{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "## Loading data\n", "\n", "The upcoming section consists of a few preparatory steps such as: (I.) preparing environment and loading packages necessary for the further steps, (II.) loading sequencing data, (III.) removing outlier and random samples to equalize a number of replicates per group and (IV.) normalizing data using a rarefaction. " ] }, { "cell_type": "code", "execution_count": 56, "metadata": {}, "outputs": [], "source": [ "import sys\n", "import copy\n", "\n", "sys.path.append(\"/home/adam/miseq/seqDataClass\")\n", "\n", "import pandas as pd\n", "import numpy as np\n", "import random\n", "\n", "#import seqDataClass.seqDataClass as seqDataClass\n", "import seqDataClass as seqDataClass" ] }, { "cell_type": "code", "execution_count": 2, "metadata": { "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Removing bad sample : Osnat056\n", "Removing bad sample : Osnat045\n", "Removing bad sample : Osnat055\n", "Removing randomly: Osnat039 from TGIRT\n", "Removing randomly: Osnat060 from ImPromII 55°C\n", "Removing randomly: Osnat061 from ImPromII 55°C\n", "Sample Osnat038 was removed from the dataset because it contains insufficient amount of sequences (34).\n", "Sample Osnat048 was removed from the dataset because it contains insufficient amount of sequences (121).\n" ] } ], "source": [ "data = seqDataClass.seqObject(mappingFile=\"/home/adam/miseq/ReverseTrans/mapping.csv\", \n", " taxonomyFile= \"/home/adam/miseq/ReverseTrans/taxonomy.csv\", \n", " otuFile=\"/home/adam/miseq/ReverseTrans/otutab.txt\", \n", " taxonomySep=',',\n", " sampleNamesColumn=\"Name\")\n", "\n", "#print(data.data.sum(axis=0))\n", "\n", "# Removing outlier samples\n", "bad_samples = [\"Osnat056\", \"Osnat045\", \"Osnat055\"]\n", "\n", "for sample in bad_samples:\n", " print(\"Removing bad sample : {}\".format(sample))\n", " data.remove_sample(category=\"Name\", sample=sample)\n", " \n", "# Randomply removing samples from the data set\n", "TGIRT = [\"Osnat037\", \"Osnat038\", \"Osnat039\", \"Osnat040\", \"Osnat041\", \"Osnat042\", \"Osnat043\"]\n", "\n", "tgirtChoice = random.sample(TGIRT, 1)\n", "\n", "for sample in tgirtChoice:\n", " print(\"Removing randomly: {} from TGIRT\".format(sample))\n", " data.remove_sample(category=\"Name\", sample=sample)\n", "\n", "promega55 = [\"Osnat059\", \"Osnat060\", \"Osnat061\", \"Osnat062\"]\n", "promega55Choice = random.sample(promega55, 2) # Randomly select an element from a list\n", "\n", "for sample in promega55Choice:\n", " print(\"Removing randomly: {} from ImPromII 55°C\".format(sample))\n", " data.remove_sample(category=\"Name\", sample=sample)\n", "\n", "data.rarefy_to_even_depth(seqDepth=10000,seed=124)\n", "\n", "#print(data.data.sum(axis=0))\n", "\n", "data.add_otu_parameter(yamlParamDictFile=\"/home/adam/miseq/ReverseTrans/GC_content_plot/otus_GC.yaml\", paramName=\"GC_content\")" ] }, { "cell_type": "code", "execution_count": 57, "metadata": {}, "outputs": [], "source": [ "data.save_otu_csv(fileName=\"/home/adam/miseq/ReverseTrans/normalized_tab.csv\")" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Saving data for downstream analysis\n", "\n", "Data is normalized by column the results are presented in a table. Following that, only an upper quartile of the classes is further normalized by row (class) and the result is used for the GC relative enrichment plot. " ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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EnzymeTGIRTSuperScriptIVPromega42Promega55
Replicate14567134671234712567
NameOsnat037Osnat040Osnat041Osnat042Osnat043Osnat044Osnat046Osnat047Osnat049Osnat050Osnat051Osnat052Osnat053Osnat054Osnat057Osnat058Osnat059Osnat062Osnat063Osnat064
DomainPhylumClassOrderFamilyGenusOTUGC_content
BacteriaCyanobacteriaOxyphotobacteriaNostocalesPhormidiaceaeTychonemaOtu00010.54784730258171213034854441812832591254294318268174981793724
ActinobacteriaActinobacteriaMicrococcalesMicrococcaceaeUnclassifiedOtu00020.572127463298301437267464377419485321336180260169232702428406433199
ProteobacteriaAlphaproteobacteriaAzospirillalesAzospirillaceaeSkermanellaOtu00030.5792081624376532442961753253562422479627139932721813515917713047
GammaproteobacteriaBetaproteobacterialesBurkholderiaceaePelomonasOtu00040.550117543020275442132126852748511494937110313352
AlphaproteobacteriaRhizobialesunculturedUnclassifiedOtu00050.55940618930241530540215140630634831213720142424931396619089107
SphingomonadalesSphingomonadaceaeSphingomonasOtu00060.52227725110212577106207116956973438107375809433257196299268587
RhizobialesBeijerinckiaceaeUnclassifiedOtu00070.5643564773100658966164977775221036680585437313116
MicrovirgaOtu00080.559406104103861221118416789149123911089059756768473937
ElsteralesunculturedUnclassifiedOtu00090.574257234185112852357431071122222118701574912635518
DeltaproteobacteriaMyxococcalesUnclassifiedUnclassifiedOtu00100.5677571121552008188551451398194403463631579090128552631
ActinobacteriaRubrobacteriaRubrobacteralesRubrobacteriaceaeRubrobacterOtu00110.60280449971231341626920211617422468545125569445838939
ActinobacteriaFrankialesGeodermatophilaceaeBlastococcusOtu00120.586797248404276204234229232336216192241814789127292295319280193
StreptomycetalesStreptomycetaceaeStreptomycesOtu00130.5819071303574607014259595686102211415236219205034
RubrobacteriaRubrobacteralesRubrobacteriaceaeRubrobacterOtu00140.59345824423753522584505756321048046565787573538
ActinobacteriaMicromonosporalesMicromonosporaceaeActinoplanesOtu00150.61029494232243961101125812749827823615321001771137370
MicrococcalesPromicromonosporaceaePromicromonosporaOtu00160.572127362756504221193457274320133173828846916
ProteobacteriaAlphaproteobacteriaRhizobialesXanthobacteraceaeBradyrhizobiumOtu00170.547030100212347527039173748561276170895329112216326
GammaproteobacteriaBetaproteobacterialesBurkholderiaceaeRalstoniaOtu00180.5338000000000000000007040145207283
DeltaproteobacteriaMyxococcalesBIrii41UnclassifiedOtu00190.56542114353214720337229254140662620352023587
GammaproteobacteriaBetaproteobacterialesBurkholderiaceaeAquabacteriumOtu00200.5454550000000000000007421155160285
AlphaproteobacteriaRhodobacteralesRhodobacteraceaeRubellimicrobiumOtu00210.5767333529123720306542594037143353129326313143
RhizobialesBeijerinckiaceaeUnclassifiedOtu00220.5767333834466634475430866856329123372725242510
SphingomonadalesSphingomonadaceaeNovosphingobiumOtu00230.52970300000010001100006719144151279
AcetobacteralesAcetobacteraceaeunculturedOtu00240.58663465277293761328192234287161320412
RhizobialesBeijerinckiaceaeunculturedOtu00250.56435633681026088206869849143317327814212212219
ActinobacteriaActinobacteriaMicrococcalesCellulomonadaceaeCellulomonasOtu00260.5819077091821117397718858566881373740164253837535
PseudonocardialesPseudonocardiaceaeSaccharothrixOtu00270.584352217442132262934261002220161249372112609
BacteroidetesBacteroidiaCytophagalesCytophagaceaeRhodocytophagaOtu00280.50827412643313435471133481114234000
ProteobacteriaGammaproteobacteriaBetaproteobacterialesBurkholderiaceaeRalstoniaOtu00290.53613130002000002816916578309375587
ActinobacteriaThermoleophiliaSolirubrobacteralesSolirubrobacteraceaeSolirubrobacterOtu00300.5850827458891049194749597134444034261281455714616968
...........................................................................
UnclassifiedUnclassifiedUnclassifiedOtu86030.59207500000000000000000000
ElusimicrobiaElusimicrobiaMVP-88UnclassifiedUnclassifiedOtu86040.54952800000000000000000000
ActinobacteriaAcidimicrobiiaunculturedUnclassifiedUnclassifiedOtu86050.59553300000000000000000000
AcidobacteriaSubgroupUnclassifiedUnclassifiedUnclassifiedOtu86060.59345810000000000000000000
UnclassifiedUnclassifiedUnclassifiedUnclassifiedUnclassifiedUnclassifiedOtu86070.47445300000000000000000000
Otu86080.51981400000000000000000000
BacteriaFirmicutesBacilliBacillalesPlanococcaceaePlanococcusOtu86090.55140200000000000000000000
PlanctomycetesPlanctomycetaciaGemmatalesGemmataceaeUnclassifiedOtu86100.54433500000000000000000000
ProteobacteriaGammaproteobacteriaBetaproteobacterialesBurkholderiaceaeUnclassifiedOtu86110.55244800000000000000000000
EntotheonellaeotaEntotheonelliaEntotheonellalesEntotheonellaceaeUnclassifiedOtu86120.55831300000000000000000000
ProteobacteriaDeltaproteobacteriaOligoflexales0319-6G20UnclassifiedOtu86130.58604700000000000000000000
AlphaproteobacteriaCaulobacteralesCaulobacteraceaeBrevundimonasOtu86140.53349910000100003110000000
GammaproteobacteriaBetaproteobacterialesTRA3-20UnclassifiedOtu86150.57209300000000000000000000
ChlamydiaeChlamydiaeChlamydialesParachlamydiaceaeUnclassifiedOtu86160.51748300000000000000000000
UnclassifiedUnclassifiedUnclassifiedUnclassifiedUnclassifiedUnclassifiedOtu86170.54205600000000000000000000
BacteriaProteobacteriaDeltaproteobacteriaOligoflexales0319-6G20UnclassifiedOtu86180.56177200000000000000000000
GemmatimonadetesBD2-11UnclassifiedUnclassifiedUnclassifiedOtu86190.60232600020000100000000000
ProteobacteriaAlphaproteobacteriaRhizobialesBeijerinckiaceaeMicrovirgaOtu86200.57425700000000000000000000
GammaproteobacteriaBetaproteobacterialesTRA3-20UnclassifiedOtu86210.56542100000000000000010000
PlanctomycetesPlanctomycetaciaIsosphaeralesIsosphaeraceaeUnclassifiedOtu86220.65484600000000000000000000
ProteobacteriaGammaproteobacteriaBetaproteobacterialesNitrosomonadaceaeMND1Otu86230.56177200010000000000000010
UnclassifiedUnclassifiedUnclassifiedUnclassifiedUnclassifiedUnclassifiedOtu86240.58910900000000000000000000
BacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeKlebsiellaOtu86250.56876500000000000000000000
ActinobacteriaAcidimicrobiiaUnclassifiedUnclassifiedUnclassifiedOtu86260.57037000000000000000000000
AcidobacteriaHolophagaeSubgroupUnclassifiedUnclassifiedOtu86270.58042001003000000000000000
PatescibacteriaMicrogenomatiaCandidatusUnclassifiedUnclassifiedOtu86280.49497500000000000000000000
PlanctomycetesPlanctomycetaciaGemmatalesGemmataceaeunculturedOtu86290.66587100000000000000000000
ProteobacteriaDeltaproteobacteriaBdellovibrionalesBdellovibrionaceaeOM27Otu86300.57002500000000000000200000
PatescibacteriaSaccharimonadiaSaccharimonadalesUnclassifiedUnclassifiedOtu86310.50617300000000000000000000
ActinobacteriaActinobacteriaUnclassifiedUnclassifiedUnclassifiedOtu86320.58292700000000000000000000
\n", "

8632 rows × 20 columns

\n", "
" ], "text/plain": [ "Enzyme TGIRT \\\n", "Replicate 1 \n", "Name Osnat037 \n", "Domain Phylum Class Order Family Genus OTU GC_content \n", "Bacteria Cyanobacteria Oxyphotobacteria Nostocales Phormidiaceae Tychonema Otu0001 0.547847 30 \n", " Actinobacteria Actinobacteria Micrococcales Micrococcaceae Unclassified Otu0002 0.572127 463 \n", " Proteobacteria Alphaproteobacteria Azospirillales Azospirillaceae Skermanella Otu0003 0.579208 162 \n", " Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Pelomonas Otu0004 0.550117 54 \n", " Alphaproteobacteria Rhizobiales uncultured Unclassified Otu0005 0.559406 189 \n", " Sphingomonadales Sphingomonadaceae Sphingomonas Otu0006 0.522277 251 \n", " Rhizobiales Beijerinckiaceae Unclassified Otu0007 0.564356 47 \n", " Microvirga Otu0008 0.559406 104 \n", " Elsterales uncultured Unclassified Otu0009 0.574257 23 \n", " Deltaproteobacteria Myxococcales Unclassified Unclassified Otu0010 0.567757 112 \n", " Actinobacteria Rubrobacteria Rubrobacterales Rubrobacteriaceae Rubrobacter Otu0011 0.602804 49 \n", " Actinobacteria Frankiales Geodermatophilaceae Blastococcus Otu0012 0.586797 248 \n", " Streptomycetales Streptomycetaceae Streptomyces Otu0013 0.581907 130 \n", " Rubrobacteria Rubrobacterales Rubrobacteriaceae Rubrobacter Otu0014 0.593458 24 \n", " Actinobacteria Micromonosporales Micromonosporaceae Actinoplanes Otu0015 0.610294 94 \n", " Micrococcales Promicromonosporaceae Promicromonospora Otu0016 0.572127 36 \n", " Proteobacteria Alphaproteobacteria Rhizobiales Xanthobacteraceae Bradyrhizobium Otu0017 0.547030 100 \n", " Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Ralstonia Otu0018 0.533800 0 \n", " Deltaproteobacteria Myxococcales BIrii41 Unclassified Otu0019 0.565421 14 \n", " Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Aquabacterium Otu0020 0.545455 0 \n", " Alphaproteobacteria Rhodobacterales Rhodobacteraceae Rubellimicrobium Otu0021 0.576733 35 \n", " Rhizobiales Beijerinckiaceae Unclassified Otu0022 0.576733 38 \n", " Sphingomonadales Sphingomonadaceae Novosphingobium Otu0023 0.529703 0 \n", " Acetobacterales Acetobacteraceae uncultured Otu0024 0.586634 6 \n", " Rhizobiales Beijerinckiaceae uncultured Otu0025 0.564356 33 \n", " Actinobacteria Actinobacteria Micrococcales Cellulomonadaceae Cellulomonas Otu0026 0.581907 70 \n", " Pseudonocardiales Pseudonocardiaceae Saccharothrix Otu0027 0.584352 21 \n", " Bacteroidetes Bacteroidia Cytophagales Cytophagaceae Rhodocytophaga Otu0028 0.508274 1 \n", " Proteobacteria Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Ralstonia Otu0029 0.536131 3 \n", " Actinobacteria Thermoleophilia Solirubrobacterales Solirubrobacteraceae Solirubrobacter Otu0030 0.585082 74 \n", "... ... \n", " Unclassified Unclassified Unclassified Otu8603 0.592075 0 \n", " Elusimicrobia Elusimicrobia MVP-88 Unclassified Unclassified Otu8604 0.549528 0 \n", " Actinobacteria Acidimicrobiia uncultured Unclassified Unclassified Otu8605 0.595533 0 \n", " Acidobacteria Subgroup Unclassified Unclassified Unclassified Otu8606 0.593458 1 \n", "Unclassified Unclassified Unclassified Unclassified Unclassified Unclassified Otu8607 0.474453 0 \n", " Otu8608 0.519814 0 \n", "Bacteria Firmicutes Bacilli Bacillales Planococcaceae Planococcus Otu8609 0.551402 0 \n", " Planctomycetes Planctomycetacia Gemmatales Gemmataceae Unclassified Otu8610 0.544335 0 \n", " Proteobacteria Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Unclassified Otu8611 0.552448 0 \n", " Entotheonellaeota Entotheonellia Entotheonellales Entotheonellaceae Unclassified Otu8612 0.558313 0 \n", " Proteobacteria Deltaproteobacteria Oligoflexales 0319-6G20 Unclassified Otu8613 0.586047 0 \n", " Alphaproteobacteria Caulobacterales Caulobacteraceae Brevundimonas Otu8614 0.533499 1 \n", " Gammaproteobacteria Betaproteobacteriales TRA3-20 Unclassified Otu8615 0.572093 0 \n", " Chlamydiae Chlamydiae Chlamydiales Parachlamydiaceae Unclassified Otu8616 0.517483 0 \n", "Unclassified Unclassified Unclassified Unclassified Unclassified Unclassified Otu8617 0.542056 0 \n", "Bacteria Proteobacteria Deltaproteobacteria Oligoflexales 0319-6G20 Unclassified Otu8618 0.561772 0 \n", " Gemmatimonadetes BD2-11 Unclassified Unclassified Unclassified Otu8619 0.602326 0 \n", " Proteobacteria Alphaproteobacteria Rhizobiales Beijerinckiaceae Microvirga Otu8620 0.574257 0 \n", " Gammaproteobacteria Betaproteobacteriales TRA3-20 Unclassified Otu8621 0.565421 0 \n", " Planctomycetes Planctomycetacia Isosphaerales Isosphaeraceae Unclassified Otu8622 0.654846 0 \n", " Proteobacteria Gammaproteobacteria Betaproteobacteriales Nitrosomonadaceae MND1 Otu8623 0.561772 0 \n", "Unclassified Unclassified Unclassified Unclassified Unclassified Unclassified Otu8624 0.589109 0 \n", "Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Klebsiella Otu8625 0.568765 0 \n", " Actinobacteria Acidimicrobiia Unclassified Unclassified Unclassified Otu8626 0.570370 0 \n", " Acidobacteria Holophagae Subgroup Unclassified Unclassified Otu8627 0.580420 0 \n", " Patescibacteria Microgenomatia Candidatus Unclassified Unclassified Otu8628 0.494975 0 \n", " Planctomycetes Planctomycetacia Gemmatales Gemmataceae uncultured Otu8629 0.665871 0 \n", " Proteobacteria Deltaproteobacteria Bdellovibrionales Bdellovibrionaceae OM27 Otu8630 0.570025 0 \n", " Patescibacteria Saccharimonadia Saccharimonadales Unclassified Unclassified Otu8631 0.506173 0 \n", " Actinobacteria Actinobacteria Unclassified Unclassified Unclassified Otu8632 0.582927 0 \n", "\n", "Enzyme \\\n", "Replicate 4 \n", "Name Osnat040 \n", "Domain Phylum Class Order Family Genus OTU GC_content \n", "Bacteria Cyanobacteria Oxyphotobacteria Nostocales Phormidiaceae Tychonema Otu0001 0.547847 258 \n", " Actinobacteria Actinobacteria Micrococcales Micrococcaceae Unclassified Otu0002 0.572127 298 \n", " Proteobacteria Alphaproteobacteria Azospirillales Azospirillaceae Skermanella Otu0003 0.579208 437 \n", " Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Pelomonas Otu0004 0.550117 3 \n", " Alphaproteobacteria Rhizobiales uncultured Unclassified Otu0005 0.559406 302 \n", " Sphingomonadales Sphingomonadaceae Sphingomonas Otu0006 0.522277 102 \n", " Rhizobiales Beijerinckiaceae Unclassified Otu0007 0.564356 73 \n", " Microvirga Otu0008 0.559406 103 \n", " Elsterales uncultured Unclassified Otu0009 0.574257 41 \n", " Deltaproteobacteria Myxococcales Unclassified Unclassified Otu0010 0.567757 155 \n", " Actinobacteria Rubrobacteria Rubrobacterales Rubrobacteriaceae Rubrobacter Otu0011 0.602804 97 \n", " Actinobacteria Frankiales Geodermatophilaceae Blastococcus Otu0012 0.586797 404 \n", " Streptomycetales Streptomycetaceae Streptomyces Otu0013 0.581907 35 \n", " Rubrobacteria Rubrobacterales Rubrobacteriaceae Rubrobacter Otu0014 0.593458 42 \n", " Actinobacteria Micromonosporales Micromonosporaceae Actinoplanes Otu0015 0.610294 232 \n", " Micrococcales Promicromonosporaceae Promicromonospora Otu0016 0.572127 27 \n", " Proteobacteria Alphaproteobacteria Rhizobiales Xanthobacteraceae Bradyrhizobium Otu0017 0.547030 21 \n", " Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Ralstonia Otu0018 0.533800 0 \n", " Deltaproteobacteria Myxococcales BIrii41 Unclassified Otu0019 0.565421 35 \n", " Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Aquabacterium Otu0020 0.545455 0 \n", " Alphaproteobacteria Rhodobacterales Rhodobacteraceae Rubellimicrobium Otu0021 0.576733 29 \n", " Rhizobiales Beijerinckiaceae Unclassified Otu0022 0.576733 34 \n", " Sphingomonadales Sphingomonadaceae Novosphingobium Otu0023 0.529703 0 \n", " Acetobacterales Acetobacteraceae uncultured Otu0024 0.586634 52 \n", " Rhizobiales Beijerinckiaceae uncultured Otu0025 0.564356 68 \n", " Actinobacteria Actinobacteria Micrococcales Cellulomonadaceae Cellulomonas Otu0026 0.581907 91 \n", " Pseudonocardiales Pseudonocardiaceae Saccharothrix Otu0027 0.584352 74 \n", " Bacteroidetes Bacteroidia Cytophagales Cytophagaceae Rhodocytophaga Otu0028 0.508274 26 \n", " Proteobacteria Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Ralstonia Otu0029 0.536131 0 \n", " Actinobacteria Thermoleophilia Solirubrobacterales Solirubrobacteraceae Solirubrobacter Otu0030 0.585082 58 \n", "... ... \n", " Unclassified Unclassified Unclassified Otu8603 0.592075 0 \n", " Elusimicrobia Elusimicrobia MVP-88 Unclassified Unclassified Otu8604 0.549528 0 \n", " Actinobacteria Acidimicrobiia uncultured Unclassified Unclassified Otu8605 0.595533 0 \n", " Acidobacteria Subgroup Unclassified Unclassified Unclassified Otu8606 0.593458 0 \n", "Unclassified Unclassified Unclassified Unclassified Unclassified Unclassified Otu8607 0.474453 0 \n", " Otu8608 0.519814 0 \n", "Bacteria Firmicutes Bacilli Bacillales Planococcaceae Planococcus Otu8609 0.551402 0 \n", " Planctomycetes Planctomycetacia Gemmatales Gemmataceae Unclassified Otu8610 0.544335 0 \n", " Proteobacteria Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Unclassified Otu8611 0.552448 0 \n", " Entotheonellaeota Entotheonellia Entotheonellales Entotheonellaceae Unclassified Otu8612 0.558313 0 \n", " Proteobacteria Deltaproteobacteria Oligoflexales 0319-6G20 Unclassified Otu8613 0.586047 0 \n", " Alphaproteobacteria Caulobacterales Caulobacteraceae Brevundimonas Otu8614 0.533499 0 \n", " Gammaproteobacteria Betaproteobacteriales TRA3-20 Unclassified Otu8615 0.572093 0 \n", " Chlamydiae Chlamydiae Chlamydiales Parachlamydiaceae Unclassified Otu8616 0.517483 0 \n", "Unclassified Unclassified Unclassified Unclassified Unclassified Unclassified Otu8617 0.542056 0 \n", "Bacteria Proteobacteria Deltaproteobacteria Oligoflexales 0319-6G20 Unclassified Otu8618 0.561772 0 \n", " Gemmatimonadetes BD2-11 Unclassified Unclassified Unclassified Otu8619 0.602326 0 \n", " Proteobacteria Alphaproteobacteria Rhizobiales Beijerinckiaceae Microvirga Otu8620 0.574257 0 \n", " Gammaproteobacteria Betaproteobacteriales TRA3-20 Unclassified Otu8621 0.565421 0 \n", " Planctomycetes Planctomycetacia Isosphaerales Isosphaeraceae Unclassified Otu8622 0.654846 0 \n", " Proteobacteria Gammaproteobacteria Betaproteobacteriales Nitrosomonadaceae MND1 Otu8623 0.561772 0 \n", "Unclassified Unclassified Unclassified Unclassified Unclassified Unclassified Otu8624 0.589109 0 \n", "Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Klebsiella Otu8625 0.568765 0 \n", " Actinobacteria Acidimicrobiia Unclassified Unclassified Unclassified Otu8626 0.570370 0 \n", " Acidobacteria Holophagae Subgroup Unclassified Unclassified Otu8627 0.580420 1 \n", " Patescibacteria Microgenomatia Candidatus Unclassified Unclassified Otu8628 0.494975 0 \n", " Planctomycetes Planctomycetacia Gemmatales Gemmataceae uncultured Otu8629 0.665871 0 \n", " Proteobacteria Deltaproteobacteria Bdellovibrionales Bdellovibrionaceae OM27 Otu8630 0.570025 0 \n", " Patescibacteria Saccharimonadia Saccharimonadales Unclassified Unclassified Otu8631 0.506173 0 \n", " Actinobacteria Actinobacteria Unclassified Unclassified Unclassified Otu8632 0.582927 0 \n", "\n", "Enzyme \\\n", "Replicate 5 \n", "Name Osnat041 \n", "Domain Phylum Class Order Family Genus OTU GC_content \n", "Bacteria Cyanobacteria Oxyphotobacteria Nostocales Phormidiaceae Tychonema Otu0001 0.547847 17 \n", " Actinobacteria Actinobacteria Micrococcales Micrococcaceae Unclassified Otu0002 0.572127 301 \n", " Proteobacteria Alphaproteobacteria Azospirillales Azospirillaceae Skermanella Otu0003 0.579208 653 \n", " Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Pelomonas Otu0004 0.550117 0 \n", " Alphaproteobacteria Rhizobiales uncultured Unclassified Otu0005 0.559406 415 \n", " Sphingomonadales Sphingomonadaceae Sphingomonas Otu0006 0.522277 125 \n", " Rhizobiales Beijerinckiaceae Unclassified Otu0007 0.564356 100 \n", " Microvirga Otu0008 0.559406 86 \n", " Elsterales uncultured Unclassified Otu0009 0.574257 85 \n", " Deltaproteobacteria Myxococcales Unclassified Unclassified Otu0010 0.567757 200 \n", " Actinobacteria Rubrobacteria Rubrobacterales Rubrobacteriaceae Rubrobacter Otu0011 0.602804 123 \n", " Actinobacteria Frankiales Geodermatophilaceae Blastococcus Otu0012 0.586797 276 \n", " Streptomycetales Streptomycetaceae Streptomyces Otu0013 0.581907 74 \n", " Rubrobacteria Rubrobacterales Rubrobacteriaceae Rubrobacter Otu0014 0.593458 37 \n", " Actinobacteria Micromonosporales Micromonosporaceae Actinoplanes Otu0015 0.610294 243 \n", " Micrococcales Promicromonosporaceae Promicromonospora Otu0016 0.572127 56 \n", " Proteobacteria Alphaproteobacteria Rhizobiales Xanthobacteraceae Bradyrhizobium Otu0017 0.547030 23 \n", " Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Ralstonia Otu0018 0.533800 0 \n", " Deltaproteobacteria Myxococcales BIrii41 Unclassified Otu0019 0.565421 32 \n", " Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Aquabacterium Otu0020 0.545455 0 \n", " Alphaproteobacteria Rhodobacterales Rhodobacteraceae Rubellimicrobium Otu0021 0.576733 12 \n", " Rhizobiales Beijerinckiaceae Unclassified Otu0022 0.576733 46 \n", " Sphingomonadales Sphingomonadaceae Novosphingobium Otu0023 0.529703 0 \n", " Acetobacterales Acetobacteraceae uncultured Otu0024 0.586634 77 \n", " Rhizobiales Beijerinckiaceae uncultured Otu0025 0.564356 102 \n", " Actinobacteria Actinobacteria Micrococcales Cellulomonadaceae Cellulomonas Otu0026 0.581907 82 \n", " Pseudonocardiales Pseudonocardiaceae Saccharothrix Otu0027 0.584352 42 \n", " Bacteroidetes Bacteroidia Cytophagales Cytophagaceae Rhodocytophaga Otu0028 0.508274 4 \n", " Proteobacteria Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Ralstonia Otu0029 0.536131 0 \n", " Actinobacteria Thermoleophilia Solirubrobacterales Solirubrobacteraceae Solirubrobacter Otu0030 0.585082 89 \n", "... ... \n", " Unclassified Unclassified Unclassified Otu8603 0.592075 0 \n", " Elusimicrobia Elusimicrobia MVP-88 Unclassified Unclassified Otu8604 0.549528 0 \n", " Actinobacteria Acidimicrobiia uncultured Unclassified Unclassified Otu8605 0.595533 0 \n", " Acidobacteria Subgroup Unclassified Unclassified Unclassified Otu8606 0.593458 0 \n", "Unclassified Unclassified Unclassified Unclassified Unclassified Unclassified Otu8607 0.474453 0 \n", " Otu8608 0.519814 0 \n", "Bacteria Firmicutes Bacilli Bacillales Planococcaceae Planococcus Otu8609 0.551402 0 \n", " Planctomycetes Planctomycetacia Gemmatales Gemmataceae Unclassified Otu8610 0.544335 0 \n", " Proteobacteria Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Unclassified Otu8611 0.552448 0 \n", " Entotheonellaeota Entotheonellia Entotheonellales Entotheonellaceae Unclassified Otu8612 0.558313 0 \n", " Proteobacteria Deltaproteobacteria Oligoflexales 0319-6G20 Unclassified Otu8613 0.586047 0 \n", " Alphaproteobacteria Caulobacterales Caulobacteraceae Brevundimonas Otu8614 0.533499 0 \n", " Gammaproteobacteria Betaproteobacteriales TRA3-20 Unclassified Otu8615 0.572093 0 \n", " Chlamydiae Chlamydiae Chlamydiales Parachlamydiaceae Unclassified Otu8616 0.517483 0 \n", "Unclassified Unclassified Unclassified Unclassified Unclassified Unclassified Otu8617 0.542056 0 \n", "Bacteria Proteobacteria Deltaproteobacteria Oligoflexales 0319-6G20 Unclassified Otu8618 0.561772 0 \n", " Gemmatimonadetes BD2-11 Unclassified Unclassified Unclassified Otu8619 0.602326 0 \n", " Proteobacteria Alphaproteobacteria Rhizobiales Beijerinckiaceae Microvirga Otu8620 0.574257 0 \n", " Gammaproteobacteria Betaproteobacteriales TRA3-20 Unclassified Otu8621 0.565421 0 \n", " Planctomycetes Planctomycetacia Isosphaerales Isosphaeraceae Unclassified Otu8622 0.654846 0 \n", " Proteobacteria Gammaproteobacteria Betaproteobacteriales Nitrosomonadaceae MND1 Otu8623 0.561772 0 \n", "Unclassified Unclassified Unclassified Unclassified Unclassified Unclassified Otu8624 0.589109 0 \n", "Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Klebsiella Otu8625 0.568765 0 \n", " Actinobacteria Acidimicrobiia Unclassified Unclassified Unclassified Otu8626 0.570370 0 \n", " Acidobacteria Holophagae Subgroup Unclassified Unclassified Otu8627 0.580420 0 \n", " Patescibacteria Microgenomatia Candidatus Unclassified Unclassified Otu8628 0.494975 0 \n", " Planctomycetes Planctomycetacia Gemmatales Gemmataceae uncultured Otu8629 0.665871 0 \n", " Proteobacteria Deltaproteobacteria Bdellovibrionales Bdellovibrionaceae OM27 Otu8630 0.570025 0 \n", " Patescibacteria Saccharimonadia Saccharimonadales Unclassified Unclassified Otu8631 0.506173 0 \n", " Actinobacteria Actinobacteria Unclassified Unclassified Unclassified Otu8632 0.582927 0 \n", "\n", "Enzyme \\\n", "Replicate 6 \n", "Name Osnat042 \n", "Domain Phylum Class Order Family Genus OTU GC_content \n", "Bacteria Cyanobacteria Oxyphotobacteria Nostocales Phormidiaceae Tychonema Otu0001 0.547847 121 \n", " Actinobacteria Actinobacteria Micrococcales Micrococcaceae Unclassified Otu0002 0.572127 437 \n", " Proteobacteria Alphaproteobacteria Azospirillales Azospirillaceae Skermanella Otu0003 0.579208 244 \n", " Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Pelomonas Otu0004 0.550117 20 \n", " Alphaproteobacteria Rhizobiales uncultured Unclassified Otu0005 0.559406 305 \n", " Sphingomonadales Sphingomonadaceae Sphingomonas Otu0006 0.522277 77 \n", " Rhizobiales Beijerinckiaceae Unclassified Otu0007 0.564356 65 \n", " Microvirga Otu0008 0.559406 122 \n", " Elsterales uncultured Unclassified Otu0009 0.574257 112 \n", " Deltaproteobacteria Myxococcales Unclassified Unclassified Otu0010 0.567757 81 \n", " Actinobacteria Rubrobacteria Rubrobacterales Rubrobacteriaceae Rubrobacter Otu0011 0.602804 134 \n", " Actinobacteria Frankiales Geodermatophilaceae Blastococcus Otu0012 0.586797 204 \n", " Streptomycetales Streptomycetaceae Streptomyces Otu0013 0.581907 60 \n", " Rubrobacteria Rubrobacterales Rubrobacteriaceae Rubrobacter Otu0014 0.593458 53 \n", " Actinobacteria Micromonosporales Micromonosporaceae Actinoplanes Otu0015 0.610294 96 \n", " Micrococcales Promicromonosporaceae Promicromonospora Otu0016 0.572127 50 \n", " Proteobacteria Alphaproteobacteria Rhizobiales Xanthobacteraceae Bradyrhizobium Otu0017 0.547030 47 \n", " Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Ralstonia Otu0018 0.533800 0 \n", " Deltaproteobacteria Myxococcales BIrii41 Unclassified Otu0019 0.565421 14 \n", " Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Aquabacterium Otu0020 0.545455 0 \n", " Alphaproteobacteria Rhodobacterales Rhodobacteraceae Rubellimicrobium Otu0021 0.576733 37 \n", " Rhizobiales Beijerinckiaceae Unclassified Otu0022 0.576733 66 \n", " Sphingomonadales Sphingomonadaceae Novosphingobium Otu0023 0.529703 0 \n", " Acetobacterales Acetobacteraceae uncultured Otu0024 0.586634 29 \n", " Rhizobiales Beijerinckiaceae uncultured Otu0025 0.564356 60 \n", " Actinobacteria Actinobacteria Micrococcales Cellulomonadaceae Cellulomonas Otu0026 0.581907 111 \n", " Pseudonocardiales Pseudonocardiaceae Saccharothrix Otu0027 0.584352 132 \n", " Bacteroidetes Bacteroidia Cytophagales Cytophagaceae Rhodocytophaga Otu0028 0.508274 33 \n", " Proteobacteria Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Ralstonia Otu0029 0.536131 0 \n", " Actinobacteria Thermoleophilia Solirubrobacterales Solirubrobacteraceae Solirubrobacter Otu0030 0.585082 104 \n", "... ... \n", " Unclassified Unclassified Unclassified Otu8603 0.592075 0 \n", " Elusimicrobia Elusimicrobia MVP-88 Unclassified Unclassified Otu8604 0.549528 0 \n", " Actinobacteria Acidimicrobiia uncultured Unclassified Unclassified Otu8605 0.595533 0 \n", " Acidobacteria Subgroup Unclassified Unclassified Unclassified Otu8606 0.593458 0 \n", "Unclassified Unclassified Unclassified Unclassified Unclassified Unclassified Otu8607 0.474453 0 \n", " Otu8608 0.519814 0 \n", "Bacteria Firmicutes Bacilli Bacillales Planococcaceae Planococcus Otu8609 0.551402 0 \n", " Planctomycetes Planctomycetacia Gemmatales Gemmataceae Unclassified Otu8610 0.544335 0 \n", " Proteobacteria Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Unclassified Otu8611 0.552448 0 \n", " Entotheonellaeota Entotheonellia Entotheonellales Entotheonellaceae Unclassified Otu8612 0.558313 0 \n", " Proteobacteria Deltaproteobacteria Oligoflexales 0319-6G20 Unclassified Otu8613 0.586047 0 \n", " Alphaproteobacteria Caulobacterales Caulobacteraceae Brevundimonas Otu8614 0.533499 0 \n", " Gammaproteobacteria Betaproteobacteriales TRA3-20 Unclassified Otu8615 0.572093 0 \n", " Chlamydiae Chlamydiae Chlamydiales Parachlamydiaceae Unclassified Otu8616 0.517483 0 \n", "Unclassified Unclassified Unclassified Unclassified Unclassified Unclassified Otu8617 0.542056 0 \n", "Bacteria Proteobacteria Deltaproteobacteria Oligoflexales 0319-6G20 Unclassified Otu8618 0.561772 0 \n", " Gemmatimonadetes BD2-11 Unclassified Unclassified Unclassified Otu8619 0.602326 2 \n", " Proteobacteria Alphaproteobacteria Rhizobiales Beijerinckiaceae Microvirga Otu8620 0.574257 0 \n", " Gammaproteobacteria Betaproteobacteriales TRA3-20 Unclassified Otu8621 0.565421 0 \n", " Planctomycetes Planctomycetacia Isosphaerales Isosphaeraceae Unclassified Otu8622 0.654846 0 \n", " Proteobacteria Gammaproteobacteria Betaproteobacteriales Nitrosomonadaceae MND1 Otu8623 0.561772 1 \n", "Unclassified Unclassified Unclassified Unclassified Unclassified Unclassified Otu8624 0.589109 0 \n", "Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Klebsiella Otu8625 0.568765 0 \n", " Actinobacteria Acidimicrobiia Unclassified Unclassified Unclassified Otu8626 0.570370 0 \n", " Acidobacteria Holophagae Subgroup Unclassified Unclassified Otu8627 0.580420 0 \n", " Patescibacteria Microgenomatia Candidatus Unclassified Unclassified Otu8628 0.494975 0 \n", " Planctomycetes Planctomycetacia Gemmatales Gemmataceae uncultured Otu8629 0.665871 0 \n", " Proteobacteria Deltaproteobacteria Bdellovibrionales Bdellovibrionaceae OM27 Otu8630 0.570025 0 \n", " Patescibacteria Saccharimonadia Saccharimonadales Unclassified Unclassified Otu8631 0.506173 0 \n", " Actinobacteria Actinobacteria Unclassified Unclassified Unclassified Otu8632 0.582927 0 \n", "\n", "Enzyme \\\n", "Replicate 7 \n", "Name Osnat043 \n", "Domain Phylum Class Order Family Genus OTU GC_content \n", "Bacteria Cyanobacteria Oxyphotobacteria Nostocales Phormidiaceae Tychonema Otu0001 0.547847 303 \n", " Actinobacteria Actinobacteria Micrococcales Micrococcaceae Unclassified Otu0002 0.572127 267 \n", " Proteobacteria Alphaproteobacteria Azospirillales Azospirillaceae Skermanella Otu0003 0.579208 296 \n", " Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Pelomonas Otu0004 0.550117 27 \n", " Alphaproteobacteria Rhizobiales uncultured Unclassified Otu0005 0.559406 402 \n", " Sphingomonadales Sphingomonadaceae Sphingomonas Otu0006 0.522277 106 \n", " Rhizobiales Beijerinckiaceae Unclassified Otu0007 0.564356 89 \n", " Microvirga Otu0008 0.559406 111 \n", " Elsterales uncultured Unclassified Otu0009 0.574257 85 \n", " Deltaproteobacteria Myxococcales Unclassified Unclassified Otu0010 0.567757 88 \n", " Actinobacteria Rubrobacteria Rubrobacterales Rubrobacteriaceae Rubrobacter Otu0011 0.602804 162 \n", " Actinobacteria Frankiales Geodermatophilaceae Blastococcus Otu0012 0.586797 234 \n", " Streptomycetales Streptomycetaceae Streptomyces Otu0013 0.581907 70 \n", " Rubrobacteria Rubrobacterales Rubrobacteriaceae Rubrobacter Otu0014 0.593458 52 \n", " Actinobacteria Micromonosporales Micromonosporaceae Actinoplanes Otu0015 0.610294 110 \n", " Micrococcales Promicromonosporaceae Promicromonospora Otu0016 0.572127 42 \n", " Proteobacteria Alphaproteobacteria Rhizobiales Xanthobacteraceae Bradyrhizobium Otu0017 0.547030 52 \n", " Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Ralstonia Otu0018 0.533800 0 \n", " Deltaproteobacteria Myxococcales BIrii41 Unclassified Otu0019 0.565421 7 \n", " Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Aquabacterium Otu0020 0.545455 0 \n", " Alphaproteobacteria Rhodobacterales Rhodobacteraceae Rubellimicrobium Otu0021 0.576733 20 \n", " Rhizobiales Beijerinckiaceae Unclassified Otu0022 0.576733 34 \n", " Sphingomonadales Sphingomonadaceae Novosphingobium Otu0023 0.529703 0 \n", " Acetobacterales Acetobacteraceae uncultured Otu0024 0.586634 37 \n", " Rhizobiales Beijerinckiaceae uncultured Otu0025 0.564356 88 \n", " Actinobacteria Actinobacteria Micrococcales Cellulomonadaceae Cellulomonas Otu0026 0.581907 73 \n", " Pseudonocardiales Pseudonocardiaceae Saccharothrix Otu0027 0.584352 26 \n", " Bacteroidetes Bacteroidia Cytophagales Cytophagaceae Rhodocytophaga Otu0028 0.508274 13 \n", " Proteobacteria Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Ralstonia Otu0029 0.536131 2 \n", " Actinobacteria Thermoleophilia Solirubrobacterales Solirubrobacteraceae Solirubrobacter Otu0030 0.585082 91 \n", "... ... \n", " Unclassified Unclassified Unclassified Otu8603 0.592075 0 \n", " Elusimicrobia Elusimicrobia MVP-88 Unclassified Unclassified Otu8604 0.549528 0 \n", " Actinobacteria Acidimicrobiia uncultured Unclassified Unclassified Otu8605 0.595533 0 \n", " Acidobacteria Subgroup Unclassified Unclassified Unclassified Otu8606 0.593458 0 \n", "Unclassified Unclassified Unclassified Unclassified Unclassified Unclassified Otu8607 0.474453 0 \n", " Otu8608 0.519814 0 \n", "Bacteria Firmicutes Bacilli Bacillales Planococcaceae Planococcus Otu8609 0.551402 0 \n", " Planctomycetes Planctomycetacia Gemmatales Gemmataceae Unclassified Otu8610 0.544335 0 \n", " Proteobacteria Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Unclassified Otu8611 0.552448 0 \n", " Entotheonellaeota Entotheonellia Entotheonellales Entotheonellaceae Unclassified Otu8612 0.558313 0 \n", " Proteobacteria Deltaproteobacteria Oligoflexales 0319-6G20 Unclassified Otu8613 0.586047 0 \n", " Alphaproteobacteria Caulobacterales Caulobacteraceae Brevundimonas Otu8614 0.533499 0 \n", " Gammaproteobacteria Betaproteobacteriales TRA3-20 Unclassified Otu8615 0.572093 0 \n", " Chlamydiae Chlamydiae Chlamydiales Parachlamydiaceae Unclassified Otu8616 0.517483 0 \n", "Unclassified Unclassified Unclassified Unclassified Unclassified Unclassified Otu8617 0.542056 0 \n", "Bacteria Proteobacteria Deltaproteobacteria Oligoflexales 0319-6G20 Unclassified Otu8618 0.561772 0 \n", " Gemmatimonadetes BD2-11 Unclassified Unclassified Unclassified Otu8619 0.602326 0 \n", " Proteobacteria Alphaproteobacteria Rhizobiales Beijerinckiaceae Microvirga Otu8620 0.574257 0 \n", " Gammaproteobacteria Betaproteobacteriales TRA3-20 Unclassified Otu8621 0.565421 0 \n", " Planctomycetes Planctomycetacia Isosphaerales Isosphaeraceae Unclassified Otu8622 0.654846 0 \n", " Proteobacteria Gammaproteobacteria Betaproteobacteriales Nitrosomonadaceae MND1 Otu8623 0.561772 0 \n", "Unclassified Unclassified Unclassified Unclassified Unclassified Unclassified Otu8624 0.589109 0 \n", "Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Klebsiella Otu8625 0.568765 0 \n", " Actinobacteria Acidimicrobiia Unclassified Unclassified Unclassified Otu8626 0.570370 0 \n", " Acidobacteria Holophagae Subgroup Unclassified Unclassified Otu8627 0.580420 3 \n", " Patescibacteria Microgenomatia Candidatus Unclassified Unclassified Otu8628 0.494975 0 \n", " Planctomycetes Planctomycetacia Gemmatales Gemmataceae uncultured Otu8629 0.665871 0 \n", " Proteobacteria Deltaproteobacteria Bdellovibrionales Bdellovibrionaceae OM27 Otu8630 0.570025 0 \n", " Patescibacteria Saccharimonadia Saccharimonadales Unclassified Unclassified Otu8631 0.506173 0 \n", " Actinobacteria Actinobacteria Unclassified Unclassified Unclassified Otu8632 0.582927 0 \n", "\n", "Enzyme SuperScriptIV \\\n", "Replicate 1 \n", "Name Osnat044 \n", "Domain Phylum Class Order Family Genus OTU GC_content \n", "Bacteria Cyanobacteria Oxyphotobacteria Nostocales Phormidiaceae Tychonema Otu0001 0.547847 48 \n", " Actinobacteria Actinobacteria Micrococcales Micrococcaceae Unclassified Otu0002 0.572127 464 \n", " Proteobacteria Alphaproteobacteria Azospirillales Azospirillaceae Skermanella Otu0003 0.579208 175 \n", " Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Pelomonas Otu0004 0.550117 54 \n", " Alphaproteobacteria Rhizobiales uncultured Unclassified Otu0005 0.559406 151 \n", " Sphingomonadales Sphingomonadaceae Sphingomonas Otu0006 0.522277 207 \n", " Rhizobiales Beijerinckiaceae Unclassified Otu0007 0.564356 66 \n", " Microvirga Otu0008 0.559406 84 \n", " Elsterales uncultured Unclassified Otu0009 0.574257 23 \n", " Deltaproteobacteria Myxococcales Unclassified Unclassified Otu0010 0.567757 55 \n", " Actinobacteria Rubrobacteria Rubrobacterales Rubrobacteriaceae Rubrobacter Otu0011 0.602804 69 \n", " Actinobacteria Frankiales Geodermatophilaceae Blastococcus Otu0012 0.586797 229 \n", " Streptomycetales Streptomycetaceae Streptomyces Otu0013 0.581907 142 \n", " Rubrobacteria Rubrobacterales Rubrobacteriaceae Rubrobacter Otu0014 0.593458 25 \n", " Actinobacteria Micromonosporales Micromonosporaceae Actinoplanes Otu0015 0.610294 112 \n", " Micrococcales Promicromonosporaceae Promicromonospora Otu0016 0.572127 21 \n", " Proteobacteria Alphaproteobacteria Rhizobiales Xanthobacteraceae Bradyrhizobium Otu0017 0.547030 70 \n", " Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Ralstonia Otu0018 0.533800 0 \n", " Deltaproteobacteria Myxococcales BIrii41 Unclassified Otu0019 0.565421 20 \n", " Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Aquabacterium Otu0020 0.545455 0 \n", " Alphaproteobacteria Rhodobacterales Rhodobacteraceae Rubellimicrobium Otu0021 0.576733 30 \n", " Rhizobiales Beijerinckiaceae Unclassified Otu0022 0.576733 47 \n", " Sphingomonadales Sphingomonadaceae Novosphingobium Otu0023 0.529703 0 \n", " Acetobacterales Acetobacteraceae uncultured Otu0024 0.586634 6 \n", " Rhizobiales Beijerinckiaceae uncultured Otu0025 0.564356 20 \n", " Actinobacteria Actinobacteria Micrococcales Cellulomonadaceae Cellulomonas Otu0026 0.581907 97 \n", " Pseudonocardiales Pseudonocardiaceae Saccharothrix Otu0027 0.584352 29 \n", " Bacteroidetes Bacteroidia Cytophagales Cytophagaceae Rhodocytophaga Otu0028 0.508274 4 \n", " Proteobacteria Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Ralstonia Otu0029 0.536131 0 \n", " Actinobacteria Thermoleophilia Solirubrobacterales Solirubrobacteraceae Solirubrobacter Otu0030 0.585082 94 \n", "... ... \n", " Unclassified Unclassified Unclassified Otu8603 0.592075 0 \n", " Elusimicrobia Elusimicrobia MVP-88 Unclassified Unclassified Otu8604 0.549528 0 \n", " Actinobacteria Acidimicrobiia uncultured Unclassified Unclassified Otu8605 0.595533 0 \n", " Acidobacteria Subgroup Unclassified Unclassified Unclassified Otu8606 0.593458 0 \n", "Unclassified Unclassified Unclassified Unclassified Unclassified Unclassified Otu8607 0.474453 0 \n", " Otu8608 0.519814 0 \n", "Bacteria Firmicutes Bacilli Bacillales Planococcaceae Planococcus Otu8609 0.551402 0 \n", " Planctomycetes Planctomycetacia Gemmatales Gemmataceae Unclassified Otu8610 0.544335 0 \n", " Proteobacteria Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Unclassified Otu8611 0.552448 0 \n", " Entotheonellaeota Entotheonellia Entotheonellales Entotheonellaceae Unclassified Otu8612 0.558313 0 \n", " Proteobacteria Deltaproteobacteria Oligoflexales 0319-6G20 Unclassified Otu8613 0.586047 0 \n", " Alphaproteobacteria Caulobacterales Caulobacteraceae Brevundimonas Otu8614 0.533499 1 \n", " Gammaproteobacteria Betaproteobacteriales TRA3-20 Unclassified Otu8615 0.572093 0 \n", " Chlamydiae Chlamydiae Chlamydiales Parachlamydiaceae Unclassified Otu8616 0.517483 0 \n", "Unclassified Unclassified Unclassified Unclassified Unclassified Unclassified Otu8617 0.542056 0 \n", "Bacteria Proteobacteria Deltaproteobacteria Oligoflexales 0319-6G20 Unclassified Otu8618 0.561772 0 \n", " Gemmatimonadetes BD2-11 Unclassified Unclassified Unclassified Otu8619 0.602326 0 \n", " Proteobacteria Alphaproteobacteria Rhizobiales Beijerinckiaceae Microvirga Otu8620 0.574257 0 \n", " Gammaproteobacteria Betaproteobacteriales TRA3-20 Unclassified Otu8621 0.565421 0 \n", " Planctomycetes Planctomycetacia Isosphaerales Isosphaeraceae Unclassified Otu8622 0.654846 0 \n", " Proteobacteria Gammaproteobacteria Betaproteobacteriales Nitrosomonadaceae MND1 Otu8623 0.561772 0 \n", "Unclassified Unclassified Unclassified Unclassified Unclassified Unclassified Otu8624 0.589109 0 \n", "Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Klebsiella Otu8625 0.568765 0 \n", " Actinobacteria Acidimicrobiia Unclassified Unclassified Unclassified Otu8626 0.570370 0 \n", " Acidobacteria Holophagae Subgroup Unclassified Unclassified Otu8627 0.580420 0 \n", " Patescibacteria Microgenomatia Candidatus Unclassified Unclassified Otu8628 0.494975 0 \n", " Planctomycetes Planctomycetacia Gemmatales Gemmataceae uncultured Otu8629 0.665871 0 \n", " Proteobacteria Deltaproteobacteria Bdellovibrionales Bdellovibrionaceae OM27 Otu8630 0.570025 0 \n", " Patescibacteria Saccharimonadia Saccharimonadales Unclassified Unclassified Otu8631 0.506173 0 \n", " Actinobacteria Actinobacteria Unclassified Unclassified Unclassified Otu8632 0.582927 0 \n", "\n", "Enzyme \\\n", "Replicate 3 \n", "Name Osnat046 \n", "Domain Phylum Class Order Family Genus OTU GC_content \n", "Bacteria Cyanobacteria Oxyphotobacteria Nostocales Phormidiaceae Tychonema Otu0001 0.547847 544 \n", " Actinobacteria Actinobacteria Micrococcales Micrococcaceae Unclassified Otu0002 0.572127 377 \n", " Proteobacteria Alphaproteobacteria Azospirillales Azospirillaceae Skermanella Otu0003 0.579208 325 \n", " Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Pelomonas Otu0004 0.550117 4 \n", " Alphaproteobacteria Rhizobiales uncultured Unclassified Otu0005 0.559406 406 \n", " Sphingomonadales Sphingomonadaceae Sphingomonas Otu0006 0.522277 116 \n", " Rhizobiales Beijerinckiaceae Unclassified Otu0007 0.564356 164 \n", " Microvirga Otu0008 0.559406 167 \n", " Elsterales uncultured Unclassified Otu0009 0.574257 57 \n", " Deltaproteobacteria Myxococcales Unclassified Unclassified Otu0010 0.567757 145 \n", " Actinobacteria Rubrobacteria Rubrobacterales Rubrobacteriaceae Rubrobacter Otu0011 0.602804 202 \n", " Actinobacteria Frankiales Geodermatophilaceae Blastococcus Otu0012 0.586797 232 \n", " Streptomycetales Streptomycetaceae Streptomyces Otu0013 0.581907 59 \n", " Rubrobacteria Rubrobacterales Rubrobacteriaceae Rubrobacter Otu0014 0.593458 84 \n", " Actinobacteria Micromonosporales Micromonosporaceae Actinoplanes Otu0015 0.610294 58 \n", " Micrococcales Promicromonosporaceae Promicromonospora Otu0016 0.572127 19 \n", " Proteobacteria Alphaproteobacteria Rhizobiales Xanthobacteraceae Bradyrhizobium Otu0017 0.547030 39 \n", " Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Ralstonia Otu0018 0.533800 0 \n", " Deltaproteobacteria Myxococcales BIrii41 Unclassified Otu0019 0.565421 33 \n", " Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Aquabacterium Otu0020 0.545455 0 \n", " Alphaproteobacteria Rhodobacterales Rhodobacteraceae Rubellimicrobium Otu0021 0.576733 65 \n", " Rhizobiales Beijerinckiaceae Unclassified Otu0022 0.576733 54 \n", " Sphingomonadales Sphingomonadaceae Novosphingobium Otu0023 0.529703 1 \n", " Acetobacterales Acetobacteraceae uncultured Otu0024 0.586634 13 \n", " Rhizobiales Beijerinckiaceae uncultured Otu0025 0.564356 68 \n", " Actinobacteria Actinobacteria Micrococcales Cellulomonadaceae Cellulomonas Otu0026 0.581907 71 \n", " Pseudonocardiales Pseudonocardiaceae Saccharothrix Otu0027 0.584352 34 \n", " Bacteroidetes Bacteroidia Cytophagales Cytophagaceae Rhodocytophaga Otu0028 0.508274 35 \n", " Proteobacteria Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Ralstonia Otu0029 0.536131 0 \n", " Actinobacteria Thermoleophilia Solirubrobacterales Solirubrobacteraceae Solirubrobacter Otu0030 0.585082 74 \n", "... ... \n", " Unclassified Unclassified Unclassified Otu8603 0.592075 0 \n", " Elusimicrobia Elusimicrobia MVP-88 Unclassified Unclassified Otu8604 0.549528 0 \n", " Actinobacteria Acidimicrobiia uncultured Unclassified Unclassified Otu8605 0.595533 0 \n", " Acidobacteria Subgroup Unclassified Unclassified Unclassified Otu8606 0.593458 0 \n", "Unclassified Unclassified Unclassified Unclassified Unclassified Unclassified Otu8607 0.474453 0 \n", " Otu8608 0.519814 0 \n", "Bacteria Firmicutes Bacilli Bacillales Planococcaceae Planococcus Otu8609 0.551402 0 \n", " Planctomycetes Planctomycetacia Gemmatales Gemmataceae Unclassified Otu8610 0.544335 0 \n", " Proteobacteria Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Unclassified Otu8611 0.552448 0 \n", " Entotheonellaeota Entotheonellia Entotheonellales Entotheonellaceae Unclassified Otu8612 0.558313 0 \n", " Proteobacteria Deltaproteobacteria Oligoflexales 0319-6G20 Unclassified Otu8613 0.586047 0 \n", " Alphaproteobacteria Caulobacterales Caulobacteraceae Brevundimonas Otu8614 0.533499 0 \n", " Gammaproteobacteria Betaproteobacteriales TRA3-20 Unclassified Otu8615 0.572093 0 \n", " Chlamydiae Chlamydiae Chlamydiales Parachlamydiaceae Unclassified Otu8616 0.517483 0 \n", "Unclassified Unclassified Unclassified Unclassified Unclassified Unclassified Otu8617 0.542056 0 \n", "Bacteria Proteobacteria Deltaproteobacteria Oligoflexales 0319-6G20 Unclassified Otu8618 0.561772 0 \n", " Gemmatimonadetes BD2-11 Unclassified Unclassified Unclassified Otu8619 0.602326 0 \n", " Proteobacteria Alphaproteobacteria Rhizobiales Beijerinckiaceae Microvirga Otu8620 0.574257 0 \n", " Gammaproteobacteria Betaproteobacteriales TRA3-20 Unclassified Otu8621 0.565421 0 \n", " Planctomycetes Planctomycetacia Isosphaerales Isosphaeraceae Unclassified Otu8622 0.654846 0 \n", " Proteobacteria Gammaproteobacteria Betaproteobacteriales Nitrosomonadaceae MND1 Otu8623 0.561772 0 \n", "Unclassified Unclassified Unclassified Unclassified Unclassified Unclassified Otu8624 0.589109 0 \n", "Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Klebsiella Otu8625 0.568765 0 \n", " Actinobacteria Acidimicrobiia Unclassified Unclassified Unclassified Otu8626 0.570370 0 \n", " Acidobacteria Holophagae Subgroup Unclassified Unclassified Otu8627 0.580420 0 \n", " Patescibacteria Microgenomatia Candidatus Unclassified Unclassified Otu8628 0.494975 0 \n", " Planctomycetes Planctomycetacia Gemmatales Gemmataceae uncultured Otu8629 0.665871 0 \n", " Proteobacteria Deltaproteobacteria Bdellovibrionales Bdellovibrionaceae OM27 Otu8630 0.570025 0 \n", " Patescibacteria Saccharimonadia Saccharimonadales Unclassified Unclassified Otu8631 0.506173 0 \n", " Actinobacteria Actinobacteria Unclassified Unclassified Unclassified Otu8632 0.582927 0 \n", "\n", "Enzyme \\\n", "Replicate 4 \n", "Name Osnat047 \n", "Domain Phylum Class Order Family Genus OTU GC_content \n", "Bacteria Cyanobacteria Oxyphotobacteria Nostocales Phormidiaceae Tychonema Otu0001 0.547847 418 \n", " Actinobacteria Actinobacteria Micrococcales Micrococcaceae Unclassified Otu0002 0.572127 419 \n", " Proteobacteria Alphaproteobacteria Azospirillales Azospirillaceae Skermanella Otu0003 0.579208 356 \n", " Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Pelomonas Otu0004 0.550117 2 \n", " Alphaproteobacteria Rhizobiales uncultured Unclassified Otu0005 0.559406 306 \n", " Sphingomonadales Sphingomonadaceae Sphingomonas Otu0006 0.522277 95 \n", " Rhizobiales Beijerinckiaceae Unclassified Otu0007 0.564356 97 \n", " Microvirga Otu0008 0.559406 89 \n", " Elsterales uncultured Unclassified Otu0009 0.574257 43 \n", " Deltaproteobacteria Myxococcales Unclassified Unclassified Otu0010 0.567757 139 \n", " Actinobacteria Rubrobacteria Rubrobacterales Rubrobacteriaceae Rubrobacter Otu0011 0.602804 116 \n", " Actinobacteria Frankiales Geodermatophilaceae Blastococcus Otu0012 0.586797 336 \n", " Streptomycetales Streptomycetaceae Streptomyces Otu0013 0.581907 59 \n", " Rubrobacteria Rubrobacterales Rubrobacteriaceae Rubrobacter Otu0014 0.593458 50 \n", " Actinobacteria Micromonosporales Micromonosporaceae Actinoplanes Otu0015 0.610294 127 \n", " Micrococcales Promicromonosporaceae Promicromonospora Otu0016 0.572127 34 \n", " Proteobacteria Alphaproteobacteria Rhizobiales Xanthobacteraceae Bradyrhizobium Otu0017 0.547030 17 \n", " Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Ralstonia Otu0018 0.533800 0 \n", " Deltaproteobacteria Myxococcales BIrii41 Unclassified Otu0019 0.565421 72 \n", " Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Aquabacterium Otu0020 0.545455 0 \n", " Alphaproteobacteria Rhodobacterales Rhodobacteraceae Rubellimicrobium Otu0021 0.576733 42 \n", " Rhizobiales Beijerinckiaceae Unclassified Otu0022 0.576733 30 \n", " Sphingomonadales Sphingomonadaceae Novosphingobium Otu0023 0.529703 0 \n", " Acetobacterales Acetobacteraceae uncultured Otu0024 0.586634 28 \n", " Rhizobiales Beijerinckiaceae uncultured Otu0025 0.564356 69 \n", " Actinobacteria Actinobacteria Micrococcales Cellulomonadaceae Cellulomonas Otu0026 0.581907 88 \n", " Pseudonocardiales Pseudonocardiaceae Saccharothrix Otu0027 0.584352 26 \n", " Bacteroidetes Bacteroidia Cytophagales Cytophagaceae Rhodocytophaga Otu0028 0.508274 47 \n", " Proteobacteria Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Ralstonia Otu0029 0.536131 0 \n", " Actinobacteria Thermoleophilia Solirubrobacterales Solirubrobacteraceae Solirubrobacter Otu0030 0.585082 95 \n", "... ... \n", " Unclassified Unclassified Unclassified Otu8603 0.592075 0 \n", " Elusimicrobia Elusimicrobia MVP-88 Unclassified Unclassified Otu8604 0.549528 0 \n", " Actinobacteria Acidimicrobiia uncultured Unclassified Unclassified Otu8605 0.595533 0 \n", " Acidobacteria Subgroup Unclassified Unclassified Unclassified Otu8606 0.593458 0 \n", "Unclassified Unclassified Unclassified Unclassified Unclassified Unclassified Otu8607 0.474453 0 \n", " Otu8608 0.519814 0 \n", "Bacteria Firmicutes Bacilli Bacillales Planococcaceae Planococcus Otu8609 0.551402 0 \n", " Planctomycetes Planctomycetacia Gemmatales Gemmataceae Unclassified Otu8610 0.544335 0 \n", " Proteobacteria Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Unclassified Otu8611 0.552448 0 \n", " Entotheonellaeota Entotheonellia Entotheonellales Entotheonellaceae Unclassified Otu8612 0.558313 0 \n", " Proteobacteria Deltaproteobacteria Oligoflexales 0319-6G20 Unclassified Otu8613 0.586047 0 \n", " Alphaproteobacteria Caulobacterales Caulobacteraceae Brevundimonas Otu8614 0.533499 0 \n", " Gammaproteobacteria Betaproteobacteriales TRA3-20 Unclassified Otu8615 0.572093 0 \n", " Chlamydiae Chlamydiae Chlamydiales Parachlamydiaceae Unclassified Otu8616 0.517483 0 \n", "Unclassified Unclassified Unclassified Unclassified Unclassified Unclassified Otu8617 0.542056 0 \n", "Bacteria Proteobacteria Deltaproteobacteria Oligoflexales 0319-6G20 Unclassified Otu8618 0.561772 0 \n", " Gemmatimonadetes BD2-11 Unclassified Unclassified Unclassified Otu8619 0.602326 0 \n", " Proteobacteria Alphaproteobacteria Rhizobiales Beijerinckiaceae Microvirga Otu8620 0.574257 0 \n", " Gammaproteobacteria Betaproteobacteriales TRA3-20 Unclassified Otu8621 0.565421 0 \n", " Planctomycetes Planctomycetacia Isosphaerales Isosphaeraceae Unclassified Otu8622 0.654846 0 \n", " Proteobacteria Gammaproteobacteria Betaproteobacteriales Nitrosomonadaceae MND1 Otu8623 0.561772 0 \n", "Unclassified Unclassified Unclassified Unclassified Unclassified Unclassified Otu8624 0.589109 0 \n", "Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Klebsiella Otu8625 0.568765 0 \n", " Actinobacteria Acidimicrobiia Unclassified Unclassified Unclassified Otu8626 0.570370 0 \n", " Acidobacteria Holophagae Subgroup Unclassified Unclassified Otu8627 0.580420 0 \n", " Patescibacteria Microgenomatia Candidatus Unclassified Unclassified Otu8628 0.494975 0 \n", " Planctomycetes Planctomycetacia Gemmatales Gemmataceae uncultured Otu8629 0.665871 0 \n", " Proteobacteria Deltaproteobacteria Bdellovibrionales Bdellovibrionaceae OM27 Otu8630 0.570025 0 \n", " Patescibacteria Saccharimonadia Saccharimonadales Unclassified Unclassified Otu8631 0.506173 0 \n", " Actinobacteria Actinobacteria Unclassified Unclassified Unclassified Otu8632 0.582927 0 \n", "\n", "Enzyme \\\n", "Replicate 6 \n", "Name Osnat049 \n", "Domain Phylum Class Order Family Genus OTU GC_content \n", "Bacteria Cyanobacteria Oxyphotobacteria Nostocales Phormidiaceae Tychonema Otu0001 0.547847 128 \n", " Actinobacteria Actinobacteria Micrococcales Micrococcaceae Unclassified Otu0002 0.572127 485 \n", " Proteobacteria Alphaproteobacteria Azospirillales Azospirillaceae Skermanella Otu0003 0.579208 242 \n", " Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Pelomonas Otu0004 0.550117 13 \n", " Alphaproteobacteria Rhizobiales uncultured Unclassified Otu0005 0.559406 348 \n", " Sphingomonadales Sphingomonadaceae Sphingomonas Otu0006 0.522277 69 \n", " Rhizobiales Beijerinckiaceae Unclassified Otu0007 0.564356 77 \n", " Microvirga Otu0008 0.559406 149 \n", " Elsterales uncultured Unclassified Otu0009 0.574257 107 \n", " Deltaproteobacteria Myxococcales Unclassified Unclassified Otu0010 0.567757 81 \n", " Actinobacteria Rubrobacteria Rubrobacterales Rubrobacteriaceae Rubrobacter Otu0011 0.602804 174 \n", " Actinobacteria Frankiales Geodermatophilaceae Blastococcus Otu0012 0.586797 216 \n", " Streptomycetales Streptomycetaceae Streptomyces Otu0013 0.581907 56 \n", " Rubrobacteria Rubrobacterales Rubrobacteriaceae Rubrobacter Otu0014 0.593458 57 \n", " Actinobacteria Micromonosporales Micromonosporaceae Actinoplanes Otu0015 0.610294 49 \n", " Micrococcales Promicromonosporaceae Promicromonospora Otu0016 0.572127 57 \n", " Proteobacteria Alphaproteobacteria Rhizobiales Xanthobacteraceae Bradyrhizobium Otu0017 0.547030 37 \n", " Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Ralstonia Otu0018 0.533800 0 \n", " Deltaproteobacteria Myxococcales BIrii41 Unclassified Otu0019 0.565421 29 \n", " Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Aquabacterium Otu0020 0.545455 0 \n", " Alphaproteobacteria Rhodobacterales Rhodobacteraceae Rubellimicrobium Otu0021 0.576733 59 \n", " Rhizobiales Beijerinckiaceae Unclassified Otu0022 0.576733 86 \n", " Sphingomonadales Sphingomonadaceae Novosphingobium Otu0023 0.529703 0 \n", " Acetobacterales Acetobacteraceae uncultured Otu0024 0.586634 19 \n", " Rhizobiales Beijerinckiaceae uncultured Otu0025 0.564356 84 \n", " Actinobacteria Actinobacteria Micrococcales Cellulomonadaceae Cellulomonas Otu0026 0.581907 58 \n", " Pseudonocardiales Pseudonocardiaceae Saccharothrix Otu0027 0.584352 100 \n", " Bacteroidetes Bacteroidia Cytophagales Cytophagaceae Rhodocytophaga Otu0028 0.508274 11 \n", " Proteobacteria Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Ralstonia Otu0029 0.536131 0 \n", " Actinobacteria Thermoleophilia Solirubrobacterales Solirubrobacteraceae Solirubrobacter Otu0030 0.585082 97 \n", "... ... \n", " Unclassified Unclassified Unclassified Otu8603 0.592075 0 \n", " Elusimicrobia Elusimicrobia MVP-88 Unclassified Unclassified Otu8604 0.549528 0 \n", " Actinobacteria Acidimicrobiia uncultured Unclassified Unclassified Otu8605 0.595533 0 \n", " Acidobacteria Subgroup Unclassified Unclassified Unclassified Otu8606 0.593458 0 \n", "Unclassified Unclassified Unclassified Unclassified Unclassified Unclassified Otu8607 0.474453 0 \n", " Otu8608 0.519814 0 \n", "Bacteria Firmicutes Bacilli Bacillales Planococcaceae Planococcus Otu8609 0.551402 0 \n", " Planctomycetes Planctomycetacia Gemmatales Gemmataceae Unclassified Otu8610 0.544335 0 \n", " Proteobacteria Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Unclassified Otu8611 0.552448 0 \n", " Entotheonellaeota Entotheonellia Entotheonellales Entotheonellaceae Unclassified Otu8612 0.558313 0 \n", " Proteobacteria Deltaproteobacteria Oligoflexales 0319-6G20 Unclassified Otu8613 0.586047 0 \n", " Alphaproteobacteria Caulobacterales Caulobacteraceae Brevundimonas Otu8614 0.533499 0 \n", " Gammaproteobacteria Betaproteobacteriales TRA3-20 Unclassified Otu8615 0.572093 0 \n", " Chlamydiae Chlamydiae Chlamydiales Parachlamydiaceae Unclassified Otu8616 0.517483 0 \n", "Unclassified Unclassified Unclassified Unclassified Unclassified Unclassified Otu8617 0.542056 0 \n", "Bacteria Proteobacteria Deltaproteobacteria Oligoflexales 0319-6G20 Unclassified Otu8618 0.561772 0 \n", " Gemmatimonadetes BD2-11 Unclassified Unclassified Unclassified Otu8619 0.602326 1 \n", " Proteobacteria Alphaproteobacteria Rhizobiales Beijerinckiaceae Microvirga Otu8620 0.574257 0 \n", " Gammaproteobacteria Betaproteobacteriales TRA3-20 Unclassified Otu8621 0.565421 0 \n", " Planctomycetes Planctomycetacia Isosphaerales Isosphaeraceae Unclassified Otu8622 0.654846 0 \n", " Proteobacteria Gammaproteobacteria Betaproteobacteriales Nitrosomonadaceae MND1 Otu8623 0.561772 0 \n", "Unclassified Unclassified Unclassified Unclassified Unclassified Unclassified Otu8624 0.589109 0 \n", "Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Klebsiella Otu8625 0.568765 0 \n", " Actinobacteria Acidimicrobiia Unclassified Unclassified Unclassified Otu8626 0.570370 0 \n", " Acidobacteria Holophagae Subgroup Unclassified Unclassified Otu8627 0.580420 0 \n", " Patescibacteria Microgenomatia Candidatus Unclassified Unclassified Otu8628 0.494975 0 \n", " Planctomycetes Planctomycetacia Gemmatales Gemmataceae uncultured Otu8629 0.665871 0 \n", " Proteobacteria Deltaproteobacteria Bdellovibrionales Bdellovibrionaceae OM27 Otu8630 0.570025 0 \n", " Patescibacteria Saccharimonadia Saccharimonadales Unclassified Unclassified Otu8631 0.506173 0 \n", " Actinobacteria Actinobacteria Unclassified Unclassified Unclassified Otu8632 0.582927 0 \n", "\n", "Enzyme \\\n", "Replicate 7 \n", "Name Osnat050 \n", "Domain Phylum Class Order Family Genus OTU GC_content \n", "Bacteria Cyanobacteria Oxyphotobacteria Nostocales Phormidiaceae Tychonema Otu0001 0.547847 325 \n", " Actinobacteria Actinobacteria Micrococcales Micrococcaceae Unclassified Otu0002 0.572127 321 \n", " Proteobacteria Alphaproteobacteria Azospirillales Azospirillaceae Skermanella Otu0003 0.579208 247 \n", " Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Pelomonas Otu0004 0.550117 21 \n", " Alphaproteobacteria Rhizobiales uncultured Unclassified Otu0005 0.559406 312 \n", " Sphingomonadales Sphingomonadaceae Sphingomonas Otu0006 0.522277 73 \n", " Rhizobiales Beijerinckiaceae Unclassified Otu0007 0.564356 75 \n", " Microvirga Otu0008 0.559406 123 \n", " Elsterales uncultured Unclassified Otu0009 0.574257 112 \n", " Deltaproteobacteria Myxococcales Unclassified Unclassified Otu0010 0.567757 94 \n", " Actinobacteria Rubrobacteria Rubrobacterales Rubrobacteriaceae Rubrobacter Otu0011 0.602804 224 \n", " Actinobacteria Frankiales Geodermatophilaceae Blastococcus Otu0012 0.586797 192 \n", " Streptomycetales Streptomycetaceae Streptomyces Otu0013 0.581907 86 \n", " Rubrobacteria Rubrobacterales Rubrobacteriaceae Rubrobacter Otu0014 0.593458 56 \n", " Actinobacteria Micromonosporales Micromonosporaceae Actinoplanes Otu0015 0.610294 82 \n", " Micrococcales Promicromonosporaceae Promicromonospora Otu0016 0.572127 27 \n", " Proteobacteria Alphaproteobacteria Rhizobiales Xanthobacteraceae Bradyrhizobium Otu0017 0.547030 48 \n", " Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Ralstonia Otu0018 0.533800 0 \n", " Deltaproteobacteria Myxococcales BIrii41 Unclassified Otu0019 0.565421 25 \n", " Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Aquabacterium Otu0020 0.545455 0 \n", " Alphaproteobacteria Rhodobacterales Rhodobacteraceae Rubellimicrobium Otu0021 0.576733 40 \n", " Rhizobiales Beijerinckiaceae Unclassified Otu0022 0.576733 68 \n", " Sphingomonadales Sphingomonadaceae Novosphingobium Otu0023 0.529703 0 \n", " Acetobacterales Acetobacteraceae uncultured Otu0024 0.586634 22 \n", " Rhizobiales Beijerinckiaceae uncultured Otu0025 0.564356 91 \n", " Actinobacteria Actinobacteria Micrococcales Cellulomonadaceae Cellulomonas Otu0026 0.581907 56 \n", " Pseudonocardiales Pseudonocardiaceae Saccharothrix Otu0027 0.584352 22 \n", " Bacteroidetes Bacteroidia Cytophagales Cytophagaceae Rhodocytophaga Otu0028 0.508274 3 \n", " Proteobacteria Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Ralstonia Otu0029 0.536131 0 \n", " Actinobacteria Thermoleophilia Solirubrobacterales Solirubrobacteraceae Solirubrobacter Otu0030 0.585082 134 \n", "... ... \n", " Unclassified Unclassified Unclassified Otu8603 0.592075 0 \n", " Elusimicrobia Elusimicrobia MVP-88 Unclassified Unclassified Otu8604 0.549528 0 \n", " Actinobacteria Acidimicrobiia uncultured Unclassified Unclassified Otu8605 0.595533 0 \n", " Acidobacteria Subgroup Unclassified Unclassified Unclassified Otu8606 0.593458 0 \n", "Unclassified Unclassified Unclassified Unclassified Unclassified Unclassified Otu8607 0.474453 0 \n", " Otu8608 0.519814 0 \n", "Bacteria Firmicutes Bacilli Bacillales Planococcaceae Planococcus Otu8609 0.551402 0 \n", " Planctomycetes Planctomycetacia Gemmatales Gemmataceae Unclassified Otu8610 0.544335 0 \n", " Proteobacteria Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Unclassified Otu8611 0.552448 0 \n", " Entotheonellaeota Entotheonellia Entotheonellales Entotheonellaceae Unclassified Otu8612 0.558313 0 \n", " Proteobacteria Deltaproteobacteria Oligoflexales 0319-6G20 Unclassified Otu8613 0.586047 0 \n", " Alphaproteobacteria Caulobacterales Caulobacteraceae Brevundimonas Otu8614 0.533499 0 \n", " Gammaproteobacteria Betaproteobacteriales TRA3-20 Unclassified Otu8615 0.572093 0 \n", " Chlamydiae Chlamydiae Chlamydiales Parachlamydiaceae Unclassified Otu8616 0.517483 0 \n", "Unclassified Unclassified Unclassified Unclassified Unclassified Unclassified Otu8617 0.542056 0 \n", "Bacteria Proteobacteria Deltaproteobacteria Oligoflexales 0319-6G20 Unclassified Otu8618 0.561772 0 \n", " Gemmatimonadetes BD2-11 Unclassified Unclassified Unclassified Otu8619 0.602326 0 \n", " Proteobacteria Alphaproteobacteria Rhizobiales Beijerinckiaceae Microvirga Otu8620 0.574257 0 \n", " Gammaproteobacteria Betaproteobacteriales TRA3-20 Unclassified Otu8621 0.565421 0 \n", " Planctomycetes Planctomycetacia Isosphaerales Isosphaeraceae Unclassified Otu8622 0.654846 0 \n", " Proteobacteria Gammaproteobacteria Betaproteobacteriales Nitrosomonadaceae MND1 Otu8623 0.561772 0 \n", "Unclassified Unclassified Unclassified Unclassified Unclassified Unclassified Otu8624 0.589109 0 \n", "Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Klebsiella Otu8625 0.568765 0 \n", " Actinobacteria Acidimicrobiia Unclassified Unclassified Unclassified Otu8626 0.570370 0 \n", " Acidobacteria Holophagae Subgroup Unclassified Unclassified Otu8627 0.580420 0 \n", " Patescibacteria Microgenomatia Candidatus Unclassified Unclassified Otu8628 0.494975 0 \n", " Planctomycetes Planctomycetacia Gemmatales Gemmataceae uncultured Otu8629 0.665871 0 \n", " Proteobacteria Deltaproteobacteria Bdellovibrionales Bdellovibrionaceae OM27 Otu8630 0.570025 0 \n", " Patescibacteria Saccharimonadia Saccharimonadales Unclassified Unclassified Otu8631 0.506173 0 \n", " Actinobacteria Actinobacteria Unclassified Unclassified Unclassified Otu8632 0.582927 0 \n", "\n", "Enzyme Promega42 \\\n", "Replicate 1 \n", "Name Osnat051 \n", "Domain Phylum Class Order Family Genus OTU GC_content \n", "Bacteria Cyanobacteria Oxyphotobacteria Nostocales Phormidiaceae Tychonema Otu0001 0.547847 9 \n", " Actinobacteria Actinobacteria Micrococcales Micrococcaceae Unclassified Otu0002 0.572127 336 \n", " Proteobacteria Alphaproteobacteria Azospirillales Azospirillaceae Skermanella Otu0003 0.579208 96 \n", " Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Pelomonas Otu0004 0.550117 268 \n", " Alphaproteobacteria Rhizobiales uncultured Unclassified Otu0005 0.559406 137 \n", " Sphingomonadales Sphingomonadaceae Sphingomonas Otu0006 0.522277 438 \n", " Rhizobiales Beijerinckiaceae Unclassified Otu0007 0.564356 22 \n", " Microvirga Otu0008 0.559406 91 \n", " Elsterales uncultured Unclassified Otu0009 0.574257 22 \n", " Deltaproteobacteria Myxococcales Unclassified Unclassified Otu0010 0.567757 40 \n", " Actinobacteria Rubrobacteria Rubrobacterales Rubrobacteriaceae Rubrobacter Otu0011 0.602804 68 \n", " Actinobacteria Frankiales Geodermatophilaceae Blastococcus Otu0012 0.586797 241 \n", " Streptomycetales Streptomycetaceae Streptomyces Otu0013 0.581907 102 \n", " Rubrobacteria Rubrobacterales Rubrobacteriaceae Rubrobacter Otu0014 0.593458 32 \n", " Actinobacteria Micromonosporales Micromonosporaceae Actinoplanes Otu0015 0.610294 78 \n", " Micrococcales Promicromonosporaceae Promicromonospora Otu0016 0.572127 43 \n", " Proteobacteria Alphaproteobacteria Rhizobiales Xanthobacteraceae Bradyrhizobium Otu0017 0.547030 56 \n", " Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Ralstonia Otu0018 0.533800 0 \n", " Deltaproteobacteria Myxococcales BIrii41 Unclassified Otu0019 0.565421 4 \n", " Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Aquabacterium Otu0020 0.545455 0 \n", " Alphaproteobacteria Rhodobacterales Rhodobacteraceae Rubellimicrobium Otu0021 0.576733 37 \n", " Rhizobiales Beijerinckiaceae Unclassified Otu0022 0.576733 56 \n", " Sphingomonadales Sphingomonadaceae Novosphingobium Otu0023 0.529703 11 \n", " Acetobacterales Acetobacteraceae uncultured Otu0024 0.586634 3 \n", " Rhizobiales Beijerinckiaceae uncultured Otu0025 0.564356 43 \n", " Actinobacteria Actinobacteria Micrococcales Cellulomonadaceae Cellulomonas Otu0026 0.581907 68 \n", " Pseudonocardiales Pseudonocardiaceae Saccharothrix Otu0027 0.584352 20 \n", " Bacteroidetes Bacteroidia Cytophagales Cytophagaceae Rhodocytophaga Otu0028 0.508274 3 \n", " Proteobacteria Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Ralstonia Otu0029 0.536131 28 \n", " Actinobacteria Thermoleophilia Solirubrobacterales Solirubrobacteraceae Solirubrobacter Otu0030 0.585082 44 \n", "... ... \n", " Unclassified Unclassified Unclassified Otu8603 0.592075 0 \n", " Elusimicrobia Elusimicrobia MVP-88 Unclassified Unclassified Otu8604 0.549528 0 \n", " Actinobacteria Acidimicrobiia uncultured Unclassified Unclassified Otu8605 0.595533 0 \n", " Acidobacteria Subgroup Unclassified Unclassified Unclassified Otu8606 0.593458 0 \n", "Unclassified Unclassified Unclassified Unclassified Unclassified Unclassified Otu8607 0.474453 0 \n", " Otu8608 0.519814 0 \n", "Bacteria Firmicutes Bacilli Bacillales Planococcaceae Planococcus Otu8609 0.551402 0 \n", " Planctomycetes Planctomycetacia Gemmatales Gemmataceae Unclassified Otu8610 0.544335 0 \n", " Proteobacteria Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Unclassified Otu8611 0.552448 0 \n", " Entotheonellaeota Entotheonellia Entotheonellales Entotheonellaceae Unclassified Otu8612 0.558313 0 \n", " Proteobacteria Deltaproteobacteria Oligoflexales 0319-6G20 Unclassified Otu8613 0.586047 0 \n", " Alphaproteobacteria Caulobacterales Caulobacteraceae Brevundimonas Otu8614 0.533499 3 \n", " Gammaproteobacteria Betaproteobacteriales TRA3-20 Unclassified Otu8615 0.572093 0 \n", " Chlamydiae Chlamydiae Chlamydiales Parachlamydiaceae Unclassified Otu8616 0.517483 0 \n", "Unclassified Unclassified Unclassified Unclassified Unclassified Unclassified Otu8617 0.542056 0 \n", "Bacteria Proteobacteria Deltaproteobacteria Oligoflexales 0319-6G20 Unclassified Otu8618 0.561772 0 \n", " Gemmatimonadetes BD2-11 Unclassified Unclassified Unclassified Otu8619 0.602326 0 \n", " Proteobacteria Alphaproteobacteria Rhizobiales Beijerinckiaceae Microvirga Otu8620 0.574257 0 \n", " Gammaproteobacteria Betaproteobacteriales TRA3-20 Unclassified Otu8621 0.565421 0 \n", " Planctomycetes Planctomycetacia Isosphaerales Isosphaeraceae Unclassified Otu8622 0.654846 0 \n", " Proteobacteria Gammaproteobacteria Betaproteobacteriales Nitrosomonadaceae MND1 Otu8623 0.561772 0 \n", "Unclassified Unclassified Unclassified Unclassified Unclassified Unclassified Otu8624 0.589109 0 \n", "Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Klebsiella Otu8625 0.568765 0 \n", " Actinobacteria Acidimicrobiia Unclassified Unclassified Unclassified Otu8626 0.570370 0 \n", " Acidobacteria Holophagae Subgroup Unclassified Unclassified Otu8627 0.580420 0 \n", " Patescibacteria Microgenomatia Candidatus Unclassified Unclassified Otu8628 0.494975 0 \n", " Planctomycetes Planctomycetacia Gemmatales Gemmataceae uncultured Otu8629 0.665871 0 \n", " Proteobacteria Deltaproteobacteria Bdellovibrionales Bdellovibrionaceae OM27 Otu8630 0.570025 0 \n", " Patescibacteria Saccharimonadia Saccharimonadales Unclassified Unclassified Otu8631 0.506173 0 \n", " Actinobacteria Actinobacteria Unclassified Unclassified Unclassified Otu8632 0.582927 0 \n", "\n", "Enzyme \\\n", "Replicate 2 \n", "Name Osnat052 \n", "Domain Phylum Class Order Family Genus OTU GC_content \n", "Bacteria Cyanobacteria Oxyphotobacteria Nostocales Phormidiaceae Tychonema Otu0001 0.547847 1254 \n", " Actinobacteria Actinobacteria Micrococcales Micrococcaceae Unclassified Otu0002 0.572127 180 \n", " Proteobacteria Alphaproteobacteria Azospirillales Azospirillaceae Skermanella Otu0003 0.579208 271 \n", " Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Pelomonas Otu0004 0.550117 5 \n", " Alphaproteobacteria Rhizobiales uncultured Unclassified Otu0005 0.559406 201 \n", " Sphingomonadales Sphingomonadaceae Sphingomonas Otu0006 0.522277 107 \n", " Rhizobiales Beijerinckiaceae Unclassified Otu0007 0.564356 103 \n", " Microvirga Otu0008 0.559406 108 \n", " Elsterales uncultured Unclassified Otu0009 0.574257 22 \n", " Deltaproteobacteria Myxococcales Unclassified Unclassified Otu0010 0.567757 346 \n", " Actinobacteria Rubrobacteria Rubrobacterales Rubrobacteriaceae Rubrobacter Otu0011 0.602804 54 \n", " Actinobacteria Frankiales Geodermatophilaceae Blastococcus Otu0012 0.586797 81 \n", " Streptomycetales Streptomycetaceae Streptomyces Otu0013 0.581907 21 \n", " Rubrobacteria Rubrobacterales Rubrobacteriaceae Rubrobacter Otu0014 0.593458 104 \n", " Actinobacteria Micromonosporales Micromonosporaceae Actinoplanes Otu0015 0.610294 23 \n", " Micrococcales Promicromonosporaceae Promicromonospora Otu0016 0.572127 20 \n", " Proteobacteria Alphaproteobacteria Rhizobiales Xanthobacteraceae Bradyrhizobium Otu0017 0.547030 12 \n", " Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Ralstonia Otu0018 0.533800 0 \n", " Deltaproteobacteria Myxococcales BIrii41 Unclassified Otu0019 0.565421 140 \n", " Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Aquabacterium Otu0020 0.545455 0 \n", " Alphaproteobacteria Rhodobacterales Rhodobacteraceae Rubellimicrobium Otu0021 0.576733 143 \n", " Rhizobiales Beijerinckiaceae Unclassified Otu0022 0.576733 32 \n", " Sphingomonadales Sphingomonadaceae Novosphingobium Otu0023 0.529703 0 \n", " Acetobacterales Acetobacteraceae uncultured Otu0024 0.586634 4 \n", " Rhizobiales Beijerinckiaceae uncultured Otu0025 0.564356 31 \n", " Actinobacteria Actinobacteria Micrococcales Cellulomonadaceae Cellulomonas Otu0026 0.581907 81 \n", " Pseudonocardiales Pseudonocardiaceae Saccharothrix Otu0027 0.584352 16 \n", " Bacteroidetes Bacteroidia Cytophagales Cytophagaceae Rhodocytophaga Otu0028 0.508274 48 \n", " Proteobacteria Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Ralstonia Otu0029 0.536131 1 \n", " Actinobacteria Thermoleophilia Solirubrobacterales Solirubrobacteraceae Solirubrobacter Otu0030 0.585082 40 \n", "... ... \n", " Unclassified Unclassified Unclassified Otu8603 0.592075 0 \n", " Elusimicrobia Elusimicrobia MVP-88 Unclassified Unclassified Otu8604 0.549528 0 \n", " Actinobacteria Acidimicrobiia uncultured Unclassified Unclassified Otu8605 0.595533 0 \n", " Acidobacteria Subgroup Unclassified Unclassified Unclassified Otu8606 0.593458 0 \n", "Unclassified Unclassified Unclassified Unclassified Unclassified Unclassified Otu8607 0.474453 0 \n", " Otu8608 0.519814 0 \n", "Bacteria Firmicutes Bacilli Bacillales Planococcaceae Planococcus Otu8609 0.551402 0 \n", " Planctomycetes Planctomycetacia Gemmatales Gemmataceae Unclassified Otu8610 0.544335 0 \n", " Proteobacteria Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Unclassified Otu8611 0.552448 0 \n", " Entotheonellaeota Entotheonellia Entotheonellales Entotheonellaceae Unclassified Otu8612 0.558313 0 \n", " Proteobacteria Deltaproteobacteria Oligoflexales 0319-6G20 Unclassified Otu8613 0.586047 0 \n", " Alphaproteobacteria Caulobacterales Caulobacteraceae Brevundimonas Otu8614 0.533499 1 \n", " Gammaproteobacteria Betaproteobacteriales TRA3-20 Unclassified Otu8615 0.572093 0 \n", " Chlamydiae Chlamydiae Chlamydiales Parachlamydiaceae Unclassified Otu8616 0.517483 0 \n", "Unclassified Unclassified Unclassified Unclassified Unclassified Unclassified Otu8617 0.542056 0 \n", "Bacteria Proteobacteria Deltaproteobacteria Oligoflexales 0319-6G20 Unclassified Otu8618 0.561772 0 \n", " Gemmatimonadetes BD2-11 Unclassified Unclassified Unclassified Otu8619 0.602326 0 \n", " Proteobacteria Alphaproteobacteria Rhizobiales Beijerinckiaceae Microvirga Otu8620 0.574257 0 \n", " Gammaproteobacteria Betaproteobacteriales TRA3-20 Unclassified Otu8621 0.565421 0 \n", " Planctomycetes Planctomycetacia Isosphaerales Isosphaeraceae Unclassified Otu8622 0.654846 0 \n", " Proteobacteria Gammaproteobacteria Betaproteobacteriales Nitrosomonadaceae MND1 Otu8623 0.561772 0 \n", "Unclassified Unclassified Unclassified Unclassified Unclassified Unclassified Otu8624 0.589109 0 \n", "Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Klebsiella Otu8625 0.568765 0 \n", " Actinobacteria Acidimicrobiia Unclassified Unclassified Unclassified Otu8626 0.570370 0 \n", " Acidobacteria Holophagae Subgroup Unclassified Unclassified Otu8627 0.580420 0 \n", " Patescibacteria Microgenomatia Candidatus Unclassified Unclassified Otu8628 0.494975 0 \n", " Planctomycetes Planctomycetacia Gemmatales Gemmataceae uncultured Otu8629 0.665871 0 \n", " Proteobacteria Deltaproteobacteria Bdellovibrionales Bdellovibrionaceae OM27 Otu8630 0.570025 0 \n", " Patescibacteria Saccharimonadia Saccharimonadales Unclassified Unclassified Otu8631 0.506173 0 \n", " Actinobacteria Actinobacteria Unclassified Unclassified Unclassified Otu8632 0.582927 0 \n", "\n", "Enzyme \\\n", "Replicate 3 \n", "Name Osnat053 \n", "Domain Phylum Class Order Family Genus OTU GC_content \n", "Bacteria Cyanobacteria Oxyphotobacteria Nostocales Phormidiaceae Tychonema Otu0001 0.547847 294 \n", " Actinobacteria Actinobacteria Micrococcales Micrococcaceae Unclassified Otu0002 0.572127 260 \n", " Proteobacteria Alphaproteobacteria Azospirillales Azospirillaceae Skermanella Otu0003 0.579208 399 \n", " Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Pelomonas Otu0004 0.550117 274 \n", " Alphaproteobacteria Rhizobiales uncultured Unclassified Otu0005 0.559406 424 \n", " Sphingomonadales Sphingomonadaceae Sphingomonas Otu0006 0.522277 375 \n", " Rhizobiales Beijerinckiaceae Unclassified Otu0007 0.564356 66 \n", " Microvirga Otu0008 0.559406 90 \n", " Elsterales uncultured Unclassified Otu0009 0.574257 118 \n", " Deltaproteobacteria Myxococcales Unclassified Unclassified Otu0010 0.567757 363 \n", " Actinobacteria Rubrobacteria Rubrobacterales Rubrobacteriaceae Rubrobacter Otu0011 0.602804 51 \n", " Actinobacteria Frankiales Geodermatophilaceae Blastococcus Otu0012 0.586797 47 \n", " Streptomycetales Streptomycetaceae Streptomyces Otu0013 0.581907 14 \n", " Rubrobacteria Rubrobacterales Rubrobacteriaceae Rubrobacter Otu0014 0.593458 80 \n", " Actinobacteria Micromonosporales Micromonosporaceae Actinoplanes Otu0015 0.610294 6 \n", " Micrococcales Promicromonosporaceae Promicromonospora Otu0016 0.572127 13 \n", " Proteobacteria Alphaproteobacteria Rhizobiales Xanthobacteraceae Bradyrhizobium Otu0017 0.547030 76 \n", " Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Ralstonia Otu0018 0.533800 0 \n", " Deltaproteobacteria Myxococcales BIrii41 Unclassified Otu0019 0.565421 66 \n", " Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Aquabacterium Otu0020 0.545455 0 \n", " Alphaproteobacteria Rhodobacterales Rhodobacteraceae Rubellimicrobium Otu0021 0.576733 35 \n", " Rhizobiales Beijerinckiaceae Unclassified Otu0022 0.576733 91 \n", " Sphingomonadales Sphingomonadaceae Novosphingobium Otu0023 0.529703 0 \n", " Acetobacterales Acetobacteraceae uncultured Otu0024 0.586634 28 \n", " Rhizobiales Beijerinckiaceae uncultured Otu0025 0.564356 73 \n", " Actinobacteria Actinobacteria Micrococcales Cellulomonadaceae Cellulomonas Otu0026 0.581907 37 \n", " Pseudonocardiales Pseudonocardiaceae Saccharothrix Otu0027 0.584352 12 \n", " Bacteroidetes Bacteroidia Cytophagales Cytophagaceae Rhodocytophaga Otu0028 0.508274 11 \n", " Proteobacteria Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Ralstonia Otu0029 0.536131 69 \n", " Actinobacteria Thermoleophilia Solirubrobacterales Solirubrobacteraceae Solirubrobacter Otu0030 0.585082 34 \n", "... ... \n", " Unclassified Unclassified Unclassified Otu8603 0.592075 0 \n", " Elusimicrobia Elusimicrobia MVP-88 Unclassified Unclassified Otu8604 0.549528 0 \n", " Actinobacteria Acidimicrobiia uncultured Unclassified Unclassified Otu8605 0.595533 0 \n", " Acidobacteria Subgroup Unclassified Unclassified Unclassified Otu8606 0.593458 0 \n", "Unclassified Unclassified Unclassified Unclassified Unclassified Unclassified Otu8607 0.474453 0 \n", " Otu8608 0.519814 0 \n", "Bacteria Firmicutes Bacilli Bacillales Planococcaceae Planococcus Otu8609 0.551402 0 \n", " Planctomycetes Planctomycetacia Gemmatales Gemmataceae Unclassified Otu8610 0.544335 0 \n", " Proteobacteria Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Unclassified Otu8611 0.552448 0 \n", " Entotheonellaeota Entotheonellia Entotheonellales Entotheonellaceae Unclassified Otu8612 0.558313 0 \n", " Proteobacteria Deltaproteobacteria Oligoflexales 0319-6G20 Unclassified Otu8613 0.586047 0 \n", " Alphaproteobacteria Caulobacterales Caulobacteraceae Brevundimonas Otu8614 0.533499 1 \n", " Gammaproteobacteria Betaproteobacteriales TRA3-20 Unclassified Otu8615 0.572093 0 \n", " Chlamydiae Chlamydiae Chlamydiales Parachlamydiaceae Unclassified Otu8616 0.517483 0 \n", "Unclassified Unclassified Unclassified Unclassified Unclassified Unclassified Otu8617 0.542056 0 \n", "Bacteria Proteobacteria Deltaproteobacteria Oligoflexales 0319-6G20 Unclassified Otu8618 0.561772 0 \n", " Gemmatimonadetes BD2-11 Unclassified Unclassified Unclassified Otu8619 0.602326 0 \n", " Proteobacteria Alphaproteobacteria Rhizobiales Beijerinckiaceae Microvirga Otu8620 0.574257 0 \n", " Gammaproteobacteria Betaproteobacteriales TRA3-20 Unclassified Otu8621 0.565421 0 \n", " Planctomycetes Planctomycetacia Isosphaerales Isosphaeraceae Unclassified Otu8622 0.654846 0 \n", " Proteobacteria Gammaproteobacteria Betaproteobacteriales Nitrosomonadaceae MND1 Otu8623 0.561772 0 \n", "Unclassified Unclassified Unclassified Unclassified Unclassified Unclassified Otu8624 0.589109 0 \n", "Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Klebsiella Otu8625 0.568765 0 \n", " Actinobacteria Acidimicrobiia Unclassified Unclassified Unclassified Otu8626 0.570370 0 \n", " Acidobacteria Holophagae Subgroup Unclassified Unclassified Otu8627 0.580420 0 \n", " Patescibacteria Microgenomatia Candidatus Unclassified Unclassified Otu8628 0.494975 0 \n", " Planctomycetes Planctomycetacia Gemmatales Gemmataceae uncultured Otu8629 0.665871 0 \n", " Proteobacteria Deltaproteobacteria Bdellovibrionales Bdellovibrionaceae OM27 Otu8630 0.570025 0 \n", " Patescibacteria Saccharimonadia Saccharimonadales Unclassified Unclassified Otu8631 0.506173 0 \n", " Actinobacteria Actinobacteria Unclassified Unclassified Unclassified Otu8632 0.582927 0 \n", "\n", "Enzyme \\\n", "Replicate 4 \n", "Name Osnat054 \n", "Domain Phylum Class Order Family Genus OTU GC_content \n", "Bacteria Cyanobacteria Oxyphotobacteria Nostocales Phormidiaceae Tychonema Otu0001 0.547847 318 \n", " Actinobacteria Actinobacteria Micrococcales Micrococcaceae Unclassified Otu0002 0.572127 169 \n", " Proteobacteria Alphaproteobacteria Azospirillales Azospirillaceae Skermanella Otu0003 0.579208 327 \n", " Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Pelomonas Otu0004 0.550117 851 \n", " Alphaproteobacteria Rhizobiales uncultured Unclassified Otu0005 0.559406 249 \n", " Sphingomonadales Sphingomonadaceae Sphingomonas Otu0006 0.522277 809 \n", " Rhizobiales Beijerinckiaceae Unclassified Otu0007 0.564356 80 \n", " Microvirga Otu0008 0.559406 59 \n", " Elsterales uncultured Unclassified Otu0009 0.574257 70 \n", " Deltaproteobacteria Myxococcales Unclassified Unclassified Otu0010 0.567757 157 \n", " Actinobacteria Rubrobacteria Rubrobacterales Rubrobacteriaceae Rubrobacter Otu0011 0.602804 25 \n", " Actinobacteria Frankiales Geodermatophilaceae Blastococcus Otu0012 0.586797 89 \n", " Streptomycetales Streptomycetaceae Streptomyces Otu0013 0.581907 15 \n", " Rubrobacteria Rubrobacterales Rubrobacteriaceae Rubrobacter Otu0014 0.593458 46 \n", " Actinobacteria Micromonosporales Micromonosporaceae Actinoplanes Otu0015 0.610294 15 \n", " Micrococcales Promicromonosporaceae Promicromonospora Otu0016 0.572127 3 \n", " Proteobacteria Alphaproteobacteria Rhizobiales Xanthobacteraceae Bradyrhizobium Otu0017 0.547030 170 \n", " Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Ralstonia Otu0018 0.533800 0 \n", " Deltaproteobacteria Myxococcales BIrii41 Unclassified Otu0019 0.565421 26 \n", " Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Aquabacterium Otu0020 0.545455 0 \n", " Alphaproteobacteria Rhodobacterales Rhodobacteraceae Rubellimicrobium Otu0021 0.576733 31 \n", " Rhizobiales Beijerinckiaceae Unclassified Otu0022 0.576733 23 \n", " Sphingomonadales Sphingomonadaceae Novosphingobium Otu0023 0.529703 0 \n", " Acetobacterales Acetobacteraceae uncultured Otu0024 0.586634 7 \n", " Rhizobiales Beijerinckiaceae uncultured Otu0025 0.564356 27 \n", " Actinobacteria Actinobacteria Micrococcales Cellulomonadaceae Cellulomonas Otu0026 0.581907 37 \n", " Pseudonocardiales Pseudonocardiaceae Saccharothrix Otu0027 0.584352 4 \n", " Bacteroidetes Bacteroidia Cytophagales Cytophagaceae Rhodocytophaga Otu0028 0.508274 1 \n", " Proteobacteria Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Ralstonia Otu0029 0.536131 165 \n", " Actinobacteria Thermoleophilia Solirubrobacterales Solirubrobacteraceae Solirubrobacter Otu0030 0.585082 26 \n", "... ... \n", " Unclassified Unclassified Unclassified Otu8603 0.592075 0 \n", " Elusimicrobia Elusimicrobia MVP-88 Unclassified Unclassified Otu8604 0.549528 0 \n", " Actinobacteria Acidimicrobiia uncultured Unclassified Unclassified Otu8605 0.595533 0 \n", " Acidobacteria Subgroup Unclassified Unclassified Unclassified Otu8606 0.593458 0 \n", "Unclassified Unclassified Unclassified Unclassified Unclassified Unclassified Otu8607 0.474453 0 \n", " Otu8608 0.519814 0 \n", "Bacteria Firmicutes Bacilli Bacillales Planococcaceae Planococcus Otu8609 0.551402 0 \n", " Planctomycetes Planctomycetacia Gemmatales Gemmataceae Unclassified Otu8610 0.544335 0 \n", " Proteobacteria Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Unclassified Otu8611 0.552448 0 \n", " Entotheonellaeota Entotheonellia Entotheonellales Entotheonellaceae Unclassified Otu8612 0.558313 0 \n", " Proteobacteria Deltaproteobacteria Oligoflexales 0319-6G20 Unclassified Otu8613 0.586047 0 \n", " Alphaproteobacteria Caulobacterales Caulobacteraceae Brevundimonas Otu8614 0.533499 0 \n", " Gammaproteobacteria Betaproteobacteriales TRA3-20 Unclassified Otu8615 0.572093 0 \n", " Chlamydiae Chlamydiae Chlamydiales Parachlamydiaceae Unclassified Otu8616 0.517483 0 \n", "Unclassified Unclassified Unclassified Unclassified Unclassified Unclassified Otu8617 0.542056 0 \n", "Bacteria Proteobacteria Deltaproteobacteria Oligoflexales 0319-6G20 Unclassified Otu8618 0.561772 0 \n", " Gemmatimonadetes BD2-11 Unclassified Unclassified Unclassified Otu8619 0.602326 0 \n", " Proteobacteria Alphaproteobacteria Rhizobiales Beijerinckiaceae Microvirga Otu8620 0.574257 0 \n", " Gammaproteobacteria Betaproteobacteriales TRA3-20 Unclassified Otu8621 0.565421 0 \n", " Planctomycetes Planctomycetacia Isosphaerales Isosphaeraceae Unclassified Otu8622 0.654846 0 \n", " Proteobacteria Gammaproteobacteria Betaproteobacteriales Nitrosomonadaceae MND1 Otu8623 0.561772 0 \n", "Unclassified Unclassified Unclassified Unclassified Unclassified Unclassified Otu8624 0.589109 0 \n", "Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Klebsiella Otu8625 0.568765 0 \n", " Actinobacteria Acidimicrobiia Unclassified Unclassified Unclassified Otu8626 0.570370 0 \n", " Acidobacteria Holophagae Subgroup Unclassified Unclassified Otu8627 0.580420 0 \n", " Patescibacteria Microgenomatia Candidatus Unclassified Unclassified Otu8628 0.494975 0 \n", " Planctomycetes Planctomycetacia Gemmatales Gemmataceae uncultured Otu8629 0.665871 0 \n", " Proteobacteria Deltaproteobacteria Bdellovibrionales Bdellovibrionaceae OM27 Otu8630 0.570025 0 \n", " Patescibacteria Saccharimonadia Saccharimonadales Unclassified Unclassified Otu8631 0.506173 0 \n", " Actinobacteria Actinobacteria Unclassified Unclassified Unclassified Otu8632 0.582927 0 \n", "\n", "Enzyme \\\n", "Replicate 7 \n", "Name Osnat057 \n", "Domain Phylum Class Order Family Genus OTU GC_content \n", "Bacteria Cyanobacteria Oxyphotobacteria Nostocales Phormidiaceae Tychonema Otu0001 0.547847 268 \n", " Actinobacteria Actinobacteria Micrococcales Micrococcaceae Unclassified Otu0002 0.572127 232 \n", " Proteobacteria Alphaproteobacteria Azospirillales Azospirillaceae Skermanella Otu0003 0.579208 218 \n", " Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Pelomonas Otu0004 0.550117 149 \n", " Alphaproteobacteria Rhizobiales uncultured Unclassified Otu0005 0.559406 313 \n", " Sphingomonadales Sphingomonadaceae Sphingomonas Otu0006 0.522277 433 \n", " Rhizobiales Beijerinckiaceae Unclassified Otu0007 0.564356 58 \n", " Microvirga Otu0008 0.559406 75 \n", " Elsterales uncultured Unclassified Otu0009 0.574257 157 \n", " Deltaproteobacteria Myxococcales Unclassified Unclassified Otu0010 0.567757 90 \n", " Actinobacteria Rubrobacteria Rubrobacterales Rubrobacteriaceae Rubrobacter Otu0011 0.602804 56 \n", " Actinobacteria Frankiales Geodermatophilaceae Blastococcus Otu0012 0.586797 127 \n", " Streptomycetales Streptomycetaceae Streptomyces Otu0013 0.581907 23 \n", " Rubrobacteria Rubrobacterales Rubrobacteriaceae Rubrobacter Otu0014 0.593458 56 \n", " Actinobacteria Micromonosporales Micromonosporaceae Actinoplanes Otu0015 0.610294 32 \n", " Micrococcales Promicromonosporaceae Promicromonospora Otu0016 0.572127 17 \n", " Proteobacteria Alphaproteobacteria Rhizobiales Xanthobacteraceae Bradyrhizobium Otu0017 0.547030 89 \n", " Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Ralstonia Otu0018 0.533800 0 \n", " Deltaproteobacteria Myxococcales BIrii41 Unclassified Otu0019 0.565421 20 \n", " Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Aquabacterium Otu0020 0.545455 0 \n", " Alphaproteobacteria Rhodobacterales Rhodobacteraceae Rubellimicrobium Otu0021 0.576733 29 \n", " Rhizobiales Beijerinckiaceae Unclassified Otu0022 0.576733 37 \n", " Sphingomonadales Sphingomonadaceae Novosphingobium Otu0023 0.529703 0 \n", " Acetobacterales Acetobacteraceae uncultured Otu0024 0.586634 16 \n", " Rhizobiales Beijerinckiaceae uncultured Otu0025 0.564356 81 \n", " Actinobacteria Actinobacteria Micrococcales Cellulomonadaceae Cellulomonas Otu0026 0.581907 40 \n", " Pseudonocardiales Pseudonocardiaceae Saccharothrix Otu0027 0.584352 9 \n", " Bacteroidetes Bacteroidia Cytophagales Cytophagaceae Rhodocytophaga Otu0028 0.508274 4 \n", " Proteobacteria Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Ralstonia Otu0029 0.536131 78 \n", " Actinobacteria Thermoleophilia Solirubrobacterales Solirubrobacteraceae Solirubrobacter Otu0030 0.585082 128 \n", "... ... \n", " Unclassified Unclassified Unclassified Otu8603 0.592075 0 \n", " Elusimicrobia Elusimicrobia MVP-88 Unclassified Unclassified Otu8604 0.549528 0 \n", " Actinobacteria Acidimicrobiia uncultured Unclassified Unclassified Otu8605 0.595533 0 \n", " Acidobacteria Subgroup Unclassified Unclassified Unclassified Otu8606 0.593458 0 \n", "Unclassified Unclassified Unclassified Unclassified Unclassified Unclassified Otu8607 0.474453 0 \n", " Otu8608 0.519814 0 \n", "Bacteria Firmicutes Bacilli Bacillales Planococcaceae Planococcus Otu8609 0.551402 0 \n", " Planctomycetes Planctomycetacia Gemmatales Gemmataceae Unclassified Otu8610 0.544335 0 \n", " Proteobacteria Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Unclassified Otu8611 0.552448 0 \n", " Entotheonellaeota Entotheonellia Entotheonellales Entotheonellaceae Unclassified Otu8612 0.558313 0 \n", " Proteobacteria Deltaproteobacteria Oligoflexales 0319-6G20 Unclassified Otu8613 0.586047 0 \n", " Alphaproteobacteria Caulobacterales Caulobacteraceae Brevundimonas Otu8614 0.533499 0 \n", " Gammaproteobacteria Betaproteobacteriales TRA3-20 Unclassified Otu8615 0.572093 0 \n", " Chlamydiae Chlamydiae Chlamydiales Parachlamydiaceae Unclassified Otu8616 0.517483 0 \n", "Unclassified Unclassified Unclassified Unclassified Unclassified Unclassified Otu8617 0.542056 0 \n", "Bacteria Proteobacteria Deltaproteobacteria Oligoflexales 0319-6G20 Unclassified Otu8618 0.561772 0 \n", " Gemmatimonadetes BD2-11 Unclassified Unclassified Unclassified Otu8619 0.602326 0 \n", " Proteobacteria Alphaproteobacteria Rhizobiales Beijerinckiaceae Microvirga Otu8620 0.574257 0 \n", " Gammaproteobacteria Betaproteobacteriales TRA3-20 Unclassified Otu8621 0.565421 0 \n", " Planctomycetes Planctomycetacia Isosphaerales Isosphaeraceae Unclassified Otu8622 0.654846 0 \n", " Proteobacteria Gammaproteobacteria Betaproteobacteriales Nitrosomonadaceae MND1 Otu8623 0.561772 0 \n", "Unclassified Unclassified Unclassified Unclassified Unclassified Unclassified Otu8624 0.589109 0 \n", "Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Klebsiella Otu8625 0.568765 0 \n", " Actinobacteria Acidimicrobiia Unclassified Unclassified Unclassified Otu8626 0.570370 0 \n", " Acidobacteria Holophagae Subgroup Unclassified Unclassified Otu8627 0.580420 0 \n", " Patescibacteria Microgenomatia Candidatus Unclassified Unclassified Otu8628 0.494975 0 \n", " Planctomycetes Planctomycetacia Gemmatales Gemmataceae uncultured Otu8629 0.665871 0 \n", " Proteobacteria Deltaproteobacteria Bdellovibrionales Bdellovibrionaceae OM27 Otu8630 0.570025 2 \n", " Patescibacteria Saccharimonadia Saccharimonadales Unclassified Unclassified Otu8631 0.506173 0 \n", " Actinobacteria Actinobacteria Unclassified Unclassified Unclassified Otu8632 0.582927 0 \n", "\n", "Enzyme Promega55 \\\n", "Replicate 1 \n", "Name Osnat058 \n", "Domain Phylum Class Order Family Genus OTU GC_content \n", "Bacteria Cyanobacteria Oxyphotobacteria Nostocales Phormidiaceae Tychonema Otu0001 0.547847 17 \n", " Actinobacteria Actinobacteria Micrococcales Micrococcaceae Unclassified Otu0002 0.572127 702 \n", " Proteobacteria Alphaproteobacteria Azospirillales Azospirillaceae Skermanella Otu0003 0.579208 135 \n", " Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Pelomonas Otu0004 0.550117 49 \n", " Alphaproteobacteria Rhizobiales uncultured Unclassified Otu0005 0.559406 96 \n", " Sphingomonadales Sphingomonadaceae Sphingomonas Otu0006 0.522277 257 \n", " Rhizobiales Beijerinckiaceae Unclassified Otu0007 0.564356 54 \n", " Microvirga Otu0008 0.559406 67 \n", " Elsterales uncultured Unclassified Otu0009 0.574257 49 \n", " Deltaproteobacteria Myxococcales Unclassified Unclassified Otu0010 0.567757 90 \n", " Actinobacteria Rubrobacteria Rubrobacterales Rubrobacteriaceae Rubrobacter Otu0011 0.602804 94 \n", " Actinobacteria Frankiales Geodermatophilaceae Blastococcus Otu0012 0.586797 292 \n", " Streptomycetales Streptomycetaceae Streptomyces Otu0013 0.581907 62 \n", " Rubrobacteria Rubrobacterales Rubrobacteriaceae Rubrobacter Otu0014 0.593458 57 \n", " Actinobacteria Micromonosporales Micromonosporaceae Actinoplanes Otu0015 0.610294 100 \n", " Micrococcales Promicromonosporaceae Promicromonospora Otu0016 0.572127 38 \n", " Proteobacteria Alphaproteobacteria Rhizobiales Xanthobacteraceae Bradyrhizobium Otu0017 0.547030 53 \n", " Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Ralstonia Otu0018 0.533800 70 \n", " Deltaproteobacteria Myxococcales BIrii41 Unclassified Otu0019 0.565421 35 \n", " Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Aquabacterium Otu0020 0.545455 74 \n", " Alphaproteobacteria Rhodobacterales Rhodobacteraceae Rubellimicrobium Otu0021 0.576733 32 \n", " Rhizobiales Beijerinckiaceae Unclassified Otu0022 0.576733 27 \n", " Sphingomonadales Sphingomonadaceae Novosphingobium Otu0023 0.529703 67 \n", " Acetobacterales Acetobacteraceae uncultured Otu0024 0.586634 1 \n", " Rhizobiales Beijerinckiaceae uncultured Otu0025 0.564356 42 \n", " Actinobacteria Actinobacteria Micrococcales Cellulomonadaceae Cellulomonas Otu0026 0.581907 164 \n", " Pseudonocardiales Pseudonocardiaceae Saccharothrix Otu0027 0.584352 37 \n", " Bacteroidetes Bacteroidia Cytophagales Cytophagaceae Rhodocytophaga Otu0028 0.508274 2 \n", " Proteobacteria Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Ralstonia Otu0029 0.536131 30 \n", " Actinobacteria Thermoleophilia Solirubrobacterales Solirubrobacteraceae Solirubrobacter Otu0030 0.585082 145 \n", "... ... \n", " Unclassified Unclassified Unclassified Otu8603 0.592075 0 \n", " Elusimicrobia Elusimicrobia MVP-88 Unclassified Unclassified Otu8604 0.549528 0 \n", " Actinobacteria Acidimicrobiia uncultured Unclassified Unclassified Otu8605 0.595533 0 \n", " Acidobacteria Subgroup Unclassified Unclassified Unclassified Otu8606 0.593458 0 \n", "Unclassified Unclassified Unclassified Unclassified Unclassified Unclassified Otu8607 0.474453 0 \n", " Otu8608 0.519814 0 \n", "Bacteria Firmicutes Bacilli Bacillales Planococcaceae Planococcus Otu8609 0.551402 0 \n", " Planctomycetes Planctomycetacia Gemmatales Gemmataceae Unclassified Otu8610 0.544335 0 \n", " Proteobacteria Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Unclassified Otu8611 0.552448 0 \n", " Entotheonellaeota Entotheonellia Entotheonellales Entotheonellaceae Unclassified Otu8612 0.558313 0 \n", " Proteobacteria Deltaproteobacteria Oligoflexales 0319-6G20 Unclassified Otu8613 0.586047 0 \n", " Alphaproteobacteria Caulobacterales Caulobacteraceae Brevundimonas Otu8614 0.533499 0 \n", " Gammaproteobacteria Betaproteobacteriales TRA3-20 Unclassified Otu8615 0.572093 0 \n", " Chlamydiae Chlamydiae Chlamydiales Parachlamydiaceae Unclassified Otu8616 0.517483 0 \n", "Unclassified Unclassified Unclassified Unclassified Unclassified Unclassified Otu8617 0.542056 0 \n", "Bacteria Proteobacteria Deltaproteobacteria Oligoflexales 0319-6G20 Unclassified Otu8618 0.561772 0 \n", " Gemmatimonadetes BD2-11 Unclassified Unclassified Unclassified Otu8619 0.602326 0 \n", " Proteobacteria Alphaproteobacteria Rhizobiales Beijerinckiaceae Microvirga Otu8620 0.574257 0 \n", " Gammaproteobacteria Betaproteobacteriales TRA3-20 Unclassified Otu8621 0.565421 1 \n", " Planctomycetes Planctomycetacia Isosphaerales Isosphaeraceae Unclassified Otu8622 0.654846 0 \n", " Proteobacteria Gammaproteobacteria Betaproteobacteriales Nitrosomonadaceae MND1 Otu8623 0.561772 0 \n", "Unclassified Unclassified Unclassified Unclassified Unclassified Unclassified Otu8624 0.589109 0 \n", "Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Klebsiella Otu8625 0.568765 0 \n", " Actinobacteria Acidimicrobiia Unclassified Unclassified Unclassified Otu8626 0.570370 0 \n", " Acidobacteria Holophagae Subgroup Unclassified Unclassified Otu8627 0.580420 0 \n", " Patescibacteria Microgenomatia Candidatus Unclassified Unclassified Otu8628 0.494975 0 \n", " Planctomycetes Planctomycetacia Gemmatales Gemmataceae uncultured Otu8629 0.665871 0 \n", " Proteobacteria Deltaproteobacteria Bdellovibrionales Bdellovibrionaceae OM27 Otu8630 0.570025 0 \n", " Patescibacteria Saccharimonadia Saccharimonadales Unclassified Unclassified Otu8631 0.506173 0 \n", " Actinobacteria Actinobacteria Unclassified Unclassified Unclassified Otu8632 0.582927 0 \n", "\n", "Enzyme \\\n", "Replicate 2 \n", "Name Osnat059 \n", "Domain Phylum Class Order Family Genus OTU GC_content \n", "Bacteria Cyanobacteria Oxyphotobacteria Nostocales Phormidiaceae Tychonema Otu0001 0.547847 498 \n", " Actinobacteria Actinobacteria Micrococcales Micrococcaceae Unclassified Otu0002 0.572127 428 \n", " Proteobacteria Alphaproteobacteria Azospirillales Azospirillaceae Skermanella Otu0003 0.579208 159 \n", " Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Pelomonas Otu0004 0.550117 37 \n", " Alphaproteobacteria Rhizobiales uncultured Unclassified Otu0005 0.559406 61 \n", " Sphingomonadales Sphingomonadaceae Sphingomonas Otu0006 0.522277 196 \n", " Rhizobiales Beijerinckiaceae Unclassified Otu0007 0.564356 37 \n", " Microvirga Otu0008 0.559406 68 \n", " Elsterales uncultured Unclassified Otu0009 0.574257 12 \n", " Deltaproteobacteria Myxococcales Unclassified Unclassified Otu0010 0.567757 128 \n", " Actinobacteria Rubrobacteria Rubrobacterales Rubrobacteriaceae Rubrobacter Otu0011 0.602804 45 \n", " Actinobacteria Frankiales Geodermatophilaceae Blastococcus Otu0012 0.586797 295 \n", " Streptomycetales Streptomycetaceae Streptomyces Otu0013 0.581907 19 \n", " Rubrobacteria Rubrobacterales Rubrobacteriaceae Rubrobacter Otu0014 0.593458 87 \n", " Actinobacteria Micromonosporales Micromonosporaceae Actinoplanes Otu0015 0.610294 177 \n", " Micrococcales Promicromonosporaceae Promicromonospora Otu0016 0.572127 28 \n", " Proteobacteria Alphaproteobacteria Rhizobiales Xanthobacteraceae Bradyrhizobium Otu0017 0.547030 29 \n", " Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Ralstonia Otu0018 0.533800 40 \n", " Deltaproteobacteria Myxococcales BIrii41 Unclassified Otu0019 0.565421 202 \n", " Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Aquabacterium Otu0020 0.545455 21 \n", " Alphaproteobacteria Rhodobacterales Rhodobacteraceae Rubellimicrobium Otu0021 0.576733 63 \n", " Rhizobiales Beijerinckiaceae Unclassified Otu0022 0.576733 25 \n", " Sphingomonadales Sphingomonadaceae Novosphingobium Otu0023 0.529703 19 \n", " Acetobacterales Acetobacteraceae uncultured Otu0024 0.586634 3 \n", " Rhizobiales Beijerinckiaceae uncultured Otu0025 0.564356 12 \n", " Actinobacteria Actinobacteria Micrococcales Cellulomonadaceae Cellulomonas Otu0026 0.581907 253 \n", " Pseudonocardiales Pseudonocardiaceae Saccharothrix Otu0027 0.584352 21 \n", " Bacteroidetes Bacteroidia Cytophagales Cytophagaceae Rhodocytophaga Otu0028 0.508274 34 \n", " Proteobacteria Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Ralstonia Otu0029 0.536131 9 \n", " Actinobacteria Thermoleophilia Solirubrobacterales Solirubrobacteraceae Solirubrobacter Otu0030 0.585082 57 \n", "... ... \n", " Unclassified Unclassified Unclassified Otu8603 0.592075 0 \n", " Elusimicrobia Elusimicrobia MVP-88 Unclassified Unclassified Otu8604 0.549528 0 \n", " Actinobacteria Acidimicrobiia uncultured Unclassified Unclassified Otu8605 0.595533 0 \n", " Acidobacteria Subgroup Unclassified Unclassified Unclassified Otu8606 0.593458 0 \n", "Unclassified Unclassified Unclassified Unclassified Unclassified Unclassified Otu8607 0.474453 0 \n", " Otu8608 0.519814 0 \n", "Bacteria Firmicutes Bacilli Bacillales Planococcaceae Planococcus Otu8609 0.551402 0 \n", " Planctomycetes Planctomycetacia Gemmatales Gemmataceae Unclassified Otu8610 0.544335 0 \n", " Proteobacteria Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Unclassified Otu8611 0.552448 0 \n", " Entotheonellaeota Entotheonellia Entotheonellales Entotheonellaceae Unclassified Otu8612 0.558313 0 \n", " Proteobacteria Deltaproteobacteria Oligoflexales 0319-6G20 Unclassified Otu8613 0.586047 0 \n", " Alphaproteobacteria Caulobacterales Caulobacteraceae Brevundimonas Otu8614 0.533499 0 \n", " Gammaproteobacteria Betaproteobacteriales TRA3-20 Unclassified Otu8615 0.572093 0 \n", " Chlamydiae Chlamydiae Chlamydiales Parachlamydiaceae Unclassified Otu8616 0.517483 0 \n", "Unclassified Unclassified Unclassified Unclassified Unclassified Unclassified Otu8617 0.542056 0 \n", "Bacteria Proteobacteria Deltaproteobacteria Oligoflexales 0319-6G20 Unclassified Otu8618 0.561772 0 \n", " Gemmatimonadetes BD2-11 Unclassified Unclassified Unclassified Otu8619 0.602326 0 \n", " Proteobacteria Alphaproteobacteria Rhizobiales Beijerinckiaceae Microvirga Otu8620 0.574257 0 \n", " Gammaproteobacteria Betaproteobacteriales TRA3-20 Unclassified Otu8621 0.565421 0 \n", " Planctomycetes Planctomycetacia Isosphaerales Isosphaeraceae Unclassified Otu8622 0.654846 0 \n", " Proteobacteria Gammaproteobacteria Betaproteobacteriales Nitrosomonadaceae MND1 Otu8623 0.561772 0 \n", "Unclassified Unclassified Unclassified Unclassified Unclassified Unclassified Otu8624 0.589109 0 \n", "Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Klebsiella Otu8625 0.568765 0 \n", " Actinobacteria Acidimicrobiia Unclassified Unclassified Unclassified Otu8626 0.570370 0 \n", " Acidobacteria Holophagae Subgroup Unclassified Unclassified Otu8627 0.580420 0 \n", " Patescibacteria Microgenomatia Candidatus Unclassified Unclassified Otu8628 0.494975 0 \n", " Planctomycetes Planctomycetacia Gemmatales Gemmataceae uncultured Otu8629 0.665871 0 \n", " Proteobacteria Deltaproteobacteria Bdellovibrionales Bdellovibrionaceae OM27 Otu8630 0.570025 0 \n", " Patescibacteria Saccharimonadia Saccharimonadales Unclassified Unclassified Otu8631 0.506173 0 \n", " Actinobacteria Actinobacteria Unclassified Unclassified Unclassified Otu8632 0.582927 0 \n", "\n", "Enzyme \\\n", "Replicate 5 \n", "Name Osnat062 \n", "Domain Phylum Class Order Family Genus OTU GC_content \n", "Bacteria Cyanobacteria Oxyphotobacteria Nostocales Phormidiaceae Tychonema Otu0001 0.547847 179 \n", " Actinobacteria Actinobacteria Micrococcales Micrococcaceae Unclassified Otu0002 0.572127 406 \n", " Proteobacteria Alphaproteobacteria Azospirillales Azospirillaceae Skermanella Otu0003 0.579208 177 \n", " Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Pelomonas Otu0004 0.550117 110 \n", " Alphaproteobacteria Rhizobiales uncultured Unclassified Otu0005 0.559406 90 \n", " Sphingomonadales Sphingomonadaceae Sphingomonas Otu0006 0.522277 299 \n", " Rhizobiales Beijerinckiaceae Unclassified Otu0007 0.564356 31 \n", " Microvirga Otu0008 0.559406 47 \n", " Elsterales uncultured Unclassified Otu0009 0.574257 63 \n", " Deltaproteobacteria Myxococcales Unclassified Unclassified Otu0010 0.567757 55 \n", " Actinobacteria Rubrobacteria Rubrobacterales Rubrobacteriaceae Rubrobacter Otu0011 0.602804 83 \n", " Actinobacteria Frankiales Geodermatophilaceae Blastococcus Otu0012 0.586797 319 \n", " Streptomycetales Streptomycetaceae Streptomyces Otu0013 0.581907 20 \n", " Rubrobacteria Rubrobacterales Rubrobacteriaceae Rubrobacter Otu0014 0.593458 57 \n", " Actinobacteria Micromonosporales Micromonosporaceae Actinoplanes Otu0015 0.610294 113 \n", " Micrococcales Promicromonosporaceae Promicromonospora Otu0016 0.572127 84 \n", " Proteobacteria Alphaproteobacteria Rhizobiales Xanthobacteraceae Bradyrhizobium Otu0017 0.547030 112 \n", " Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Ralstonia Otu0018 0.533800 145 \n", " Deltaproteobacteria Myxococcales BIrii41 Unclassified Otu0019 0.565421 35 \n", " Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Aquabacterium Otu0020 0.545455 155 \n", " Alphaproteobacteria Rhodobacterales Rhodobacteraceae Rubellimicrobium Otu0021 0.576733 13 \n", " Rhizobiales Beijerinckiaceae Unclassified Otu0022 0.576733 24 \n", " Sphingomonadales Sphingomonadaceae Novosphingobium Otu0023 0.529703 144 \n", " Acetobacterales Acetobacteraceae uncultured Otu0024 0.586634 20 \n", " Rhizobiales Beijerinckiaceae uncultured Otu0025 0.564356 21 \n", " Actinobacteria Actinobacteria Micrococcales Cellulomonadaceae Cellulomonas Otu0026 0.581907 83 \n", " Pseudonocardiales Pseudonocardiaceae Saccharothrix Otu0027 0.584352 12 \n", " Bacteroidetes Bacteroidia Cytophagales Cytophagaceae Rhodocytophaga Otu0028 0.508274 0 \n", " Proteobacteria Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Ralstonia Otu0029 0.536131 37 \n", " Actinobacteria Thermoleophilia Solirubrobacterales Solirubrobacteraceae Solirubrobacter Otu0030 0.585082 146 \n", "... ... \n", " Unclassified Unclassified Unclassified Otu8603 0.592075 0 \n", " Elusimicrobia Elusimicrobia MVP-88 Unclassified Unclassified Otu8604 0.549528 0 \n", " Actinobacteria Acidimicrobiia uncultured Unclassified Unclassified Otu8605 0.595533 0 \n", " Acidobacteria Subgroup Unclassified Unclassified Unclassified Otu8606 0.593458 0 \n", "Unclassified Unclassified Unclassified Unclassified Unclassified Unclassified Otu8607 0.474453 0 \n", " Otu8608 0.519814 0 \n", "Bacteria Firmicutes Bacilli Bacillales Planococcaceae Planococcus Otu8609 0.551402 0 \n", " Planctomycetes Planctomycetacia Gemmatales Gemmataceae Unclassified Otu8610 0.544335 0 \n", " Proteobacteria Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Unclassified Otu8611 0.552448 0 \n", " Entotheonellaeota Entotheonellia Entotheonellales Entotheonellaceae Unclassified Otu8612 0.558313 0 \n", " Proteobacteria Deltaproteobacteria Oligoflexales 0319-6G20 Unclassified Otu8613 0.586047 0 \n", " Alphaproteobacteria Caulobacterales Caulobacteraceae Brevundimonas Otu8614 0.533499 0 \n", " Gammaproteobacteria Betaproteobacteriales TRA3-20 Unclassified Otu8615 0.572093 0 \n", " Chlamydiae Chlamydiae Chlamydiales Parachlamydiaceae Unclassified Otu8616 0.517483 0 \n", "Unclassified Unclassified Unclassified Unclassified Unclassified Unclassified Otu8617 0.542056 0 \n", "Bacteria Proteobacteria Deltaproteobacteria Oligoflexales 0319-6G20 Unclassified Otu8618 0.561772 0 \n", " Gemmatimonadetes BD2-11 Unclassified Unclassified Unclassified Otu8619 0.602326 0 \n", " Proteobacteria Alphaproteobacteria Rhizobiales Beijerinckiaceae Microvirga Otu8620 0.574257 0 \n", " Gammaproteobacteria Betaproteobacteriales TRA3-20 Unclassified Otu8621 0.565421 0 \n", " Planctomycetes Planctomycetacia Isosphaerales Isosphaeraceae Unclassified Otu8622 0.654846 0 \n", " Proteobacteria Gammaproteobacteria Betaproteobacteriales Nitrosomonadaceae MND1 Otu8623 0.561772 0 \n", "Unclassified Unclassified Unclassified Unclassified Unclassified Unclassified Otu8624 0.589109 0 \n", "Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Klebsiella Otu8625 0.568765 0 \n", " Actinobacteria Acidimicrobiia Unclassified Unclassified Unclassified Otu8626 0.570370 0 \n", " Acidobacteria Holophagae Subgroup Unclassified Unclassified Otu8627 0.580420 0 \n", " Patescibacteria Microgenomatia Candidatus Unclassified Unclassified Otu8628 0.494975 0 \n", " Planctomycetes Planctomycetacia Gemmatales Gemmataceae uncultured Otu8629 0.665871 0 \n", " Proteobacteria Deltaproteobacteria Bdellovibrionales Bdellovibrionaceae OM27 Otu8630 0.570025 0 \n", " Patescibacteria Saccharimonadia Saccharimonadales Unclassified Unclassified Otu8631 0.506173 0 \n", " Actinobacteria Actinobacteria Unclassified Unclassified Unclassified Otu8632 0.582927 0 \n", "\n", "Enzyme \\\n", "Replicate 6 \n", "Name Osnat063 \n", "Domain Phylum Class Order Family Genus OTU GC_content \n", "Bacteria Cyanobacteria Oxyphotobacteria Nostocales Phormidiaceae Tychonema Otu0001 0.547847 37 \n", " Actinobacteria Actinobacteria Micrococcales Micrococcaceae Unclassified Otu0002 0.572127 433 \n", " Proteobacteria Alphaproteobacteria Azospirillales Azospirillaceae Skermanella Otu0003 0.579208 130 \n", " Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Pelomonas Otu0004 0.550117 313 \n", " Alphaproteobacteria Rhizobiales uncultured Unclassified Otu0005 0.559406 89 \n", " Sphingomonadales Sphingomonadaceae Sphingomonas Otu0006 0.522277 268 \n", " Rhizobiales Beijerinckiaceae Unclassified Otu0007 0.564356 31 \n", " Microvirga Otu0008 0.559406 39 \n", " Elsterales uncultured Unclassified Otu0009 0.574257 55 \n", " Deltaproteobacteria Myxococcales Unclassified Unclassified Otu0010 0.567757 26 \n", " Actinobacteria Rubrobacteria Rubrobacterales Rubrobacteriaceae Rubrobacter Otu0011 0.602804 89 \n", " Actinobacteria Frankiales Geodermatophilaceae Blastococcus Otu0012 0.586797 280 \n", " Streptomycetales Streptomycetaceae Streptomyces Otu0013 0.581907 50 \n", " Rubrobacteria Rubrobacterales Rubrobacteriaceae Rubrobacter Otu0014 0.593458 35 \n", " Actinobacteria Micromonosporales Micromonosporaceae Actinoplanes Otu0015 0.610294 73 \n", " Micrococcales Promicromonosporaceae Promicromonospora Otu0016 0.572127 69 \n", " Proteobacteria Alphaproteobacteria Rhizobiales Xanthobacteraceae Bradyrhizobium Otu0017 0.547030 216 \n", " Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Ralstonia Otu0018 0.533800 207 \n", " Deltaproteobacteria Myxococcales BIrii41 Unclassified Otu0019 0.565421 8 \n", " Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Aquabacterium Otu0020 0.545455 160 \n", " Alphaproteobacteria Rhodobacterales Rhodobacteraceae Rubellimicrobium Otu0021 0.576733 14 \n", " Rhizobiales Beijerinckiaceae Unclassified Otu0022 0.576733 25 \n", " Sphingomonadales Sphingomonadaceae Novosphingobium Otu0023 0.529703 151 \n", " Acetobacterales Acetobacteraceae uncultured Otu0024 0.586634 4 \n", " Rhizobiales Beijerinckiaceae uncultured Otu0025 0.564356 22 \n", " Actinobacteria Actinobacteria Micrococcales Cellulomonadaceae Cellulomonas Otu0026 0.581907 75 \n", " Pseudonocardiales Pseudonocardiaceae Saccharothrix Otu0027 0.584352 60 \n", " Bacteroidetes Bacteroidia Cytophagales Cytophagaceae Rhodocytophaga Otu0028 0.508274 0 \n", " Proteobacteria Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Ralstonia Otu0029 0.536131 55 \n", " Actinobacteria Thermoleophilia Solirubrobacterales Solirubrobacteraceae Solirubrobacter Otu0030 0.585082 169 \n", "... ... \n", " Unclassified Unclassified Unclassified Otu8603 0.592075 0 \n", " Elusimicrobia Elusimicrobia MVP-88 Unclassified Unclassified Otu8604 0.549528 0 \n", " Actinobacteria Acidimicrobiia uncultured Unclassified Unclassified Otu8605 0.595533 0 \n", " Acidobacteria Subgroup Unclassified Unclassified Unclassified Otu8606 0.593458 0 \n", "Unclassified Unclassified Unclassified Unclassified Unclassified Unclassified Otu8607 0.474453 0 \n", " Otu8608 0.519814 0 \n", "Bacteria Firmicutes Bacilli Bacillales Planococcaceae Planococcus Otu8609 0.551402 0 \n", " Planctomycetes Planctomycetacia Gemmatales Gemmataceae Unclassified Otu8610 0.544335 0 \n", " Proteobacteria Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Unclassified Otu8611 0.552448 0 \n", " Entotheonellaeota Entotheonellia Entotheonellales Entotheonellaceae Unclassified Otu8612 0.558313 0 \n", " Proteobacteria Deltaproteobacteria Oligoflexales 0319-6G20 Unclassified Otu8613 0.586047 0 \n", " Alphaproteobacteria Caulobacterales Caulobacteraceae Brevundimonas Otu8614 0.533499 0 \n", " Gammaproteobacteria Betaproteobacteriales TRA3-20 Unclassified Otu8615 0.572093 0 \n", " Chlamydiae Chlamydiae Chlamydiales Parachlamydiaceae Unclassified Otu8616 0.517483 0 \n", "Unclassified Unclassified Unclassified Unclassified Unclassified Unclassified Otu8617 0.542056 0 \n", "Bacteria Proteobacteria Deltaproteobacteria Oligoflexales 0319-6G20 Unclassified Otu8618 0.561772 0 \n", " Gemmatimonadetes BD2-11 Unclassified Unclassified Unclassified Otu8619 0.602326 0 \n", " Proteobacteria Alphaproteobacteria Rhizobiales Beijerinckiaceae Microvirga Otu8620 0.574257 0 \n", " Gammaproteobacteria Betaproteobacteriales TRA3-20 Unclassified Otu8621 0.565421 0 \n", " Planctomycetes Planctomycetacia Isosphaerales Isosphaeraceae Unclassified Otu8622 0.654846 0 \n", " Proteobacteria Gammaproteobacteria Betaproteobacteriales Nitrosomonadaceae MND1 Otu8623 0.561772 1 \n", "Unclassified Unclassified Unclassified Unclassified Unclassified Unclassified Otu8624 0.589109 0 \n", "Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Klebsiella Otu8625 0.568765 0 \n", " Actinobacteria Acidimicrobiia Unclassified Unclassified Unclassified Otu8626 0.570370 0 \n", " Acidobacteria Holophagae Subgroup Unclassified Unclassified Otu8627 0.580420 0 \n", " Patescibacteria Microgenomatia Candidatus Unclassified Unclassified Otu8628 0.494975 0 \n", " Planctomycetes Planctomycetacia Gemmatales Gemmataceae uncultured Otu8629 0.665871 0 \n", " Proteobacteria Deltaproteobacteria Bdellovibrionales Bdellovibrionaceae OM27 Otu8630 0.570025 0 \n", " Patescibacteria Saccharimonadia Saccharimonadales Unclassified Unclassified Otu8631 0.506173 0 \n", " Actinobacteria Actinobacteria Unclassified Unclassified Unclassified Otu8632 0.582927 0 \n", "\n", "Enzyme \n", "Replicate 7 \n", "Name Osnat064 \n", "Domain Phylum Class Order Family Genus OTU GC_content \n", "Bacteria Cyanobacteria Oxyphotobacteria Nostocales Phormidiaceae Tychonema Otu0001 0.547847 24 \n", " Actinobacteria Actinobacteria Micrococcales Micrococcaceae Unclassified Otu0002 0.572127 199 \n", " Proteobacteria Alphaproteobacteria Azospirillales Azospirillaceae Skermanella Otu0003 0.579208 47 \n", " Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Pelomonas Otu0004 0.550117 352 \n", " Alphaproteobacteria Rhizobiales uncultured Unclassified Otu0005 0.559406 107 \n", " Sphingomonadales Sphingomonadaceae Sphingomonas Otu0006 0.522277 587 \n", " Rhizobiales Beijerinckiaceae Unclassified Otu0007 0.564356 16 \n", " Microvirga Otu0008 0.559406 37 \n", " Elsterales uncultured Unclassified Otu0009 0.574257 18 \n", " Deltaproteobacteria Myxococcales Unclassified Unclassified Otu0010 0.567757 31 \n", " Actinobacteria Rubrobacteria Rubrobacterales Rubrobacteriaceae Rubrobacter Otu0011 0.602804 39 \n", " Actinobacteria Frankiales Geodermatophilaceae Blastococcus Otu0012 0.586797 193 \n", " Streptomycetales Streptomycetaceae Streptomyces Otu0013 0.581907 34 \n", " Rubrobacteria Rubrobacterales Rubrobacteriaceae Rubrobacter Otu0014 0.593458 38 \n", " Actinobacteria Micromonosporales Micromonosporaceae Actinoplanes Otu0015 0.610294 70 \n", " Micrococcales Promicromonosporaceae Promicromonospora Otu0016 0.572127 16 \n", " Proteobacteria Alphaproteobacteria Rhizobiales Xanthobacteraceae Bradyrhizobium Otu0017 0.547030 326 \n", " Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Ralstonia Otu0018 0.533800 283 \n", " Deltaproteobacteria Myxococcales BIrii41 Unclassified Otu0019 0.565421 7 \n", " Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Aquabacterium Otu0020 0.545455 285 \n", " Alphaproteobacteria Rhodobacterales Rhodobacteraceae Rubellimicrobium Otu0021 0.576733 3 \n", " Rhizobiales Beijerinckiaceae Unclassified Otu0022 0.576733 10 \n", " Sphingomonadales Sphingomonadaceae Novosphingobium Otu0023 0.529703 279 \n", " Acetobacterales Acetobacteraceae uncultured Otu0024 0.586634 12 \n", " Rhizobiales Beijerinckiaceae uncultured Otu0025 0.564356 19 \n", " Actinobacteria Actinobacteria Micrococcales Cellulomonadaceae Cellulomonas Otu0026 0.581907 35 \n", " Pseudonocardiales Pseudonocardiaceae Saccharothrix Otu0027 0.584352 9 \n", " Bacteroidetes Bacteroidia Cytophagales Cytophagaceae Rhodocytophaga Otu0028 0.508274 0 \n", " Proteobacteria Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Ralstonia Otu0029 0.536131 87 \n", " Actinobacteria Thermoleophilia Solirubrobacterales Solirubrobacteraceae Solirubrobacter Otu0030 0.585082 68 \n", "... ... \n", " Unclassified Unclassified Unclassified Otu8603 0.592075 0 \n", " Elusimicrobia Elusimicrobia MVP-88 Unclassified Unclassified Otu8604 0.549528 0 \n", " Actinobacteria Acidimicrobiia uncultured Unclassified Unclassified Otu8605 0.595533 0 \n", " Acidobacteria Subgroup Unclassified Unclassified Unclassified Otu8606 0.593458 0 \n", "Unclassified Unclassified Unclassified Unclassified Unclassified Unclassified Otu8607 0.474453 0 \n", " Otu8608 0.519814 0 \n", "Bacteria Firmicutes Bacilli Bacillales Planococcaceae Planococcus Otu8609 0.551402 0 \n", " Planctomycetes Planctomycetacia Gemmatales Gemmataceae Unclassified Otu8610 0.544335 0 \n", " Proteobacteria Gammaproteobacteria Betaproteobacteriales Burkholderiaceae Unclassified Otu8611 0.552448 0 \n", " Entotheonellaeota Entotheonellia Entotheonellales Entotheonellaceae Unclassified Otu8612 0.558313 0 \n", " Proteobacteria Deltaproteobacteria Oligoflexales 0319-6G20 Unclassified Otu8613 0.586047 0 \n", " Alphaproteobacteria Caulobacterales Caulobacteraceae Brevundimonas Otu8614 0.533499 0 \n", " Gammaproteobacteria Betaproteobacteriales TRA3-20 Unclassified Otu8615 0.572093 0 \n", " Chlamydiae Chlamydiae Chlamydiales Parachlamydiaceae Unclassified Otu8616 0.517483 0 \n", "Unclassified Unclassified Unclassified Unclassified Unclassified Unclassified Otu8617 0.542056 0 \n", "Bacteria Proteobacteria Deltaproteobacteria Oligoflexales 0319-6G20 Unclassified Otu8618 0.561772 0 \n", " Gemmatimonadetes BD2-11 Unclassified Unclassified Unclassified Otu8619 0.602326 0 \n", " Proteobacteria Alphaproteobacteria Rhizobiales Beijerinckiaceae Microvirga Otu8620 0.574257 0 \n", " Gammaproteobacteria Betaproteobacteriales TRA3-20 Unclassified Otu8621 0.565421 0 \n", " Planctomycetes Planctomycetacia Isosphaerales Isosphaeraceae Unclassified Otu8622 0.654846 0 \n", " Proteobacteria Gammaproteobacteria Betaproteobacteriales Nitrosomonadaceae MND1 Otu8623 0.561772 0 \n", "Unclassified Unclassified Unclassified Unclassified Unclassified Unclassified Otu8624 0.589109 0 \n", "Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Klebsiella Otu8625 0.568765 0 \n", " Actinobacteria Acidimicrobiia Unclassified Unclassified Unclassified Otu8626 0.570370 0 \n", " Acidobacteria Holophagae Subgroup Unclassified Unclassified Otu8627 0.580420 0 \n", " Patescibacteria Microgenomatia Candidatus Unclassified Unclassified Otu8628 0.494975 0 \n", " Planctomycetes Planctomycetacia Gemmatales Gemmataceae uncultured Otu8629 0.665871 0 \n", " Proteobacteria Deltaproteobacteria Bdellovibrionales Bdellovibrionaceae OM27 Otu8630 0.570025 0 \n", " Patescibacteria Saccharimonadia Saccharimonadales Unclassified Unclassified Otu8631 0.506173 0 \n", " Actinobacteria Actinobacteria Unclassified Unclassified Unclassified Otu8632 0.582927 0 \n", "\n", "[8632 rows x 20 columns]" ] }, "execution_count": 3, "metadata": {}, "output_type": "execute_result" } ], "source": [ "data.data" ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [], "source": [ "# A copy of the original data frame\n", "df1 = data.data.copy()" ] }, { "cell_type": "code", "execution_count": 5, "metadata": {}, "outputs": [], "source": [ "# Calculating a sum per enzyme category to normalize \n", "df2 = df1.groupby(\"Class\").sum()\n", "\n", "# Standard deviation per enzyme group\n", "df2_std = df2.std(level=\"Enzyme\", axis=1)\n", "\n", "# Making a sum on the class and enzyme level\n", "#df2 = df1.sum(level=\"Class\", axis=0)\n", "df2_ave = df2.sum(level=\"Enzyme\", axis=1)" ] }, { "cell_type": "code", "execution_count": 6, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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EnzymeTGIRTSuperScriptIVPromega42Promega55
Class
0319-7L14392332527442
ABY10000
AKAU40494301
Acidimicrobiia1858151812031617
Acidobacteriia359444257259
Actinobacteria1135310105586411263
Alphaproteobacteria1238512148129439302
Anaerolineae89113191175
Armatimonadia21619
BD2-1142482633
BD7-110474
Babeliae9181110
Bacilli5206631356656
Bacteroidia3005230728251817
Berkelbacteria0120
Blastocatellia328309336243
Chlamydiae362523
Chloroflexia789666441825
Chthonomonadetes0000
Clostridia1681313
Coriobacteriia0010
Dehalococcoidia971557098
Deinococci29448928
Deltaproteobacteria3001314143302154
Elusimicrobia2260
Entotheonellia164221125122
Erysipelotrichia0501
FFCH59090100
Fibrobacteria36464535
Fimbriimonadia43326929
...............
Nitrospira70743234
OLB1456442324
OM1900000
Oxyphotobacteria87717112798962
P2-11E3373
Parcubacteria2031
Phycisphaerae1718101128
Pla48384
Planctomycetacia283247357710
Rhodothermia510011
Rubrobacteria1974238013511505
S01341147311675
SHA-26416412
Saccharimonadia304913057
Sericytochromatia27335325
Spirochaetia0001
Subgroup501681385284
Synergistia0000
TK10611522275583
Thermoanaerobaculia146122117127
Thermodesulfovibrionia0000
Thermoleophilia3562373327454643
Thermoplasmata451414
Unclassified1216129212111210
Verrucomicrobiae102913911310620
WS61200
WWE30000
Woesearchaeia0002
uncultured28314166
vadinHA491177
\n", "

81 rows × 4 columns

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" ], "text/plain": [ "Enzyme TGIRT SuperScriptIV Promega42 Promega55\n", "Class \n", "0319-7L14 392 332 527 442\n", "ABY1 0 0 0 0\n", "AKAU4049 4 3 0 1\n", "Acidimicrobiia 1858 1518 1203 1617\n", "Acidobacteriia 359 444 257 259\n", "Actinobacteria 11353 10105 5864 11263\n", "Alphaproteobacteria 12385 12148 12943 9302\n", "Anaerolineae 89 113 191 175\n", "Armatimonadia 2 1 6 19\n", "BD2-11 42 48 26 33\n", "BD7-11 0 4 7 4\n", "Babeliae 9 18 11 10\n", "Bacilli 520 663 1356 656\n", "Bacteroidia 3005 2307 2825 1817\n", "Berkelbacteria 0 1 2 0\n", "Blastocatellia 328 309 336 243\n", "Chlamydiae 3 6 25 23\n", "Chloroflexia 789 666 441 825\n", "Chthonomonadetes 0 0 0 0\n", "Clostridia 16 8 13 13\n", "Coriobacteriia 0 0 1 0\n", "Dehalococcoidia 97 155 70 98\n", "Deinococci 29 44 89 28\n", "Deltaproteobacteria 3001 3141 4330 2154\n", "Elusimicrobia 2 2 6 0\n", "Entotheonellia 164 221 125 122\n", "Erysipelotrichia 0 5 0 1\n", "FFCH5909 0 1 0 0\n", "Fibrobacteria 36 46 45 35\n", "Fimbriimonadia 43 32 69 29\n", "... ... ... ... ...\n", "Nitrospira 70 74 32 34\n", "OLB14 56 44 23 24\n", "OM190 0 0 0 0\n", "Oxyphotobacteria 877 1711 2798 962\n", "P2-11E 3 3 7 3\n", "Parcubacteria 2 0 3 1\n", "Phycisphaerae 17 18 101 128\n", "Pla4 8 3 8 4\n", "Planctomycetacia 283 247 357 710\n", "Rhodothermia 5 10 0 11\n", "Rubrobacteria 1974 2380 1351 1505\n", "S0134 114 73 116 75\n", "SHA-26 4 16 4 12\n", "Saccharimonadia 30 49 130 57\n", "Sericytochromatia 27 33 53 25\n", "Spirochaetia 0 0 0 1\n", "Subgroup 501 681 385 284\n", "Synergistia 0 0 0 0\n", "TK10 611 522 275 583\n", "Thermoanaerobaculia 146 122 117 127\n", "Thermodesulfovibrionia 0 0 0 0\n", "Thermoleophilia 3562 3733 2745 4643\n", "Thermoplasmata 4 5 14 14\n", "Unclassified 1216 1292 1211 1210\n", "Verrucomicrobiae 1029 1391 1310 620\n", "WS6 1 2 0 0\n", "WWE3 0 0 0 0\n", "Woesearchaeia 0 0 0 2\n", "uncultured 28 31 41 66\n", "vadinHA49 1 1 7 7\n", "\n", "[81 rows x 4 columns]" ] }, "execution_count": 6, "metadata": {}, "output_type": "execute_result" } ], "source": [ "df2_ave" ] }, { "cell_type": "code", "execution_count": 7, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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EnzymeTGIRTSuperScriptIVPromega42Promega55
Class
0319-7L1456.38971550.25733885.20739481.041964
ABY10.0000000.0000000.0000000.000000
AKAU40491.0954450.8944270.0000000.447214
Acidimicrobiia55.41028846.301188109.91724247.300106
Acidobacteriia28.45522818.08867029.3649456.942622
Actinobacteria274.296919223.156895445.351771581.639321
Alphaproteobacteria382.188435303.496787481.747652232.488279
Anaerolineae5.80517012.7003947.5630688.093207
Armatimonadia0.5477230.4472140.4472142.863564
BD2-116.7305278.8204315.7619447.987490
BD7-110.0000001.0954451.3416410.836660
Babeliae1.3038400.5477231.9235381.870829
Bacilli65.07687874.751589133.78415560.870354
Bacteroidia194.803747143.224649141.663333188.279845
Berkelbacteria0.0000000.4472140.8944270.000000
Blastocatellia36.92966333.89985331.54679114.876155
Chlamydiae0.5477230.8366607.5166484.878524
Chloroflexia33.72980933.71498239.23263912.389512
Chthonomonadetes0.0000000.0000000.0000000.000000
Clostridia2.2803513.0495902.7928482.701851
Coriobacteriia0.0000000.0000000.4472140.000000
Dehalococcoidia9.47628614.5258395.87367011.104053
Deinococci3.9623234.14728819.9173292.966479
Deltaproteobacteria48.86409778.349856440.766945215.612384
Elusimicrobia0.8944270.5477231.7888540.000000
Entotheonellia23.48829534.62946723.43074922.074873
Erysipelotrichia0.0000002.2360680.0000000.447214
FFCH59090.0000000.4472140.0000000.000000
Fibrobacteria2.9495762.4899803.0000003.082207
Fimbriimonadia3.6469174.0987807.5960523.834058
...............
Nitrospira8.6890749.8081604.0373263.768289
OLB142.9495763.4928504.7222882.167948
OM1900.0000000.0000000.0000000.000000
Oxyphotobacteria139.263419212.430459523.532520243.335776
P2-11E0.8944270.8944273.1304951.341641
Parcubacteria0.5477230.0000001.3416410.447214
Phycisphaerae1.3416413.0495905.63027511.058933
Pla40.5477231.3416413.0495900.836660
Planctomycetacia16.53178816.57709320.32978150.906778
Rhodothermia2.2360681.2247450.0000004.381780
Rubrobacteria158.676400193.53035967.31047571.333723
S013430.65452718.79627632.64506113.619838
SHA-260.8366601.4832400.8366601.949359
Saccharimonadia9.11043416.45296319.7989904.393177
Sericytochromatia2.0736443.3615479.0719354.898979
Spirochaetia0.0000000.0000000.0000000.447214
Subgroup42.71065444.54997251.20058637.036469
Synergistia0.0000000.0000000.0000000.000000
TK1043.88849538.44866725.95187945.970643
Thermoanaerobaculia16.26960411.56719511.43678310.285913
Thermodesulfovibrionia0.0000000.0000000.0000000.000000
Thermoleophilia174.316666190.525064254.825430135.417133
Thermoplasmata0.8366601.0000003.7013512.588436
Unclassified40.13352733.32866640.94752721.505813
Verrucomicrobiae49.726251112.83926684.88227143.312816
WS60.4472140.8944270.0000000.000000
WWE30.0000000.0000000.0000000.000000
Woesearchaeia0.0000000.0000000.0000000.894427
uncultured2.7018511.9235384.4384683.420526
vadinHA490.4472140.4472141.9493591.673320
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81 rows × 4 columns

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" ], "text/plain": [ "Enzyme TGIRT SuperScriptIV Promega42 Promega55\n", "Class \n", "0319-7L14 56.389715 50.257338 85.207394 81.041964\n", "ABY1 0.000000 0.000000 0.000000 0.000000\n", "AKAU4049 1.095445 0.894427 0.000000 0.447214\n", "Acidimicrobiia 55.410288 46.301188 109.917242 47.300106\n", "Acidobacteriia 28.455228 18.088670 29.364945 6.942622\n", "Actinobacteria 274.296919 223.156895 445.351771 581.639321\n", "Alphaproteobacteria 382.188435 303.496787 481.747652 232.488279\n", "Anaerolineae 5.805170 12.700394 7.563068 8.093207\n", "Armatimonadia 0.547723 0.447214 0.447214 2.863564\n", "BD2-11 6.730527 8.820431 5.761944 7.987490\n", "BD7-11 0.000000 1.095445 1.341641 0.836660\n", "Babeliae 1.303840 0.547723 1.923538 1.870829\n", "Bacilli 65.076878 74.751589 133.784155 60.870354\n", "Bacteroidia 194.803747 143.224649 141.663333 188.279845\n", "Berkelbacteria 0.000000 0.447214 0.894427 0.000000\n", "Blastocatellia 36.929663 33.899853 31.546791 14.876155\n", "Chlamydiae 0.547723 0.836660 7.516648 4.878524\n", "Chloroflexia 33.729809 33.714982 39.232639 12.389512\n", "Chthonomonadetes 0.000000 0.000000 0.000000 0.000000\n", "Clostridia 2.280351 3.049590 2.792848 2.701851\n", "Coriobacteriia 0.000000 0.000000 0.447214 0.000000\n", "Dehalococcoidia 9.476286 14.525839 5.873670 11.104053\n", "Deinococci 3.962323 4.147288 19.917329 2.966479\n", "Deltaproteobacteria 48.864097 78.349856 440.766945 215.612384\n", "Elusimicrobia 0.894427 0.547723 1.788854 0.000000\n", "Entotheonellia 23.488295 34.629467 23.430749 22.074873\n", "Erysipelotrichia 0.000000 2.236068 0.000000 0.447214\n", "FFCH5909 0.000000 0.447214 0.000000 0.000000\n", "Fibrobacteria 2.949576 2.489980 3.000000 3.082207\n", "Fimbriimonadia 3.646917 4.098780 7.596052 3.834058\n", "... ... ... ... ...\n", "Nitrospira 8.689074 9.808160 4.037326 3.768289\n", "OLB14 2.949576 3.492850 4.722288 2.167948\n", "OM190 0.000000 0.000000 0.000000 0.000000\n", "Oxyphotobacteria 139.263419 212.430459 523.532520 243.335776\n", "P2-11E 0.894427 0.894427 3.130495 1.341641\n", "Parcubacteria 0.547723 0.000000 1.341641 0.447214\n", "Phycisphaerae 1.341641 3.049590 5.630275 11.058933\n", "Pla4 0.547723 1.341641 3.049590 0.836660\n", "Planctomycetacia 16.531788 16.577093 20.329781 50.906778\n", "Rhodothermia 2.236068 1.224745 0.000000 4.381780\n", "Rubrobacteria 158.676400 193.530359 67.310475 71.333723\n", "S0134 30.654527 18.796276 32.645061 13.619838\n", "SHA-26 0.836660 1.483240 0.836660 1.949359\n", "Saccharimonadia 9.110434 16.452963 19.798990 4.393177\n", "Sericytochromatia 2.073644 3.361547 9.071935 4.898979\n", "Spirochaetia 0.000000 0.000000 0.000000 0.447214\n", "Subgroup 42.710654 44.549972 51.200586 37.036469\n", "Synergistia 0.000000 0.000000 0.000000 0.000000\n", "TK10 43.888495 38.448667 25.951879 45.970643\n", "Thermoanaerobaculia 16.269604 11.567195 11.436783 10.285913\n", "Thermodesulfovibrionia 0.000000 0.000000 0.000000 0.000000\n", "Thermoleophilia 174.316666 190.525064 254.825430 135.417133\n", "Thermoplasmata 0.836660 1.000000 3.701351 2.588436\n", "Unclassified 40.133527 33.328666 40.947527 21.505813\n", "Verrucomicrobiae 49.726251 112.839266 84.882271 43.312816\n", "WS6 0.447214 0.894427 0.000000 0.000000\n", "WWE3 0.000000 0.000000 0.000000 0.000000\n", "Woesearchaeia 0.000000 0.000000 0.000000 0.894427\n", "uncultured 2.701851 1.923538 4.438468 3.420526\n", "vadinHA49 0.447214 0.447214 1.949359 1.673320\n", "\n", "[81 rows x 4 columns]" ] }, "execution_count": 7, "metadata": {}, "output_type": "execute_result" } ], "source": [ "df2_std" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "The data frame is simplified to only a class level information, OTU names, GC content and the four enzymatic conditions. " ] }, { "cell_type": "code", "execution_count": 8, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "/home/adam/Programs/anaconda3/lib/python3.6/site-packages/pandas/core/generic.py:3812: PerformanceWarning: dropping on a non-lexsorted multi-index without a level parameter may impact performance.\n", " new_axis = axis.drop(labels, errors=errors)\n" ] }, { "data": { "text/html": [ "
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EnzymeClassOTUGC_contentTGIRTSuperScriptIV...Promega42Promega55
Replicate1456713...1234712567
NameOsnat037Osnat040Osnat041Osnat042Osnat043Osnat044Osnat046...Osnat051Osnat052Osnat053Osnat054Osnat057Osnat058Osnat059Osnat062Osnat063Osnat064
0OxyphotobacteriaOtu00010.5478470.0342080.2941850.0193840.1379700.3454960.0280540.317943...0.0032170.4481770.1050750.1136530.0957830.0176720.5176720.1860710.0384620.024948
1ActinobacteriaOtu00020.5721270.0407820.0262490.0265130.0384920.0235180.0459180.037308...0.0572990.0306960.0443380.0288200.0395630.0623280.0380010.0360470.0384440.017668
2AlphaproteobacteriaOtu00030.5792080.0130800.0352850.0527250.0197010.0239000.0144060.026753...0.0074170.0209380.0308270.0252650.0168430.0145130.0170930.0190280.0139750.005053
3GammaproteobacteriaOtu00040.5501170.0209630.0011650.0000000.0077640.0104810.0193340.001432...0.0449140.0008380.0459190.1426180.0249710.0064390.0048620.0144550.0411300.046255
4AlphaproteobacteriaOtu00050.5594060.0152600.0243840.0335080.0246270.0324590.0124300.033421...0.0105850.0155300.0327590.0192380.0241830.0103200.0065580.0096750.0095680.011503
5AlphaproteobacteriaOtu00060.5222770.0202660.0082360.0100930.0062170.0085590.0170400.009549...0.0338410.0082670.0289730.0625050.0334540.0276280.0210710.0321440.0288110.063105
6AlphaproteobacteriaOtu00070.5643560.0037950.0058940.0080740.0052480.0071860.0054330.013500...0.0017000.0079580.0050990.0061810.0044810.0058050.0039780.0033330.0033330.001720
7AlphaproteobacteriaOtu00080.5594060.0083970.0083170.0069440.0098510.0089620.0069150.013747...0.0070310.0083440.0069540.0045580.0057950.0072030.0073100.0050530.0041930.003978
8AlphaproteobacteriaOtu00090.5742570.0018570.0033100.0068630.0090430.0068630.0018930.004692...0.0017000.0017000.0091170.0054080.0121300.0052680.0012900.0067730.0059130.001935
9DeltaproteobacteriaOtu00100.5677570.0373210.0516490.0666440.0269910.0293240.0175100.046164...0.0092380.0799080.0838340.0362590.0207850.0417830.0594240.0255340.0120710.014392
10RubrobacteriaOtu00110.6028040.0248230.0491390.0623100.0678820.0820670.0289920.084874...0.0503330.0399700.0377500.0185050.0414510.0624580.0299000.0551500.0591360.025914
11ActinobacteriaOtu00120.5867970.0218440.0355850.0243110.0179690.0206110.0226620.022959...0.0410980.0138130.0080150.0151770.0216580.0259260.0261920.0283230.0248600.017136
12ActinobacteriaOtu00130.5819070.0114510.0030830.0065180.0052850.0061660.0140520.005839...0.0173940.0035810.0023870.0025580.0039220.0055050.0016870.0017760.0044390.003019
13RubrobacteriaOtu00140.5934580.0121580.0212770.0187440.0268490.0263420.0105040.035294...0.0236860.0769800.0592150.0340490.0414510.0378740.0578070.0378740.0232560.025249
14ActinobacteriaOtu00150.6102940.0082800.0204350.0214040.0084560.0096890.0110840.005740...0.0133020.0039220.0010230.0025580.0054570.0088790.0157150.0100330.0064810.006215
15ActinobacteriaOtu00160.5721270.0031710.0023780.0049330.0044040.0036990.0020780.001880...0.0073330.0034110.0022170.0005120.0028990.0033740.0024860.0074580.0061260.001421
16AlphaproteobacteriaOtu00170.5470300.0080740.0016960.0018570.0037950.0041990.0057620.003210...0.0043270.0009270.0058720.0131350.0068760.0056980.0031180.0120400.0232210.035046
17GammaproteobacteriaOtu00180.5338000.0000000.0000000.0000000.0000000.0000000.0000000.000000...0.0000000.0000000.0000000.0000000.0000000.0091980.0052560.0190540.0272010.037188
18DeltaproteobacteriaOtu00190.5654210.0046650.0116630.0106630.0046650.0023330.0063670.010506...0.0009240.0323330.0152420.0060050.0046190.0162490.0937790.0162490.0037140.003250
19GammaproteobacteriaOtu00200.5454550.0000000.0000000.0000000.0000000.0000000.0000000.000000...0.0000000.0000000.0000000.0000000.0000000.0097240.0027600.0203680.0210250.037451
20AlphaproteobacteriaOtu00210.5767330.0028260.0023420.0009690.0029870.0016150.0024700.005351...0.0028590.0110480.0027040.0023950.0022410.0034400.0067730.0013980.0015050.000323
21AlphaproteobacteriaOtu00220.5767330.0030680.0027450.0037140.0053290.0027450.0038690.004445...0.0043270.0024720.0070310.0017770.0028590.0029030.0026880.0025800.0026880.001075
22AlphaproteobacteriaOtu00230.5297030.0000000.0000000.0000000.0000000.0000000.0000000.000082...0.0008500.0000000.0000000.0000000.0000000.0072030.0020430.0154810.0162330.029994
23AlphaproteobacteriaOtu00240.5866340.0004840.0041990.0062170.0023420.0029870.0004940.001070...0.0002320.0003090.0021630.0005410.0012360.0001080.0003230.0021500.0004300.001290
24AlphaproteobacteriaOtu00250.5643560.0026650.0054910.0082360.0048450.0071050.0016460.005598...0.0033220.0023950.0056400.0020860.0062580.0045150.0012900.0022580.0023650.002043
25ActinobacteriaOtu00260.5819070.0061660.0080160.0072230.0097770.0064300.0095990.007026...0.0115960.0138130.0063100.0063100.0068210.0145610.0224630.0073690.0066590.003108
26ActinobacteriaOtu00270.5843520.0018500.0065180.0036990.0116270.0022900.0028700.003365...0.0034110.0027290.0020460.0006820.0015350.0032850.0018650.0010650.0053270.000799
27BacteroidiaOtu00280.5082740.0003330.0086520.0013310.0109820.0043260.0017340.015171...0.0010620.0169910.0038940.0003540.0014160.0011010.0187120.0000000.0000000.000000
28GammaproteobacteriaOtu00290.5361310.0011650.0000000.0000000.0000000.0007760.0000000.000000...0.0046920.0001680.0115640.0276520.0130720.0039420.0011830.0048620.0072270.011432
29ThermoleophiliaOtu00300.5850820.0207750.0162830.0249860.0291970.0255470.0251810.019823...0.0160290.0145720.0123860.0094720.0466300.0312300.0122770.0314450.0363990.014646
..................................................................
8602ThermoleophiliaOtu86030.5920750.0000000.0000000.0000000.0000000.0000000.0000000.000000...0.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.000000
8603ElusimicrobiaOtu86040.5495280.0000000.0000000.0000000.0000000.0000000.0000000.000000...0.0000000.0000000.0000000.0000000.000000NaNNaNNaNNaNNaN
8604AcidimicrobiiaOtu86050.5955330.0000000.0000000.0000000.0000000.0000000.0000000.000000...0.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.000000
8605SubgroupOtu86060.5934580.0019960.0000000.0000000.0000000.0000000.0000000.000000...0.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.000000
8606UnclassifiedOtu86070.4744530.0000000.0000000.0000000.0000000.0000000.0000000.000000...0.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.000000
8607UnclassifiedOtu86080.5198140.0000000.0000000.0000000.0000000.0000000.0000000.000000...0.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.000000
8608BacilliOtu86090.5514020.0000000.0000000.0000000.0000000.0000000.0000000.000000...0.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.000000
8609PlanctomycetaciaOtu86100.5443350.0000000.0000000.0000000.0000000.0000000.0000000.000000...0.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.000000
8610GammaproteobacteriaOtu86110.5524480.0000000.0000000.0000000.0000000.0000000.0000000.000000...0.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.000000
8611EntotheonelliaOtu86120.5583130.0000000.0000000.0000000.0000000.0000000.0000000.000000...0.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.000000
8612DeltaproteobacteriaOtu86130.5860470.0000000.0000000.0000000.0000000.0000000.0000000.000000...0.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.000000
8613AlphaproteobacteriaOtu86140.5334990.0000810.0000000.0000000.0000000.0000000.0000820.000000...0.0002320.0000770.0000770.0000000.0000000.0000000.0000000.0000000.0000000.000000
8614GammaproteobacteriaOtu86150.5720930.0000000.0000000.0000000.0000000.0000000.0000000.000000...0.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.000000
8615ChlamydiaeOtu86160.5174830.0000000.0000000.0000000.0000000.0000000.0000000.000000...0.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.000000
8616UnclassifiedOtu86170.5420560.0000000.0000000.0000000.0000000.0000000.0000000.000000...0.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.000000
8617DeltaproteobacteriaOtu86180.5617720.0000000.0000000.0000000.0000000.0000000.0000000.000000...0.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.000000
8618BD2-11Otu86190.6023260.0000000.0000000.0000000.0476190.0000000.0000000.000000...0.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.000000
8619AlphaproteobacteriaOtu86200.5742570.0000000.0000000.0000000.0000000.0000000.0000000.000000...0.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.000000
8620GammaproteobacteriaOtu86210.5654210.0000000.0000000.0000000.0000000.0000000.0000000.000000...0.0000000.0000000.0000000.0000000.0000000.0001310.0000000.0000000.0000000.000000
8621PlanctomycetaciaOtu86220.6548460.0000000.0000000.0000000.0000000.0000000.0000000.000000...0.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.000000
8622GammaproteobacteriaOtu86230.5617720.0000000.0000000.0000000.0003880.0000000.0000000.000000...0.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0001310.000000
8623UnclassifiedOtu86240.5891090.0000000.0000000.0000000.0000000.0000000.0000000.000000...0.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.000000
8624GammaproteobacteriaOtu86250.5687650.0000000.0000000.0000000.0000000.0000000.0000000.000000...0.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.000000
8625AcidimicrobiiaOtu86260.5703700.0000000.0000000.0000000.0000000.0000000.0000000.000000...0.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.000000
8626HolophagaeOtu86270.5804200.0000000.0052360.0000000.0000000.0157070.0000000.000000...0.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.000000
8627MicrogenomatiaOtu86280.4949750.0000000.0000000.0000000.0000000.000000NaNNaN...0.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.000000
8628PlanctomycetaciaOtu86290.6658710.0000000.0000000.0000000.0000000.0000000.0000000.000000...0.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.000000
8629DeltaproteobacteriaOtu86300.5700250.0000000.0000000.0000000.0000000.0000000.0000000.000000...0.0000000.0000000.0000000.0000000.0004620.0000000.0000000.0000000.0000000.000000
8630SaccharimonadiaOtu86310.5061730.0000000.0000000.0000000.0000000.0000000.0000000.000000...0.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.000000
8631ActinobacteriaOtu86320.5829270.0000000.0000000.0000000.0000000.0000000.0000000.000000...0.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.000000
\n", "

8632 rows × 23 columns

\n", "
" ], "text/plain": [ "Enzyme Class OTU GC_content TGIRT \\\n", "Replicate 1 4 \n", "Name Osnat037 Osnat040 \n", "0 Oxyphotobacteria Otu0001 0.547847 0.034208 0.294185 \n", "1 Actinobacteria Otu0002 0.572127 0.040782 0.026249 \n", "2 Alphaproteobacteria Otu0003 0.579208 0.013080 0.035285 \n", "3 Gammaproteobacteria Otu0004 0.550117 0.020963 0.001165 \n", "4 Alphaproteobacteria Otu0005 0.559406 0.015260 0.024384 \n", "5 Alphaproteobacteria Otu0006 0.522277 0.020266 0.008236 \n", "6 Alphaproteobacteria Otu0007 0.564356 0.003795 0.005894 \n", "7 Alphaproteobacteria Otu0008 0.559406 0.008397 0.008317 \n", "8 Alphaproteobacteria Otu0009 0.574257 0.001857 0.003310 \n", "9 Deltaproteobacteria Otu0010 0.567757 0.037321 0.051649 \n", "10 Rubrobacteria Otu0011 0.602804 0.024823 0.049139 \n", "11 Actinobacteria Otu0012 0.586797 0.021844 0.035585 \n", "12 Actinobacteria Otu0013 0.581907 0.011451 0.003083 \n", "13 Rubrobacteria Otu0014 0.593458 0.012158 0.021277 \n", "14 Actinobacteria Otu0015 0.610294 0.008280 0.020435 \n", "15 Actinobacteria Otu0016 0.572127 0.003171 0.002378 \n", "16 Alphaproteobacteria Otu0017 0.547030 0.008074 0.001696 \n", "17 Gammaproteobacteria Otu0018 0.533800 0.000000 0.000000 \n", "18 Deltaproteobacteria Otu0019 0.565421 0.004665 0.011663 \n", "19 Gammaproteobacteria Otu0020 0.545455 0.000000 0.000000 \n", "20 Alphaproteobacteria Otu0021 0.576733 0.002826 0.002342 \n", "21 Alphaproteobacteria Otu0022 0.576733 0.003068 0.002745 \n", "22 Alphaproteobacteria Otu0023 0.529703 0.000000 0.000000 \n", "23 Alphaproteobacteria Otu0024 0.586634 0.000484 0.004199 \n", "24 Alphaproteobacteria Otu0025 0.564356 0.002665 0.005491 \n", "25 Actinobacteria Otu0026 0.581907 0.006166 0.008016 \n", "26 Actinobacteria Otu0027 0.584352 0.001850 0.006518 \n", "27 Bacteroidia Otu0028 0.508274 0.000333 0.008652 \n", "28 Gammaproteobacteria Otu0029 0.536131 0.001165 0.000000 \n", "29 Thermoleophilia Otu0030 0.585082 0.020775 0.016283 \n", "... ... ... ... ... ... \n", "8602 Thermoleophilia Otu8603 0.592075 0.000000 0.000000 \n", "8603 Elusimicrobia Otu8604 0.549528 0.000000 0.000000 \n", "8604 Acidimicrobiia Otu8605 0.595533 0.000000 0.000000 \n", "8605 Subgroup Otu8606 0.593458 0.001996 0.000000 \n", "8606 Unclassified Otu8607 0.474453 0.000000 0.000000 \n", "8607 Unclassified Otu8608 0.519814 0.000000 0.000000 \n", "8608 Bacilli Otu8609 0.551402 0.000000 0.000000 \n", "8609 Planctomycetacia Otu8610 0.544335 0.000000 0.000000 \n", "8610 Gammaproteobacteria Otu8611 0.552448 0.000000 0.000000 \n", "8611 Entotheonellia Otu8612 0.558313 0.000000 0.000000 \n", "8612 Deltaproteobacteria Otu8613 0.586047 0.000000 0.000000 \n", "8613 Alphaproteobacteria Otu8614 0.533499 0.000081 0.000000 \n", "8614 Gammaproteobacteria Otu8615 0.572093 0.000000 0.000000 \n", "8615 Chlamydiae Otu8616 0.517483 0.000000 0.000000 \n", "8616 Unclassified Otu8617 0.542056 0.000000 0.000000 \n", "8617 Deltaproteobacteria Otu8618 0.561772 0.000000 0.000000 \n", "8618 BD2-11 Otu8619 0.602326 0.000000 0.000000 \n", "8619 Alphaproteobacteria Otu8620 0.574257 0.000000 0.000000 \n", "8620 Gammaproteobacteria Otu8621 0.565421 0.000000 0.000000 \n", "8621 Planctomycetacia Otu8622 0.654846 0.000000 0.000000 \n", "8622 Gammaproteobacteria Otu8623 0.561772 0.000000 0.000000 \n", "8623 Unclassified Otu8624 0.589109 0.000000 0.000000 \n", "8624 Gammaproteobacteria Otu8625 0.568765 0.000000 0.000000 \n", "8625 Acidimicrobiia Otu8626 0.570370 0.000000 0.000000 \n", "8626 Holophagae Otu8627 0.580420 0.000000 0.005236 \n", "8627 Microgenomatia Otu8628 0.494975 0.000000 0.000000 \n", "8628 Planctomycetacia Otu8629 0.665871 0.000000 0.000000 \n", "8629 Deltaproteobacteria Otu8630 0.570025 0.000000 0.000000 \n", "8630 Saccharimonadia Otu8631 0.506173 0.000000 0.000000 \n", "8631 Actinobacteria Otu8632 0.582927 0.000000 0.000000 \n", "\n", "Enzyme SuperScriptIV ... \\\n", "Replicate 5 6 7 1 3 ... \n", "Name Osnat041 Osnat042 Osnat043 Osnat044 Osnat046 ... \n", "0 0.019384 0.137970 0.345496 0.028054 0.317943 ... \n", "1 0.026513 0.038492 0.023518 0.045918 0.037308 ... \n", "2 0.052725 0.019701 0.023900 0.014406 0.026753 ... \n", "3 0.000000 0.007764 0.010481 0.019334 0.001432 ... \n", "4 0.033508 0.024627 0.032459 0.012430 0.033421 ... \n", "5 0.010093 0.006217 0.008559 0.017040 0.009549 ... \n", "6 0.008074 0.005248 0.007186 0.005433 0.013500 ... \n", "7 0.006944 0.009851 0.008962 0.006915 0.013747 ... \n", "8 0.006863 0.009043 0.006863 0.001893 0.004692 ... \n", "9 0.066644 0.026991 0.029324 0.017510 0.046164 ... \n", "10 0.062310 0.067882 0.082067 0.028992 0.084874 ... \n", "11 0.024311 0.017969 0.020611 0.022662 0.022959 ... \n", "12 0.006518 0.005285 0.006166 0.014052 0.005839 ... \n", "13 0.018744 0.026849 0.026342 0.010504 0.035294 ... \n", "14 0.021404 0.008456 0.009689 0.011084 0.005740 ... \n", "15 0.004933 0.004404 0.003699 0.002078 0.001880 ... \n", "16 0.001857 0.003795 0.004199 0.005762 0.003210 ... \n", "17 0.000000 0.000000 0.000000 0.000000 0.000000 ... \n", "18 0.010663 0.004665 0.002333 0.006367 0.010506 ... \n", "19 0.000000 0.000000 0.000000 0.000000 0.000000 ... \n", "20 0.000969 0.002987 0.001615 0.002470 0.005351 ... \n", "21 0.003714 0.005329 0.002745 0.003869 0.004445 ... \n", "22 0.000000 0.000000 0.000000 0.000000 0.000082 ... \n", "23 0.006217 0.002342 0.002987 0.000494 0.001070 ... \n", "24 0.008236 0.004845 0.007105 0.001646 0.005598 ... \n", "25 0.007223 0.009777 0.006430 0.009599 0.007026 ... \n", "26 0.003699 0.011627 0.002290 0.002870 0.003365 ... \n", "27 0.001331 0.010982 0.004326 0.001734 0.015171 ... \n", "28 0.000000 0.000000 0.000776 0.000000 0.000000 ... \n", "29 0.024986 0.029197 0.025547 0.025181 0.019823 ... \n", "... ... ... ... ... ... ... \n", "8602 0.000000 0.000000 0.000000 0.000000 0.000000 ... \n", "8603 0.000000 0.000000 0.000000 0.000000 0.000000 ... \n", "8604 0.000000 0.000000 0.000000 0.000000 0.000000 ... \n", "8605 0.000000 0.000000 0.000000 0.000000 0.000000 ... \n", "8606 0.000000 0.000000 0.000000 0.000000 0.000000 ... \n", "8607 0.000000 0.000000 0.000000 0.000000 0.000000 ... \n", "8608 0.000000 0.000000 0.000000 0.000000 0.000000 ... \n", "8609 0.000000 0.000000 0.000000 0.000000 0.000000 ... \n", "8610 0.000000 0.000000 0.000000 0.000000 0.000000 ... \n", "8611 0.000000 0.000000 0.000000 0.000000 0.000000 ... \n", "8612 0.000000 0.000000 0.000000 0.000000 0.000000 ... \n", "8613 0.000000 0.000000 0.000000 0.000082 0.000000 ... \n", "8614 0.000000 0.000000 0.000000 0.000000 0.000000 ... \n", "8615 0.000000 0.000000 0.000000 0.000000 0.000000 ... \n", "8616 0.000000 0.000000 0.000000 0.000000 0.000000 ... \n", "8617 0.000000 0.000000 0.000000 0.000000 0.000000 ... \n", "8618 0.000000 0.047619 0.000000 0.000000 0.000000 ... \n", "8619 0.000000 0.000000 0.000000 0.000000 0.000000 ... \n", "8620 0.000000 0.000000 0.000000 0.000000 0.000000 ... \n", "8621 0.000000 0.000000 0.000000 0.000000 0.000000 ... \n", "8622 0.000000 0.000388 0.000000 0.000000 0.000000 ... \n", "8623 0.000000 0.000000 0.000000 0.000000 0.000000 ... \n", "8624 0.000000 0.000000 0.000000 0.000000 0.000000 ... \n", "8625 0.000000 0.000000 0.000000 0.000000 0.000000 ... \n", "8626 0.000000 0.000000 0.015707 0.000000 0.000000 ... \n", "8627 0.000000 0.000000 0.000000 NaN NaN ... \n", "8628 0.000000 0.000000 0.000000 0.000000 0.000000 ... \n", "8629 0.000000 0.000000 0.000000 0.000000 0.000000 ... \n", "8630 0.000000 0.000000 0.000000 0.000000 0.000000 ... \n", "8631 0.000000 0.000000 0.000000 0.000000 0.000000 ... \n", "\n", "Enzyme Promega42 Promega55 \\\n", "Replicate 1 2 3 4 7 1 \n", "Name Osnat051 Osnat052 Osnat053 Osnat054 Osnat057 Osnat058 \n", "0 0.003217 0.448177 0.105075 0.113653 0.095783 0.017672 \n", "1 0.057299 0.030696 0.044338 0.028820 0.039563 0.062328 \n", "2 0.007417 0.020938 0.030827 0.025265 0.016843 0.014513 \n", "3 0.044914 0.000838 0.045919 0.142618 0.024971 0.006439 \n", "4 0.010585 0.015530 0.032759 0.019238 0.024183 0.010320 \n", "5 0.033841 0.008267 0.028973 0.062505 0.033454 0.027628 \n", "6 0.001700 0.007958 0.005099 0.006181 0.004481 0.005805 \n", "7 0.007031 0.008344 0.006954 0.004558 0.005795 0.007203 \n", "8 0.001700 0.001700 0.009117 0.005408 0.012130 0.005268 \n", "9 0.009238 0.079908 0.083834 0.036259 0.020785 0.041783 \n", "10 0.050333 0.039970 0.037750 0.018505 0.041451 0.062458 \n", "11 0.041098 0.013813 0.008015 0.015177 0.021658 0.025926 \n", "12 0.017394 0.003581 0.002387 0.002558 0.003922 0.005505 \n", "13 0.023686 0.076980 0.059215 0.034049 0.041451 0.037874 \n", "14 0.013302 0.003922 0.001023 0.002558 0.005457 0.008879 \n", "15 0.007333 0.003411 0.002217 0.000512 0.002899 0.003374 \n", "16 0.004327 0.000927 0.005872 0.013135 0.006876 0.005698 \n", "17 0.000000 0.000000 0.000000 0.000000 0.000000 0.009198 \n", "18 0.000924 0.032333 0.015242 0.006005 0.004619 0.016249 \n", "19 0.000000 0.000000 0.000000 0.000000 0.000000 0.009724 \n", "20 0.002859 0.011048 0.002704 0.002395 0.002241 0.003440 \n", "21 0.004327 0.002472 0.007031 0.001777 0.002859 0.002903 \n", "22 0.000850 0.000000 0.000000 0.000000 0.000000 0.007203 \n", "23 0.000232 0.000309 0.002163 0.000541 0.001236 0.000108 \n", "24 0.003322 0.002395 0.005640 0.002086 0.006258 0.004515 \n", "25 0.011596 0.013813 0.006310 0.006310 0.006821 0.014561 \n", "26 0.003411 0.002729 0.002046 0.000682 0.001535 0.003285 \n", "27 0.001062 0.016991 0.003894 0.000354 0.001416 0.001101 \n", "28 0.004692 0.000168 0.011564 0.027652 0.013072 0.003942 \n", "29 0.016029 0.014572 0.012386 0.009472 0.046630 0.031230 \n", "... ... ... ... ... ... ... \n", "8602 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 \n", "8603 0.000000 0.000000 0.000000 0.000000 0.000000 NaN \n", "8604 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 \n", "8605 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 \n", "8606 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 \n", "8607 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 \n", "8608 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 \n", "8609 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 \n", "8610 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 \n", "8611 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 \n", "8612 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 \n", "8613 0.000232 0.000077 0.000077 0.000000 0.000000 0.000000 \n", "8614 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 \n", "8615 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 \n", "8616 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 \n", "8617 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 \n", "8618 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 \n", "8619 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 \n", "8620 0.000000 0.000000 0.000000 0.000000 0.000000 0.000131 \n", "8621 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 \n", "8622 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 \n", "8623 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 \n", "8624 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 \n", "8625 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 \n", "8626 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 \n", "8627 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 \n", "8628 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 \n", "8629 0.000000 0.000000 0.000000 0.000000 0.000462 0.000000 \n", "8630 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 \n", "8631 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 \n", "\n", "Enzyme \n", "Replicate 2 5 6 7 \n", "Name Osnat059 Osnat062 Osnat063 Osnat064 \n", "0 0.517672 0.186071 0.038462 0.024948 \n", "1 0.038001 0.036047 0.038444 0.017668 \n", "2 0.017093 0.019028 0.013975 0.005053 \n", "3 0.004862 0.014455 0.041130 0.046255 \n", "4 0.006558 0.009675 0.009568 0.011503 \n", "5 0.021071 0.032144 0.028811 0.063105 \n", "6 0.003978 0.003333 0.003333 0.001720 \n", "7 0.007310 0.005053 0.004193 0.003978 \n", "8 0.001290 0.006773 0.005913 0.001935 \n", "9 0.059424 0.025534 0.012071 0.014392 \n", "10 0.029900 0.055150 0.059136 0.025914 \n", "11 0.026192 0.028323 0.024860 0.017136 \n", "12 0.001687 0.001776 0.004439 0.003019 \n", "13 0.057807 0.037874 0.023256 0.025249 \n", "14 0.015715 0.010033 0.006481 0.006215 \n", "15 0.002486 0.007458 0.006126 0.001421 \n", "16 0.003118 0.012040 0.023221 0.035046 \n", "17 0.005256 0.019054 0.027201 0.037188 \n", "18 0.093779 0.016249 0.003714 0.003250 \n", "19 0.002760 0.020368 0.021025 0.037451 \n", "20 0.006773 0.001398 0.001505 0.000323 \n", "21 0.002688 0.002580 0.002688 0.001075 \n", "22 0.002043 0.015481 0.016233 0.029994 \n", "23 0.000323 0.002150 0.000430 0.001290 \n", "24 0.001290 0.002258 0.002365 0.002043 \n", "25 0.022463 0.007369 0.006659 0.003108 \n", "26 0.001865 0.001065 0.005327 0.000799 \n", "27 0.018712 0.000000 0.000000 0.000000 \n", "28 0.001183 0.004862 0.007227 0.011432 \n", "29 0.012277 0.031445 0.036399 0.014646 \n", "... ... ... ... ... \n", "8602 0.000000 0.000000 0.000000 0.000000 \n", "8603 NaN NaN NaN NaN \n", "8604 0.000000 0.000000 0.000000 0.000000 \n", "8605 0.000000 0.000000 0.000000 0.000000 \n", "8606 0.000000 0.000000 0.000000 0.000000 \n", "8607 0.000000 0.000000 0.000000 0.000000 \n", "8608 0.000000 0.000000 0.000000 0.000000 \n", "8609 0.000000 0.000000 0.000000 0.000000 \n", "8610 0.000000 0.000000 0.000000 0.000000 \n", "8611 0.000000 0.000000 0.000000 0.000000 \n", "8612 0.000000 0.000000 0.000000 0.000000 \n", "8613 0.000000 0.000000 0.000000 0.000000 \n", "8614 0.000000 0.000000 0.000000 0.000000 \n", "8615 0.000000 0.000000 0.000000 0.000000 \n", "8616 0.000000 0.000000 0.000000 0.000000 \n", "8617 0.000000 0.000000 0.000000 0.000000 \n", "8618 0.000000 0.000000 0.000000 0.000000 \n", "8619 0.000000 0.000000 0.000000 0.000000 \n", "8620 0.000000 0.000000 0.000000 0.000000 \n", "8621 0.000000 0.000000 0.000000 0.000000 \n", "8622 0.000000 0.000000 0.000131 0.000000 \n", "8623 0.000000 0.000000 0.000000 0.000000 \n", "8624 0.000000 0.000000 0.000000 0.000000 \n", "8625 0.000000 0.000000 0.000000 0.000000 \n", "8626 0.000000 0.000000 0.000000 0.000000 \n", "8627 0.000000 0.000000 0.000000 0.000000 \n", "8628 0.000000 0.000000 0.000000 0.000000 \n", "8629 0.000000 0.000000 0.000000 0.000000 \n", "8630 0.000000 0.000000 0.000000 0.000000 \n", "8631 0.000000 0.000000 0.000000 0.000000 \n", "\n", "[8632 rows x 23 columns]" ] }, "execution_count": 8, "metadata": {}, "output_type": "execute_result" } ], "source": [ "# Copy of the original data frame\n", "df2 = df1.copy()\n", "# Dividing the per/enzyme values by an average to normalize them\n", "df2 = df2.div(df2_ave)\n", "\n", "# Sorting out the rest\n", "df2 = df2.reset_index()\n", "df3 = df2.drop([\"Domain\",\"Phylum\", \"Order\", \"Family\", \"Genus\"], axis=1)\n", "df3" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "The resulting data frame is \"melted\" such that the enzymatic conditions become a new column and the GC content and value are the only two numerical value columns." ] }, { "cell_type": "code", "execution_count": 9, "metadata": {}, "outputs": [], "source": [ "df4 = df3.melt(id_vars=[\"Class\", \"OTU\", \"GC_content\"])" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "By summarizing within each Class and Enzyme category, we should receive either 1 or 0 if a group is not present in a given category. " ] }, { "cell_type": "code", "execution_count": 10, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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GC_contentvalue
ClassEnzyme
0319-7L14Promega42164.0679461.0
Promega55164.0679461.0
SuperScriptIV164.0679461.0
TGIRT164.0679461.0
ABY1Promega422.6167080.0
Promega552.6167080.0
SuperScriptIV2.6167080.0
TGIRT2.6167080.0
AKAU4049Promega425.9418600.0
Promega555.9418601.0
SuperScriptIV5.9418601.0
TGIRT5.9418601.0
AcidimicrobiiaPromega42754.6504891.0
Promega55754.6504891.0
SuperScriptIV754.6504891.0
TGIRT754.6504891.0
AcidobacteriiaPromega4285.6965171.0
Promega5585.6965171.0
SuperScriptIV85.6965171.0
TGIRT85.6965171.0
ActinobacteriaPromega421776.3562191.0
Promega551776.3562191.0
SuperScriptIV1776.3562191.0
TGIRT1776.3562191.0
AlphaproteobacteriaPromega422091.3239691.0
Promega552091.3239691.0
SuperScriptIV2091.3239691.0
TGIRT2091.3239691.0
AnaerolineaePromega42223.9743481.0
Promega55223.9743481.0
............
ThermoplasmataSuperScriptIV28.8341971.0
TGIRT28.8341971.0
UnclassifiedPromega422280.2895571.0
Promega552280.2895571.0
SuperScriptIV2280.2895571.0
TGIRT2280.2895571.0
VerrucomicrobiaePromega42760.3901221.0
Promega55760.3901221.0
SuperScriptIV760.3901221.0
TGIRT760.3901221.0
WS6Promega4214.6548980.0
Promega5514.6548980.0
SuperScriptIV14.6548981.0
TGIRT14.6548981.0
WWE3Promega422.5618810.0
Promega552.5618810.0
SuperScriptIV2.5618810.0
TGIRT2.5618810.0
WoesearchaeiaPromega422.6349610.0
Promega552.6349611.0
SuperScriptIV2.6349610.0
TGIRT2.6349610.0
unculturedPromega42301.1654281.0
Promega55301.1654281.0
SuperScriptIV301.1654281.0
TGIRT301.1654281.0
vadinHA49Promega4217.0509861.0
Promega5517.0509861.0
SuperScriptIV17.0509861.0
TGIRT17.0509861.0
\n", "

324 rows × 2 columns

\n", "
" ], "text/plain": [ " GC_content value\n", "Class Enzyme \n", "0319-7L14 Promega42 164.067946 1.0\n", " Promega55 164.067946 1.0\n", " SuperScriptIV 164.067946 1.0\n", " TGIRT 164.067946 1.0\n", "ABY1 Promega42 2.616708 0.0\n", " Promega55 2.616708 0.0\n", " SuperScriptIV 2.616708 0.0\n", " TGIRT 2.616708 0.0\n", "AKAU4049 Promega42 5.941860 0.0\n", " Promega55 5.941860 1.0\n", " SuperScriptIV 5.941860 1.0\n", " TGIRT 5.941860 1.0\n", "Acidimicrobiia Promega42 754.650489 1.0\n", " Promega55 754.650489 1.0\n", " SuperScriptIV 754.650489 1.0\n", " TGIRT 754.650489 1.0\n", "Acidobacteriia Promega42 85.696517 1.0\n", " Promega55 85.696517 1.0\n", " SuperScriptIV 85.696517 1.0\n", " TGIRT 85.696517 1.0\n", "Actinobacteria Promega42 1776.356219 1.0\n", " Promega55 1776.356219 1.0\n", " SuperScriptIV 1776.356219 1.0\n", " TGIRT 1776.356219 1.0\n", "Alphaproteobacteria Promega42 2091.323969 1.0\n", " Promega55 2091.323969 1.0\n", " SuperScriptIV 2091.323969 1.0\n", " TGIRT 2091.323969 1.0\n", "Anaerolineae Promega42 223.974348 1.0\n", " Promega55 223.974348 1.0\n", "... ... ...\n", "Thermoplasmata SuperScriptIV 28.834197 1.0\n", " TGIRT 28.834197 1.0\n", "Unclassified Promega42 2280.289557 1.0\n", " Promega55 2280.289557 1.0\n", " SuperScriptIV 2280.289557 1.0\n", " TGIRT 2280.289557 1.0\n", "Verrucomicrobiae Promega42 760.390122 1.0\n", " Promega55 760.390122 1.0\n", " SuperScriptIV 760.390122 1.0\n", " TGIRT 760.390122 1.0\n", "WS6 Promega42 14.654898 0.0\n", " Promega55 14.654898 0.0\n", " SuperScriptIV 14.654898 1.0\n", " TGIRT 14.654898 1.0\n", "WWE3 Promega42 2.561881 0.0\n", " Promega55 2.561881 0.0\n", " SuperScriptIV 2.561881 0.0\n", " TGIRT 2.561881 0.0\n", "Woesearchaeia Promega42 2.634961 0.0\n", " Promega55 2.634961 1.0\n", " SuperScriptIV 2.634961 0.0\n", " TGIRT 2.634961 0.0\n", "uncultured Promega42 301.165428 1.0\n", " Promega55 301.165428 1.0\n", " SuperScriptIV 301.165428 1.0\n", " TGIRT 301.165428 1.0\n", "vadinHA49 Promega42 17.050986 1.0\n", " Promega55 17.050986 1.0\n", " SuperScriptIV 17.050986 1.0\n", " TGIRT 17.050986 1.0\n", "\n", "[324 rows x 2 columns]" ] }, "execution_count": 10, "metadata": {}, "output_type": "execute_result" } ], "source": [ "df4.groupby([\"Class\", \"Enzyme\"]).sum()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Multiplying a GC content value of each OTU by the OTU's relative abundance within a given Class and Enzyme group, we receive the OTU's proportional contribution to the overall Class GC content. By summarizing the GC content over a Class, we obtain it's weighted average GC content. The Class normalized count is discarded. " ] }, { "cell_type": "code", "execution_count": 11, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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GC_content
ClassEnzyme
0319-7L14Promega420.580750
Promega550.582987
SuperScriptIV0.581233
TGIRT0.582942
ABY1Promega420.000000
Promega550.000000
SuperScriptIV0.000000
TGIRT0.000000
AKAU4049Promega420.000000
Promega550.593023
SuperScriptIV0.593798
TGIRT0.594186
AcidimicrobiiaPromega420.585221
Promega550.586662
SuperScriptIV0.588191
TGIRT0.587488
AcidobacteriiaPromega420.555791
Promega550.561708
SuperScriptIV0.561813
TGIRT0.559804
ActinobacteriaPromega420.583321
Promega550.583805
SuperScriptIV0.584725
TGIRT0.586320
AlphaproteobacteriaPromega420.554835
Promega550.553426
SuperScriptIV0.562606
TGIRT0.563610
AnaerolineaePromega420.552375
Promega550.559423
.........
ThermoplasmataSuperScriptIV0.580311
TGIRT0.577720
UnclassifiedPromega420.492766
Promega550.507756
SuperScriptIV0.505267
TGIRT0.503933
VerrucomicrobiaePromega420.534486
Promega550.533333
SuperScriptIV0.532315
TGIRT0.532096
WS6Promega420.000000
Promega550.000000
SuperScriptIV0.496296
TGIRT0.496296
WWE3Promega420.000000
Promega550.000000
SuperScriptIV0.000000
TGIRT0.000000
WoesearchaeiaPromega420.000000
Promega550.526992
SuperScriptIV0.000000
TGIRT0.000000
unculturedPromega420.608757
Promega550.612651
SuperScriptIV0.611116
TGIRT0.616270
vadinHA49Promega420.568613
Promega550.569948
SuperScriptIV0.570093
TGIRT0.570093
\n", "

324 rows × 1 columns

\n", "
" ], "text/plain": [ " GC_content\n", "Class Enzyme \n", "0319-7L14 Promega42 0.580750\n", " Promega55 0.582987\n", " SuperScriptIV 0.581233\n", " TGIRT 0.582942\n", "ABY1 Promega42 0.000000\n", " Promega55 0.000000\n", " SuperScriptIV 0.000000\n", " TGIRT 0.000000\n", "AKAU4049 Promega42 0.000000\n", " Promega55 0.593023\n", " SuperScriptIV 0.593798\n", " TGIRT 0.594186\n", "Acidimicrobiia Promega42 0.585221\n", " Promega55 0.586662\n", " SuperScriptIV 0.588191\n", " TGIRT 0.587488\n", "Acidobacteriia Promega42 0.555791\n", " Promega55 0.561708\n", " SuperScriptIV 0.561813\n", " TGIRT 0.559804\n", "Actinobacteria Promega42 0.583321\n", " Promega55 0.583805\n", " SuperScriptIV 0.584725\n", " TGIRT 0.586320\n", "Alphaproteobacteria Promega42 0.554835\n", " Promega55 0.553426\n", " SuperScriptIV 0.562606\n", " TGIRT 0.563610\n", "Anaerolineae Promega42 0.552375\n", " Promega55 0.559423\n", "... ...\n", "Thermoplasmata SuperScriptIV 0.580311\n", " TGIRT 0.577720\n", "Unclassified Promega42 0.492766\n", " Promega55 0.507756\n", " SuperScriptIV 0.505267\n", " TGIRT 0.503933\n", "Verrucomicrobiae Promega42 0.534486\n", " Promega55 0.533333\n", " SuperScriptIV 0.532315\n", " TGIRT 0.532096\n", "WS6 Promega42 0.000000\n", " Promega55 0.000000\n", " SuperScriptIV 0.496296\n", " TGIRT 0.496296\n", "WWE3 Promega42 0.000000\n", " Promega55 0.000000\n", " SuperScriptIV 0.000000\n", " TGIRT 0.000000\n", "Woesearchaeia Promega42 0.000000\n", " Promega55 0.526992\n", " SuperScriptIV 0.000000\n", " TGIRT 0.000000\n", "uncultured Promega42 0.608757\n", " Promega55 0.612651\n", " SuperScriptIV 0.611116\n", " TGIRT 0.616270\n", "vadinHA49 Promega42 0.568613\n", " Promega55 0.569948\n", " SuperScriptIV 0.570093\n", " TGIRT 0.570093\n", "\n", "[324 rows x 1 columns]" ] }, "execution_count": 11, "metadata": {}, "output_type": "execute_result" } ], "source": [ "df4.GC_content = df4.GC_content*df4.value\n", "df5 = df4.groupby([\"Class\",\"Enzyme\"]).sum()\n", "df5 = df5.drop(\"value\", axis=1)\n", "df5 " ] }, { "cell_type": "code", "execution_count": 43, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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Average
ClassEnzyme
0319-7L14Promega42527
Promega55442
SuperScriptIV332
TGIRT392
ABY1Promega420
Promega550
SuperScriptIV0
TGIRT0
AKAU4049Promega420
Promega551
SuperScriptIV3
TGIRT4
AcidimicrobiiaPromega421203
Promega551617
SuperScriptIV1518
TGIRT1858
AcidobacteriiaPromega42257
Promega55259
SuperScriptIV444
TGIRT359
ActinobacteriaPromega425864
Promega5511263
SuperScriptIV10105
TGIRT11353
AlphaproteobacteriaPromega4212943
Promega559302
SuperScriptIV12148
TGIRT12385
AnaerolineaePromega42191
Promega55175
.........
ThermoplasmataSuperScriptIV5
TGIRT4
UnclassifiedPromega421211
Promega551210
SuperScriptIV1292
TGIRT1216
VerrucomicrobiaePromega421310
Promega55620
SuperScriptIV1391
TGIRT1029
WS6Promega420
Promega550
SuperScriptIV2
TGIRT1
WWE3Promega420
Promega550
SuperScriptIV0
TGIRT0
WoesearchaeiaPromega420
Promega552
SuperScriptIV0
TGIRT0
unculturedPromega4241
Promega5566
SuperScriptIV31
TGIRT28
vadinHA49Promega427
Promega557
SuperScriptIV1
TGIRT1
\n", "

324 rows × 1 columns

\n", "
" ], "text/plain": [ " Average\n", "Class Enzyme \n", "0319-7L14 Promega42 527\n", " Promega55 442\n", " SuperScriptIV 332\n", " TGIRT 392\n", "ABY1 Promega42 0\n", " Promega55 0\n", " SuperScriptIV 0\n", " TGIRT 0\n", "AKAU4049 Promega42 0\n", " Promega55 1\n", " SuperScriptIV 3\n", " TGIRT 4\n", "Acidimicrobiia Promega42 1203\n", " Promega55 1617\n", " SuperScriptIV 1518\n", " TGIRT 1858\n", "Acidobacteriia Promega42 257\n", " Promega55 259\n", " SuperScriptIV 444\n", " TGIRT 359\n", "Actinobacteria Promega42 5864\n", " Promega55 11263\n", " SuperScriptIV 10105\n", " TGIRT 11353\n", "Alphaproteobacteria Promega42 12943\n", " Promega55 9302\n", " SuperScriptIV 12148\n", " TGIRT 12385\n", "Anaerolineae Promega42 191\n", " Promega55 175\n", "... ...\n", "Thermoplasmata SuperScriptIV 5\n", " TGIRT 4\n", "Unclassified Promega42 1211\n", " Promega55 1210\n", " SuperScriptIV 1292\n", " TGIRT 1216\n", "Verrucomicrobiae Promega42 1310\n", " Promega55 620\n", " SuperScriptIV 1391\n", " TGIRT 1029\n", "WS6 Promega42 0\n", " Promega55 0\n", " SuperScriptIV 2\n", " TGIRT 1\n", "WWE3 Promega42 0\n", " Promega55 0\n", " SuperScriptIV 0\n", " TGIRT 0\n", "Woesearchaeia Promega42 0\n", " Promega55 2\n", " SuperScriptIV 0\n", " TGIRT 0\n", "uncultured Promega42 41\n", " Promega55 66\n", " SuperScriptIV 31\n", " TGIRT 28\n", "vadinHA49 Promega42 7\n", " Promega55 7\n", " SuperScriptIV 1\n", " TGIRT 1\n", "\n", "[324 rows x 1 columns]" ] }, "execution_count": 43, "metadata": {}, "output_type": "execute_result" } ], "source": [ "df2_ave2 = df2_ave.reset_index()\n", "df2_ave2 = df2_ave2.melt(id_vars=\"Class\")\n", "df2_ave2 = df2_ave2.set_index([\"Class\", \"Enzyme\"])\n", "df2_ave2 = df2_ave2.sort_values([\"Class\", \"Enzyme\"])\n", "# Renaming the values column to have neater output\n", "df2_ave2.rename(columns={\"value\":\"Average\"},level=0, inplace=True)\n", "df2_ave2" ] }, { "cell_type": "code", "execution_count": 42, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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StdDev
ClassEnzyme
0319-7L14Promega4285.207394
Promega5581.041964
SuperScriptIV50.257338
TGIRT56.389715
ABY1Promega420.000000
Promega550.000000
SuperScriptIV0.000000
TGIRT0.000000
AKAU4049Promega420.000000
Promega550.447214
SuperScriptIV0.894427
TGIRT1.095445
AcidimicrobiiaPromega42109.917242
Promega5547.300106
SuperScriptIV46.301188
TGIRT55.410288
AcidobacteriiaPromega4229.364945
Promega556.942622
SuperScriptIV18.088670
TGIRT28.455228
ActinobacteriaPromega42445.351771
Promega55581.639321
SuperScriptIV223.156895
TGIRT274.296919
AlphaproteobacteriaPromega42481.747652
Promega55232.488279
SuperScriptIV303.496787
TGIRT382.188435
AnaerolineaePromega427.563068
Promega558.093207
.........
ThermoplasmataSuperScriptIV1.000000
TGIRT0.836660
UnclassifiedPromega4240.947527
Promega5521.505813
SuperScriptIV33.328666
TGIRT40.133527
VerrucomicrobiaePromega4284.882271
Promega5543.312816
SuperScriptIV112.839266
TGIRT49.726251
WS6Promega420.000000
Promega550.000000
SuperScriptIV0.894427
TGIRT0.447214
WWE3Promega420.000000
Promega550.000000
SuperScriptIV0.000000
TGIRT0.000000
WoesearchaeiaPromega420.000000
Promega550.894427
SuperScriptIV0.000000
TGIRT0.000000
unculturedPromega424.438468
Promega553.420526
SuperScriptIV1.923538
TGIRT2.701851
vadinHA49Promega421.949359
Promega551.673320
SuperScriptIV0.447214
TGIRT0.447214
\n", "

324 rows × 1 columns

\n", "
" ], "text/plain": [ " StdDev\n", "Class Enzyme \n", "0319-7L14 Promega42 85.207394\n", " Promega55 81.041964\n", " SuperScriptIV 50.257338\n", " TGIRT 56.389715\n", "ABY1 Promega42 0.000000\n", " Promega55 0.000000\n", " SuperScriptIV 0.000000\n", " TGIRT 0.000000\n", "AKAU4049 Promega42 0.000000\n", " Promega55 0.447214\n", " SuperScriptIV 0.894427\n", " TGIRT 1.095445\n", "Acidimicrobiia Promega42 109.917242\n", " Promega55 47.300106\n", " SuperScriptIV 46.301188\n", " TGIRT 55.410288\n", "Acidobacteriia Promega42 29.364945\n", " Promega55 6.942622\n", " SuperScriptIV 18.088670\n", " TGIRT 28.455228\n", "Actinobacteria Promega42 445.351771\n", " Promega55 581.639321\n", " SuperScriptIV 223.156895\n", " TGIRT 274.296919\n", "Alphaproteobacteria Promega42 481.747652\n", " Promega55 232.488279\n", " SuperScriptIV 303.496787\n", " TGIRT 382.188435\n", "Anaerolineae Promega42 7.563068\n", " Promega55 8.093207\n", "... ...\n", "Thermoplasmata SuperScriptIV 1.000000\n", " TGIRT 0.836660\n", "Unclassified Promega42 40.947527\n", " Promega55 21.505813\n", " SuperScriptIV 33.328666\n", " TGIRT 40.133527\n", "Verrucomicrobiae Promega42 84.882271\n", " Promega55 43.312816\n", " SuperScriptIV 112.839266\n", " TGIRT 49.726251\n", "WS6 Promega42 0.000000\n", " Promega55 0.000000\n", " SuperScriptIV 0.894427\n", " TGIRT 0.447214\n", "WWE3 Promega42 0.000000\n", " Promega55 0.000000\n", " SuperScriptIV 0.000000\n", " TGIRT 0.000000\n", "Woesearchaeia Promega42 0.000000\n", " Promega55 0.894427\n", " SuperScriptIV 0.000000\n", " TGIRT 0.000000\n", "uncultured Promega42 4.438468\n", " Promega55 3.420526\n", " SuperScriptIV 1.923538\n", " TGIRT 2.701851\n", "vadinHA49 Promega42 1.949359\n", " Promega55 1.673320\n", " SuperScriptIV 0.447214\n", " TGIRT 0.447214\n", "\n", "[324 rows x 1 columns]" ] }, "execution_count": 42, "metadata": {}, "output_type": "execute_result" } ], "source": [ "df2_std2 = df2_std.reset_index()\n", "df2_std2 = df2_std2.melt(id_vars=\"Class\")\n", "df2_std2 = df2_std2.set_index([\"Class\", \"Enzyme\"])\n", "df2_std2 = df2_std2.sort_values([\"Class\", \"Enzyme\"])\n", "# Renaming the values column to have neater output\n", "df2_std2.rename(columns={\"value\":\"StdDev\"},level=0, inplace=True)\n", "df2_std2" ] }, { "cell_type": "code", "execution_count": 44, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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AverageStdDevGC_content
ClassEnzyme
0319-7L14Promega4252785.2073940.580750
Promega5544281.0419640.582987
SuperScriptIV33250.2573380.581233
TGIRT39256.3897150.582942
ABY1Promega4200.0000000.000000
Promega5500.0000000.000000
SuperScriptIV00.0000000.000000
TGIRT00.0000000.000000
AKAU4049Promega4200.0000000.000000
Promega5510.4472140.593023
SuperScriptIV30.8944270.593798
TGIRT41.0954450.594186
AcidimicrobiiaPromega421203109.9172420.585221
Promega55161747.3001060.586662
SuperScriptIV151846.3011880.588191
TGIRT185855.4102880.587488
AcidobacteriiaPromega4225729.3649450.555791
Promega552596.9426220.561708
SuperScriptIV44418.0886700.561813
TGIRT35928.4552280.559804
ActinobacteriaPromega425864445.3517710.583321
Promega5511263581.6393210.583805
SuperScriptIV10105223.1568950.584725
TGIRT11353274.2969190.586320
AlphaproteobacteriaPromega4212943481.7476520.554835
Promega559302232.4882790.553426
SuperScriptIV12148303.4967870.562606
TGIRT12385382.1884350.563610
AnaerolineaePromega421917.5630680.552375
Promega551758.0932070.559423
...............
ThermoplasmataSuperScriptIV51.0000000.580311
TGIRT40.8366600.577720
UnclassifiedPromega42121140.9475270.492766
Promega55121021.5058130.507756
SuperScriptIV129233.3286660.505267
TGIRT121640.1335270.503933
VerrucomicrobiaePromega42131084.8822710.534486
Promega5562043.3128160.533333
SuperScriptIV1391112.8392660.532315
TGIRT102949.7262510.532096
WS6Promega4200.0000000.000000
Promega5500.0000000.000000
SuperScriptIV20.8944270.496296
TGIRT10.4472140.496296
WWE3Promega4200.0000000.000000
Promega5500.0000000.000000
SuperScriptIV00.0000000.000000
TGIRT00.0000000.000000
WoesearchaeiaPromega4200.0000000.000000
Promega5520.8944270.526992
SuperScriptIV00.0000000.000000
TGIRT00.0000000.000000
unculturedPromega42414.4384680.608757
Promega55663.4205260.612651
SuperScriptIV311.9235380.611116
TGIRT282.7018510.616270
vadinHA49Promega4271.9493590.568613
Promega5571.6733200.569948
SuperScriptIV10.4472140.570093
TGIRT10.4472140.570093
\n", "

324 rows × 3 columns

\n", "
" ], "text/plain": [ " Average StdDev GC_content\n", "Class Enzyme \n", "0319-7L14 Promega42 527 85.207394 0.580750\n", " Promega55 442 81.041964 0.582987\n", " SuperScriptIV 332 50.257338 0.581233\n", " TGIRT 392 56.389715 0.582942\n", "ABY1 Promega42 0 0.000000 0.000000\n", " Promega55 0 0.000000 0.000000\n", " SuperScriptIV 0 0.000000 0.000000\n", " TGIRT 0 0.000000 0.000000\n", "AKAU4049 Promega42 0 0.000000 0.000000\n", " Promega55 1 0.447214 0.593023\n", " SuperScriptIV 3 0.894427 0.593798\n", " TGIRT 4 1.095445 0.594186\n", "Acidimicrobiia Promega42 1203 109.917242 0.585221\n", " Promega55 1617 47.300106 0.586662\n", " SuperScriptIV 1518 46.301188 0.588191\n", " TGIRT 1858 55.410288 0.587488\n", "Acidobacteriia Promega42 257 29.364945 0.555791\n", " Promega55 259 6.942622 0.561708\n", " SuperScriptIV 444 18.088670 0.561813\n", " TGIRT 359 28.455228 0.559804\n", "Actinobacteria Promega42 5864 445.351771 0.583321\n", " Promega55 11263 581.639321 0.583805\n", " SuperScriptIV 10105 223.156895 0.584725\n", " TGIRT 11353 274.296919 0.586320\n", "Alphaproteobacteria Promega42 12943 481.747652 0.554835\n", " Promega55 9302 232.488279 0.553426\n", " SuperScriptIV 12148 303.496787 0.562606\n", " TGIRT 12385 382.188435 0.563610\n", "Anaerolineae Promega42 191 7.563068 0.552375\n", " Promega55 175 8.093207 0.559423\n", "... ... ... ...\n", "Thermoplasmata SuperScriptIV 5 1.000000 0.580311\n", " TGIRT 4 0.836660 0.577720\n", "Unclassified Promega42 1211 40.947527 0.492766\n", " Promega55 1210 21.505813 0.507756\n", " SuperScriptIV 1292 33.328666 0.505267\n", " TGIRT 1216 40.133527 0.503933\n", "Verrucomicrobiae Promega42 1310 84.882271 0.534486\n", " Promega55 620 43.312816 0.533333\n", " SuperScriptIV 1391 112.839266 0.532315\n", " TGIRT 1029 49.726251 0.532096\n", "WS6 Promega42 0 0.000000 0.000000\n", " Promega55 0 0.000000 0.000000\n", " SuperScriptIV 2 0.894427 0.496296\n", " TGIRT 1 0.447214 0.496296\n", "WWE3 Promega42 0 0.000000 0.000000\n", " Promega55 0 0.000000 0.000000\n", " SuperScriptIV 0 0.000000 0.000000\n", " TGIRT 0 0.000000 0.000000\n", "Woesearchaeia Promega42 0 0.000000 0.000000\n", " Promega55 2 0.894427 0.526992\n", " SuperScriptIV 0 0.000000 0.000000\n", " TGIRT 0 0.000000 0.000000\n", "uncultured Promega42 41 4.438468 0.608757\n", " Promega55 66 3.420526 0.612651\n", " SuperScriptIV 31 1.923538 0.611116\n", " TGIRT 28 2.701851 0.616270\n", "vadinHA49 Promega42 7 1.949359 0.568613\n", " Promega55 7 1.673320 0.569948\n", " SuperScriptIV 1 0.447214 0.570093\n", " TGIRT 1 0.447214 0.570093\n", "\n", "[324 rows x 3 columns]" ] }, "execution_count": 44, "metadata": {}, "output_type": "execute_result" } ], "source": [ "dfFinal = pd.concat([df2_ave2, df2_std2, df5],axis=1)\n", "dfFinal" ] }, { "cell_type": "code", "execution_count": 45, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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AverageStdDevGC_content
EnzymePromega42Promega55SuperScriptIVTGIRTPromega42Promega55SuperScriptIVTGIRTPromega42Promega55SuperScriptIVTGIRT
Class
0319-7L1452744233239285.20739481.04196450.25733856.3897150.5807500.5829870.5812330.582942
ABY100000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.000000
AKAU404901340.0000000.4472140.8944271.0954450.0000000.5930230.5937980.594186
Acidimicrobiia1203161715181858109.91724247.30010646.30118855.4102880.5852210.5866620.5881910.587488
Acidobacteriia25725944435929.3649456.94262218.08867028.4552280.5557910.5617080.5618130.559804
Actinobacteria5864112631010511353445.351771581.639321223.156895274.2969190.5833210.5838050.5847250.586320
Alphaproteobacteria1294393021214812385481.747652232.488279303.496787382.1884350.5548350.5534260.5626060.563610
Anaerolineae191175113897.5630688.09320712.7003945.8051700.5523750.5594230.5612380.564171
Armatimonadia619120.4472142.8635640.4472140.5477230.5790680.5798350.5941320.575936
BD2-11263348425.7619447.9874908.8204316.7305270.6098610.6102530.6088900.610935
BD7-1174401.3416410.8366601.0954450.0000000.5792220.5780890.5818280.000000
Babeliae11101891.9235381.8708290.5477231.3038400.5812750.5667290.5794060.567681
Bacilli1356656663520133.78415560.87035474.75158965.0768780.5228740.5337930.5312690.537584
Bacteroidia2825181723073005141.663333188.279845143.224649194.8037470.5143520.5143830.5137380.508924
Berkelbacteria20100.8944270.0000000.4472140.0000000.5099010.0000000.5198020.000000
Blastocatellia33624330932831.54679114.87615533.89985336.9296630.5435840.5464200.5481640.549827
Chlamydiae2523637.5166484.8785240.8366600.5477230.5022780.5000510.5089570.503497
Chloroflexia44182566678939.23263912.38951233.71498233.7298090.6391460.6447710.6396640.640914
Chthonomonadetes00000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.000000
Clostridia13138162.7928482.7018513.0495902.2803510.5306630.5214770.5099520.516354
Coriobacteriia10000.4472140.0000000.0000000.0000000.5808820.0000000.0000000.000000
Dehalococcoidia7098155975.87367011.10405314.5258399.4762860.5781480.5778600.5775430.578580
Deinococci8928442919.9173292.9664794.1472883.9623230.5653570.5742200.5613800.564073
Deltaproteobacteria4330215431413001440.766945215.61238478.34985648.8640970.5639300.5660200.5652180.565658
Elusimicrobia60221.7888540.0000000.5477230.8944270.5476580.0000000.5424530.544811
Entotheonellia12512222116423.43074922.07487334.62946723.4882950.5767940.5766640.5762620.575045
Erysipelotrichia01500.0000000.4472142.2360680.0000000.0000000.5186920.5170160.000000
FFCH590900100.0000000.0000000.4472140.0000000.0000000.0000000.6346150.000000
Fibrobacteria453546363.0000003.0822072.4899802.9495760.5544490.5548410.5538320.553822
Fimbriimonadia692932437.5960523.8340584.0987803.6469170.5424530.5433260.5368590.541226
.......................................
Nitrospira323474704.0373263.7682899.8081608.6890740.6007360.5995530.5995220.599818
OLB14232444564.7222882.1679483.4928502.9495760.5869570.5851110.5849730.585082
OM19000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.000000
Oxyphotobacteria27989621711877523.532520243.335776212.430459139.2634190.5460750.5447380.5460600.545485
P2-11E73333.1304951.3416410.8944270.8944270.5753090.5851850.5786010.581893
Parcubacteria31021.3416410.4472140.0000000.5477230.5000000.4963330.0000000.493845
Phycisphaerae10112818175.63027511.0589333.0495901.3416410.5765350.5731420.5727570.577386
Pla484383.0495900.8366601.3416410.5477230.6037300.6095570.6076150.603730
Planctomycetacia35771024728320.32978150.90677816.57709316.5317880.5982060.6247580.6071470.619704
Rhodothermia0111050.0000004.3817801.2247452.2360680.0000000.5713970.5838860.566825
Rubrobacteria135115052380197467.31047571.333723193.530359158.6764000.5976080.6003720.6010170.601583
S0134116757311432.64506113.61983818.79627630.6545270.5891860.6030750.5995250.598523
SHA-264121640.8366601.9493591.4832400.8366600.6026500.6405680.6093570.613068
Saccharimonadia13057493019.7989904.39317716.4529639.1104340.5030400.5017560.4960030.496590
Sericytochromatia532533279.0719354.8989793.3615472.0736440.5326180.5298300.5344900.530035
Spirochaetia01000.0000000.4472140.0000000.0000000.0000000.5617720.0000000.000000
Subgroup38528468150151.20058637.03646944.54997242.7106540.5801260.5806210.5797170.580671
Synergistia00000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.000000
TK1027558352261125.95187945.97064338.44866743.8884950.6148150.6286710.6184170.616980
Thermoanaerobaculia11712712214611.43678310.28591311.56719516.2696040.5822420.5828200.5830030.582521
Thermodesulfovibrionia00000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.000000
Thermoleophilia2745464337333562254.825430135.417133190.525064174.3166660.5890960.5889530.5894920.589915
Thermoplasmata1414543.7013512.5884361.0000000.8366600.5838270.5727240.5803110.577720
Unclassified121112101292121640.94752721.50581333.32866640.1335270.4927660.5077560.5052670.503933
Verrucomicrobiae13106201391102984.88227143.312816112.83926649.7262510.5344860.5333330.5323150.532096
WS600210.0000000.0000000.8944270.4472140.0000000.0000000.4962960.496296
WWE300000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.000000
Woesearchaeia02000.0000000.8944270.0000000.0000000.0000000.5269920.0000000.000000
uncultured416631284.4384683.4205261.9235382.7018510.6087570.6126510.6111160.616270
vadinHA4977111.9493591.6733200.4472140.4472140.5686130.5699480.5700930.570093
\n", "

81 rows × 12 columns

\n", "
" ], "text/plain": [ " Average StdDev \\\n", "Enzyme Promega42 Promega55 SuperScriptIV TGIRT Promega42 \n", "Class \n", "0319-7L14 527 442 332 392 85.207394 \n", "ABY1 0 0 0 0 0.000000 \n", "AKAU4049 0 1 3 4 0.000000 \n", "Acidimicrobiia 1203 1617 1518 1858 109.917242 \n", "Acidobacteriia 257 259 444 359 29.364945 \n", "Actinobacteria 5864 11263 10105 11353 445.351771 \n", "Alphaproteobacteria 12943 9302 12148 12385 481.747652 \n", "Anaerolineae 191 175 113 89 7.563068 \n", "Armatimonadia 6 19 1 2 0.447214 \n", "BD2-11 26 33 48 42 5.761944 \n", "BD7-11 7 4 4 0 1.341641 \n", "Babeliae 11 10 18 9 1.923538 \n", "Bacilli 1356 656 663 520 133.784155 \n", "Bacteroidia 2825 1817 2307 3005 141.663333 \n", "Berkelbacteria 2 0 1 0 0.894427 \n", "Blastocatellia 336 243 309 328 31.546791 \n", "Chlamydiae 25 23 6 3 7.516648 \n", "Chloroflexia 441 825 666 789 39.232639 \n", "Chthonomonadetes 0 0 0 0 0.000000 \n", "Clostridia 13 13 8 16 2.792848 \n", "Coriobacteriia 1 0 0 0 0.447214 \n", "Dehalococcoidia 70 98 155 97 5.873670 \n", "Deinococci 89 28 44 29 19.917329 \n", "Deltaproteobacteria 4330 2154 3141 3001 440.766945 \n", "Elusimicrobia 6 0 2 2 1.788854 \n", "Entotheonellia 125 122 221 164 23.430749 \n", "Erysipelotrichia 0 1 5 0 0.000000 \n", "FFCH5909 0 0 1 0 0.000000 \n", "Fibrobacteria 45 35 46 36 3.000000 \n", "Fimbriimonadia 69 29 32 43 7.596052 \n", "... ... ... ... ... ... \n", "Nitrospira 32 34 74 70 4.037326 \n", "OLB14 23 24 44 56 4.722288 \n", "OM190 0 0 0 0 0.000000 \n", "Oxyphotobacteria 2798 962 1711 877 523.532520 \n", "P2-11E 7 3 3 3 3.130495 \n", "Parcubacteria 3 1 0 2 1.341641 \n", "Phycisphaerae 101 128 18 17 5.630275 \n", "Pla4 8 4 3 8 3.049590 \n", "Planctomycetacia 357 710 247 283 20.329781 \n", "Rhodothermia 0 11 10 5 0.000000 \n", "Rubrobacteria 1351 1505 2380 1974 67.310475 \n", "S0134 116 75 73 114 32.645061 \n", "SHA-26 4 12 16 4 0.836660 \n", "Saccharimonadia 130 57 49 30 19.798990 \n", "Sericytochromatia 53 25 33 27 9.071935 \n", "Spirochaetia 0 1 0 0 0.000000 \n", "Subgroup 385 284 681 501 51.200586 \n", "Synergistia 0 0 0 0 0.000000 \n", "TK10 275 583 522 611 25.951879 \n", "Thermoanaerobaculia 117 127 122 146 11.436783 \n", "Thermodesulfovibrionia 0 0 0 0 0.000000 \n", "Thermoleophilia 2745 4643 3733 3562 254.825430 \n", "Thermoplasmata 14 14 5 4 3.701351 \n", "Unclassified 1211 1210 1292 1216 40.947527 \n", "Verrucomicrobiae 1310 620 1391 1029 84.882271 \n", "WS6 0 0 2 1 0.000000 \n", "WWE3 0 0 0 0 0.000000 \n", "Woesearchaeia 0 2 0 0 0.000000 \n", "uncultured 41 66 31 28 4.438468 \n", "vadinHA49 7 7 1 1 1.949359 \n", "\n", " GC_content \\\n", "Enzyme Promega55 SuperScriptIV TGIRT Promega42 \n", "Class \n", "0319-7L14 81.041964 50.257338 56.389715 0.580750 \n", "ABY1 0.000000 0.000000 0.000000 0.000000 \n", "AKAU4049 0.447214 0.894427 1.095445 0.000000 \n", "Acidimicrobiia 47.300106 46.301188 55.410288 0.585221 \n", "Acidobacteriia 6.942622 18.088670 28.455228 0.555791 \n", "Actinobacteria 581.639321 223.156895 274.296919 0.583321 \n", "Alphaproteobacteria 232.488279 303.496787 382.188435 0.554835 \n", "Anaerolineae 8.093207 12.700394 5.805170 0.552375 \n", "Armatimonadia 2.863564 0.447214 0.547723 0.579068 \n", "BD2-11 7.987490 8.820431 6.730527 0.609861 \n", "BD7-11 0.836660 1.095445 0.000000 0.579222 \n", "Babeliae 1.870829 0.547723 1.303840 0.581275 \n", "Bacilli 60.870354 74.751589 65.076878 0.522874 \n", "Bacteroidia 188.279845 143.224649 194.803747 0.514352 \n", "Berkelbacteria 0.000000 0.447214 0.000000 0.509901 \n", "Blastocatellia 14.876155 33.899853 36.929663 0.543584 \n", "Chlamydiae 4.878524 0.836660 0.547723 0.502278 \n", "Chloroflexia 12.389512 33.714982 33.729809 0.639146 \n", "Chthonomonadetes 0.000000 0.000000 0.000000 0.000000 \n", "Clostridia 2.701851 3.049590 2.280351 0.530663 \n", "Coriobacteriia 0.000000 0.000000 0.000000 0.580882 \n", "Dehalococcoidia 11.104053 14.525839 9.476286 0.578148 \n", "Deinococci 2.966479 4.147288 3.962323 0.565357 \n", "Deltaproteobacteria 215.612384 78.349856 48.864097 0.563930 \n", "Elusimicrobia 0.000000 0.547723 0.894427 0.547658 \n", "Entotheonellia 22.074873 34.629467 23.488295 0.576794 \n", "Erysipelotrichia 0.447214 2.236068 0.000000 0.000000 \n", "FFCH5909 0.000000 0.447214 0.000000 0.000000 \n", "Fibrobacteria 3.082207 2.489980 2.949576 0.554449 \n", "Fimbriimonadia 3.834058 4.098780 3.646917 0.542453 \n", "... ... ... ... ... \n", "Nitrospira 3.768289 9.808160 8.689074 0.600736 \n", "OLB14 2.167948 3.492850 2.949576 0.586957 \n", "OM190 0.000000 0.000000 0.000000 0.000000 \n", "Oxyphotobacteria 243.335776 212.430459 139.263419 0.546075 \n", "P2-11E 1.341641 0.894427 0.894427 0.575309 \n", "Parcubacteria 0.447214 0.000000 0.547723 0.500000 \n", "Phycisphaerae 11.058933 3.049590 1.341641 0.576535 \n", "Pla4 0.836660 1.341641 0.547723 0.603730 \n", "Planctomycetacia 50.906778 16.577093 16.531788 0.598206 \n", "Rhodothermia 4.381780 1.224745 2.236068 0.000000 \n", "Rubrobacteria 71.333723 193.530359 158.676400 0.597608 \n", "S0134 13.619838 18.796276 30.654527 0.589186 \n", "SHA-26 1.949359 1.483240 0.836660 0.602650 \n", "Saccharimonadia 4.393177 16.452963 9.110434 0.503040 \n", "Sericytochromatia 4.898979 3.361547 2.073644 0.532618 \n", "Spirochaetia 0.447214 0.000000 0.000000 0.000000 \n", "Subgroup 37.036469 44.549972 42.710654 0.580126 \n", "Synergistia 0.000000 0.000000 0.000000 0.000000 \n", "TK10 45.970643 38.448667 43.888495 0.614815 \n", "Thermoanaerobaculia 10.285913 11.567195 16.269604 0.582242 \n", "Thermodesulfovibrionia 0.000000 0.000000 0.000000 0.000000 \n", "Thermoleophilia 135.417133 190.525064 174.316666 0.589096 \n", "Thermoplasmata 2.588436 1.000000 0.836660 0.583827 \n", "Unclassified 21.505813 33.328666 40.133527 0.492766 \n", "Verrucomicrobiae 43.312816 112.839266 49.726251 0.534486 \n", "WS6 0.000000 0.894427 0.447214 0.000000 \n", "WWE3 0.000000 0.000000 0.000000 0.000000 \n", "Woesearchaeia 0.894427 0.000000 0.000000 0.000000 \n", "uncultured 3.420526 1.923538 2.701851 0.608757 \n", "vadinHA49 1.673320 0.447214 0.447214 0.568613 \n", "\n", " \n", "Enzyme Promega55 SuperScriptIV TGIRT \n", "Class \n", "0319-7L14 0.582987 0.581233 0.582942 \n", "ABY1 0.000000 0.000000 0.000000 \n", "AKAU4049 0.593023 0.593798 0.594186 \n", "Acidimicrobiia 0.586662 0.588191 0.587488 \n", "Acidobacteriia 0.561708 0.561813 0.559804 \n", "Actinobacteria 0.583805 0.584725 0.586320 \n", "Alphaproteobacteria 0.553426 0.562606 0.563610 \n", "Anaerolineae 0.559423 0.561238 0.564171 \n", "Armatimonadia 0.579835 0.594132 0.575936 \n", "BD2-11 0.610253 0.608890 0.610935 \n", "BD7-11 0.578089 0.581828 0.000000 \n", "Babeliae 0.566729 0.579406 0.567681 \n", "Bacilli 0.533793 0.531269 0.537584 \n", "Bacteroidia 0.514383 0.513738 0.508924 \n", "Berkelbacteria 0.000000 0.519802 0.000000 \n", "Blastocatellia 0.546420 0.548164 0.549827 \n", "Chlamydiae 0.500051 0.508957 0.503497 \n", "Chloroflexia 0.644771 0.639664 0.640914 \n", "Chthonomonadetes 0.000000 0.000000 0.000000 \n", "Clostridia 0.521477 0.509952 0.516354 \n", "Coriobacteriia 0.000000 0.000000 0.000000 \n", "Dehalococcoidia 0.577860 0.577543 0.578580 \n", "Deinococci 0.574220 0.561380 0.564073 \n", "Deltaproteobacteria 0.566020 0.565218 0.565658 \n", "Elusimicrobia 0.000000 0.542453 0.544811 \n", "Entotheonellia 0.576664 0.576262 0.575045 \n", "Erysipelotrichia 0.518692 0.517016 0.000000 \n", "FFCH5909 0.000000 0.634615 0.000000 \n", "Fibrobacteria 0.554841 0.553832 0.553822 \n", "Fimbriimonadia 0.543326 0.536859 0.541226 \n", "... ... ... ... \n", "Nitrospira 0.599553 0.599522 0.599818 \n", "OLB14 0.585111 0.584973 0.585082 \n", "OM190 0.000000 0.000000 0.000000 \n", "Oxyphotobacteria 0.544738 0.546060 0.545485 \n", "P2-11E 0.585185 0.578601 0.581893 \n", "Parcubacteria 0.496333 0.000000 0.493845 \n", "Phycisphaerae 0.573142 0.572757 0.577386 \n", "Pla4 0.609557 0.607615 0.603730 \n", "Planctomycetacia 0.624758 0.607147 0.619704 \n", "Rhodothermia 0.571397 0.583886 0.566825 \n", "Rubrobacteria 0.600372 0.601017 0.601583 \n", "S0134 0.603075 0.599525 0.598523 \n", "SHA-26 0.640568 0.609357 0.613068 \n", "Saccharimonadia 0.501756 0.496003 0.496590 \n", "Sericytochromatia 0.529830 0.534490 0.530035 \n", "Spirochaetia 0.561772 0.000000 0.000000 \n", "Subgroup 0.580621 0.579717 0.580671 \n", "Synergistia 0.000000 0.000000 0.000000 \n", "TK10 0.628671 0.618417 0.616980 \n", "Thermoanaerobaculia 0.582820 0.583003 0.582521 \n", "Thermodesulfovibrionia 0.000000 0.000000 0.000000 \n", "Thermoleophilia 0.588953 0.589492 0.589915 \n", "Thermoplasmata 0.572724 0.580311 0.577720 \n", "Unclassified 0.507756 0.505267 0.503933 \n", "Verrucomicrobiae 0.533333 0.532315 0.532096 \n", "WS6 0.000000 0.496296 0.496296 \n", "WWE3 0.000000 0.000000 0.000000 \n", "Woesearchaeia 0.526992 0.000000 0.000000 \n", "uncultured 0.612651 0.611116 0.616270 \n", "vadinHA49 0.569948 0.570093 0.570093 \n", "\n", "[81 rows x 12 columns]" ] }, "execution_count": 45, "metadata": {}, "output_type": "execute_result" } ], "source": [ "dfFinal = dfFinal.reset_index()\n", "dfFinal = dfFinal.pivot(index=\"Class\", columns=\"Enzyme\")\n", "dfFinal" ] }, { "cell_type": "code", "execution_count": 46, "metadata": {}, "outputs": [], "source": [ "dfFinal.to_csv(\"GC_class_whole.csv\")" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Only bacterial classes that account for the upper quartile of the dataset will be plotted. The remaining groups are summarized and labeled as \"Low abundance\"." ] }, { "cell_type": "code", "execution_count": 61, "metadata": {}, "outputs": [], "source": [ "# Using row sums to normalize each class\n", "rowSums = dfFinal.sum(axis=1, level=0)[\"Average\"]\n", "\n", "# 85 % quantile\n", "quantile85 = rowSums.quantile(q=0.5)\n", "rowSumsVector = rowSums <= quantile85\n", "\n", "# Upper 85% quantile rows\n", "df3 = dfFinal.loc[rowSums >= quantile85, :]\n", "la = dfFinal.loc[rowSums < quantile85, :].sum(axis=0)" ] }, { "cell_type": "code", "execution_count": 62, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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AverageStdDevGC_content
EnzymePromega42Promega55SuperScriptIVTGIRTPromega42Promega55SuperScriptIVTGIRTPromega42Promega55SuperScriptIVTGIRT
0319-7L14527.0442.0332.0392.085.20739481.04196450.25733856.3897150.5807500.5829870.5812330.582942
Acidimicrobiia1203.01617.01518.01858.0109.91724247.30010646.30118855.4102880.5852210.5866620.5881910.587488
Acidobacteriia257.0259.0444.0359.029.3649456.94262218.08867028.4552280.5557910.5617080.5618130.559804
Actinobacteria5864.011263.010105.011353.0445.351771581.639321223.156895274.2969190.5833210.5838050.5847250.586320
Alphaproteobacteria12943.09302.012148.012385.0481.747652232.488279303.496787382.1884350.5548350.5534260.5626060.563610
Anaerolineae191.0175.0113.089.07.5630688.09320712.7003945.8051700.5523750.5594230.5612380.564171
BD2-1126.033.048.042.05.7619447.9874908.8204316.7305270.6098610.6102530.6088900.610935
Bacilli1356.0656.0663.0520.0133.78415560.87035474.75158965.0768780.5228740.5337930.5312690.537584
Bacteroidia2825.01817.02307.03005.0141.663333188.279845143.224649194.8037470.5143520.5143830.5137380.508924
Blastocatellia336.0243.0309.0328.031.54679114.87615533.89985336.9296630.5435840.5464200.5481640.549827
Chloroflexia441.0825.0666.0789.039.23263912.38951233.71498233.7298090.6391460.6447710.6396640.640914
Dehalococcoidia70.098.0155.097.05.87367011.10405314.5258399.4762860.5781480.5778600.5775430.578580
Deinococci89.028.044.029.019.9173292.9664794.1472883.9623230.5653570.5742200.5613800.564073
Deltaproteobacteria4330.02154.03141.03001.0440.766945215.61238478.34985648.8640970.5639300.5660200.5652180.565658
Entotheonellia125.0122.0221.0164.023.43074922.07487334.62946723.4882950.5767940.5766640.5762620.575045
Fibrobacteria45.035.046.036.03.0000003.0822072.4899802.9495760.5544490.5548410.5538320.553822
Fimbriimonadia69.029.032.043.07.5960523.8340584.0987803.6469170.5424530.5433260.5368590.541226
Gammaproteobacteria5967.07610.02793.02576.0556.201672552.65359980.198504162.0808440.5430560.5368290.5442280.545745
Gemmatimonadetes532.0591.0518.0463.0111.57643177.212046105.991981106.9242720.6260240.6290100.6260450.628619
Gitt-GS-136270.0171.0239.0274.032.89376825.67489016.51363114.8727940.5609480.5618900.5610700.560207
Holophagae235.0139.0308.0191.025.41653014.30734112.09545436.8334090.5672140.5666780.5680340.568013
JG30-KF-CM6676.0145.0175.0175.011.27829814.35270012.8452337.2456880.5967720.5974730.5970700.597318
KD4-96298.0264.0370.0406.021.17309612.19426135.68613226.4707390.5696510.5693400.5692420.568869
Ktedonobacteria26.041.061.052.03.5637064.4384684.0865635.3197740.5786460.5789460.5805070.580245
Longimicrobia328.0217.0213.0197.036.95673112.19836125.51078219.1650720.6151910.6160980.6153480.614556
MB-A2-10861.0101.067.099.014.75466018.6868943.4351134.1472880.6089170.6085270.6082360.605956
Nitriliruptoria253.0380.0410.0408.017.84096414.74788112.4096744.5607020.5765690.5786540.5768600.577517
Nitrospira32.034.074.070.04.0373263.7682899.8081608.6890740.6007360.5995530.5995220.599818
Oxyphotobacteria2798.0962.01711.0877.0523.532520243.335776212.430459139.2634190.5460750.5447380.5460600.545485
Phycisphaerae101.0128.018.017.05.63027511.0589333.0495901.3416410.5765350.5731420.5727570.577386
Planctomycetacia357.0710.0247.0283.020.32978150.90677816.57709316.5317880.5982060.6247580.6071470.619704
Rubrobacteria1351.01505.02380.01974.067.31047571.333723193.530359158.6764000.5976080.6003720.6010170.601583
S0134116.075.073.0114.032.64506113.61983818.79627630.6545270.5891860.6030750.5995250.598523
Saccharimonadia130.057.049.030.019.7989904.39317716.4529639.1104340.5030400.5017560.4960030.496590
Subgroup385.0284.0681.0501.051.20058637.03646944.54997242.7106540.5801260.5806210.5797170.580671
TK10275.0583.0522.0611.025.95187945.97064338.44866743.8884950.6148150.6286710.6184170.616980
Thermoanaerobaculia117.0127.0122.0146.011.43678310.28591311.56719516.2696040.5822420.5828200.5830030.582521
Thermoleophilia2745.04643.03733.03562.0254.825430135.417133190.525064174.3166660.5890960.5889530.5894920.589915
Unclassified1211.01210.01292.01216.040.94752721.50581333.32866640.1335270.4927660.5077560.5052670.503933
Verrucomicrobiae1310.0620.01391.01029.084.88227143.312816112.83926649.7262510.5344860.5333330.5323150.532096
uncultured41.066.031.028.04.4384683.4205261.9235382.7018510.6087570.6126510.6111160.616270
Low abundance288.0239.0230.0211.068.92516552.14258935.39258232.70225913.21660814.89519614.01345411.626262
\n", "
" ], "text/plain": [ " Average StdDev \\\n", "Enzyme Promega42 Promega55 SuperScriptIV TGIRT Promega42 \n", "0319-7L14 527.0 442.0 332.0 392.0 85.207394 \n", "Acidimicrobiia 1203.0 1617.0 1518.0 1858.0 109.917242 \n", "Acidobacteriia 257.0 259.0 444.0 359.0 29.364945 \n", "Actinobacteria 5864.0 11263.0 10105.0 11353.0 445.351771 \n", "Alphaproteobacteria 12943.0 9302.0 12148.0 12385.0 481.747652 \n", "Anaerolineae 191.0 175.0 113.0 89.0 7.563068 \n", "BD2-11 26.0 33.0 48.0 42.0 5.761944 \n", "Bacilli 1356.0 656.0 663.0 520.0 133.784155 \n", "Bacteroidia 2825.0 1817.0 2307.0 3005.0 141.663333 \n", "Blastocatellia 336.0 243.0 309.0 328.0 31.546791 \n", "Chloroflexia 441.0 825.0 666.0 789.0 39.232639 \n", "Dehalococcoidia 70.0 98.0 155.0 97.0 5.873670 \n", "Deinococci 89.0 28.0 44.0 29.0 19.917329 \n", "Deltaproteobacteria 4330.0 2154.0 3141.0 3001.0 440.766945 \n", "Entotheonellia 125.0 122.0 221.0 164.0 23.430749 \n", "Fibrobacteria 45.0 35.0 46.0 36.0 3.000000 \n", "Fimbriimonadia 69.0 29.0 32.0 43.0 7.596052 \n", "Gammaproteobacteria 5967.0 7610.0 2793.0 2576.0 556.201672 \n", "Gemmatimonadetes 532.0 591.0 518.0 463.0 111.576431 \n", "Gitt-GS-136 270.0 171.0 239.0 274.0 32.893768 \n", "Holophagae 235.0 139.0 308.0 191.0 25.416530 \n", "JG30-KF-CM66 76.0 145.0 175.0 175.0 11.278298 \n", "KD4-96 298.0 264.0 370.0 406.0 21.173096 \n", "Ktedonobacteria 26.0 41.0 61.0 52.0 3.563706 \n", "Longimicrobia 328.0 217.0 213.0 197.0 36.956731 \n", "MB-A2-108 61.0 101.0 67.0 99.0 14.754660 \n", "Nitriliruptoria 253.0 380.0 410.0 408.0 17.840964 \n", "Nitrospira 32.0 34.0 74.0 70.0 4.037326 \n", "Oxyphotobacteria 2798.0 962.0 1711.0 877.0 523.532520 \n", "Phycisphaerae 101.0 128.0 18.0 17.0 5.630275 \n", "Planctomycetacia 357.0 710.0 247.0 283.0 20.329781 \n", "Rubrobacteria 1351.0 1505.0 2380.0 1974.0 67.310475 \n", "S0134 116.0 75.0 73.0 114.0 32.645061 \n", "Saccharimonadia 130.0 57.0 49.0 30.0 19.798990 \n", "Subgroup 385.0 284.0 681.0 501.0 51.200586 \n", "TK10 275.0 583.0 522.0 611.0 25.951879 \n", "Thermoanaerobaculia 117.0 127.0 122.0 146.0 11.436783 \n", "Thermoleophilia 2745.0 4643.0 3733.0 3562.0 254.825430 \n", "Unclassified 1211.0 1210.0 1292.0 1216.0 40.947527 \n", "Verrucomicrobiae 1310.0 620.0 1391.0 1029.0 84.882271 \n", "uncultured 41.0 66.0 31.0 28.0 4.438468 \n", "Low abundance 288.0 239.0 230.0 211.0 68.925165 \n", "\n", " GC_content \\\n", "Enzyme Promega55 SuperScriptIV TGIRT Promega42 \n", "0319-7L14 81.041964 50.257338 56.389715 0.580750 \n", "Acidimicrobiia 47.300106 46.301188 55.410288 0.585221 \n", "Acidobacteriia 6.942622 18.088670 28.455228 0.555791 \n", "Actinobacteria 581.639321 223.156895 274.296919 0.583321 \n", "Alphaproteobacteria 232.488279 303.496787 382.188435 0.554835 \n", "Anaerolineae 8.093207 12.700394 5.805170 0.552375 \n", "BD2-11 7.987490 8.820431 6.730527 0.609861 \n", "Bacilli 60.870354 74.751589 65.076878 0.522874 \n", "Bacteroidia 188.279845 143.224649 194.803747 0.514352 \n", "Blastocatellia 14.876155 33.899853 36.929663 0.543584 \n", "Chloroflexia 12.389512 33.714982 33.729809 0.639146 \n", "Dehalococcoidia 11.104053 14.525839 9.476286 0.578148 \n", "Deinococci 2.966479 4.147288 3.962323 0.565357 \n", "Deltaproteobacteria 215.612384 78.349856 48.864097 0.563930 \n", "Entotheonellia 22.074873 34.629467 23.488295 0.576794 \n", "Fibrobacteria 3.082207 2.489980 2.949576 0.554449 \n", "Fimbriimonadia 3.834058 4.098780 3.646917 0.542453 \n", "Gammaproteobacteria 552.653599 80.198504 162.080844 0.543056 \n", "Gemmatimonadetes 77.212046 105.991981 106.924272 0.626024 \n", "Gitt-GS-136 25.674890 16.513631 14.872794 0.560948 \n", "Holophagae 14.307341 12.095454 36.833409 0.567214 \n", "JG30-KF-CM66 14.352700 12.845233 7.245688 0.596772 \n", "KD4-96 12.194261 35.686132 26.470739 0.569651 \n", "Ktedonobacteria 4.438468 4.086563 5.319774 0.578646 \n", "Longimicrobia 12.198361 25.510782 19.165072 0.615191 \n", "MB-A2-108 18.686894 3.435113 4.147288 0.608917 \n", "Nitriliruptoria 14.747881 12.409674 4.560702 0.576569 \n", "Nitrospira 3.768289 9.808160 8.689074 0.600736 \n", "Oxyphotobacteria 243.335776 212.430459 139.263419 0.546075 \n", "Phycisphaerae 11.058933 3.049590 1.341641 0.576535 \n", "Planctomycetacia 50.906778 16.577093 16.531788 0.598206 \n", "Rubrobacteria 71.333723 193.530359 158.676400 0.597608 \n", "S0134 13.619838 18.796276 30.654527 0.589186 \n", "Saccharimonadia 4.393177 16.452963 9.110434 0.503040 \n", "Subgroup 37.036469 44.549972 42.710654 0.580126 \n", "TK10 45.970643 38.448667 43.888495 0.614815 \n", "Thermoanaerobaculia 10.285913 11.567195 16.269604 0.582242 \n", "Thermoleophilia 135.417133 190.525064 174.316666 0.589096 \n", "Unclassified 21.505813 33.328666 40.133527 0.492766 \n", "Verrucomicrobiae 43.312816 112.839266 49.726251 0.534486 \n", "uncultured 3.420526 1.923538 2.701851 0.608757 \n", "Low abundance 52.142589 35.392582 32.702259 13.216608 \n", "\n", " \n", "Enzyme Promega55 SuperScriptIV TGIRT \n", "0319-7L14 0.582987 0.581233 0.582942 \n", "Acidimicrobiia 0.586662 0.588191 0.587488 \n", "Acidobacteriia 0.561708 0.561813 0.559804 \n", "Actinobacteria 0.583805 0.584725 0.586320 \n", "Alphaproteobacteria 0.553426 0.562606 0.563610 \n", "Anaerolineae 0.559423 0.561238 0.564171 \n", "BD2-11 0.610253 0.608890 0.610935 \n", "Bacilli 0.533793 0.531269 0.537584 \n", "Bacteroidia 0.514383 0.513738 0.508924 \n", "Blastocatellia 0.546420 0.548164 0.549827 \n", "Chloroflexia 0.644771 0.639664 0.640914 \n", "Dehalococcoidia 0.577860 0.577543 0.578580 \n", "Deinococci 0.574220 0.561380 0.564073 \n", "Deltaproteobacteria 0.566020 0.565218 0.565658 \n", "Entotheonellia 0.576664 0.576262 0.575045 \n", "Fibrobacteria 0.554841 0.553832 0.553822 \n", "Fimbriimonadia 0.543326 0.536859 0.541226 \n", "Gammaproteobacteria 0.536829 0.544228 0.545745 \n", "Gemmatimonadetes 0.629010 0.626045 0.628619 \n", "Gitt-GS-136 0.561890 0.561070 0.560207 \n", "Holophagae 0.566678 0.568034 0.568013 \n", "JG30-KF-CM66 0.597473 0.597070 0.597318 \n", "KD4-96 0.569340 0.569242 0.568869 \n", "Ktedonobacteria 0.578946 0.580507 0.580245 \n", "Longimicrobia 0.616098 0.615348 0.614556 \n", "MB-A2-108 0.608527 0.608236 0.605956 \n", "Nitriliruptoria 0.578654 0.576860 0.577517 \n", "Nitrospira 0.599553 0.599522 0.599818 \n", "Oxyphotobacteria 0.544738 0.546060 0.545485 \n", "Phycisphaerae 0.573142 0.572757 0.577386 \n", "Planctomycetacia 0.624758 0.607147 0.619704 \n", "Rubrobacteria 0.600372 0.601017 0.601583 \n", "S0134 0.603075 0.599525 0.598523 \n", "Saccharimonadia 0.501756 0.496003 0.496590 \n", "Subgroup 0.580621 0.579717 0.580671 \n", "TK10 0.628671 0.618417 0.616980 \n", "Thermoanaerobaculia 0.582820 0.583003 0.582521 \n", "Thermoleophilia 0.588953 0.589492 0.589915 \n", "Unclassified 0.507756 0.505267 0.503933 \n", "Verrucomicrobiae 0.533333 0.532315 0.532096 \n", "uncultured 0.612651 0.611116 0.616270 \n", "Low abundance 14.895196 14.013454 11.626262 " ] }, "execution_count": 62, "metadata": {}, "output_type": "execute_result" } ], "source": [ "# Pulling lower quantile rows together and appending them to the upper quantile data frame\n", "la = la.to_frame(name=\"Low abundance\")\n", "la = la.transpose()\n", "\n", "df3 = df3.append(la)\n", "df3" ] }, { "cell_type": "code", "execution_count": 58, "metadata": {}, "outputs": [], "source": [ "df3.to_csv(\"GC_class_forFigure.csv\")" ] }, { "cell_type": "code", "execution_count": 63, "metadata": {}, "outputs": [], "source": [ "df3.to_csv(\"barplot_data_class.csv\")" ] }, { "cell_type": "code", "execution_count": 55, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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indexvariablevalue
00319-7L14level_00
1Acidimicrobiialevel_01
2Acidobacteriialevel_02
3Actinobacterialevel_03
4Alphaproteobacterialevel_04
5Anaerolineaelevel_05
6BD2-11level_06
7Bacillilevel_07
8Bacteroidialevel_08
9Blastocatellialevel_09
10Chloroflexialevel_010
11Dehalococcoidialevel_011
12Deinococcilevel_012
13Deltaproteobacterialevel_013
14Entotheonellialevel_014
15Fibrobacterialevel_015
16Fimbriimonadialevel_016
17Gammaproteobacterialevel_017
18Gemmatimonadeteslevel_018
19Gitt-GS-136level_019
20Holophagaelevel_020
21JG30-KF-CM66level_021
22KD4-96level_022
23Ktedonobacterialevel_023
24Longimicrobialevel_024
25MB-A2-108level_025
26Nitriliruptorialevel_026
27Nitrospiralevel_027
28Oxyphotobacterialevel_028
29Phycisphaeraelevel_029
............
6018Deinococcivalue0.564073
6019Deltaproteobacteriavalue0.565658
6020Entotheonelliavalue0.575045
6021Fibrobacteriavalue0.553822
6022Fimbriimonadiavalue0.541226
6023Gammaproteobacteriavalue0.545745
6024Gemmatimonadetesvalue0.628619
6025Gitt-GS-136value0.560207
6026Holophagaevalue0.568013
6027JG30-KF-CM66value0.597318
6028KD4-96value0.568869
6029Ktedonobacteriavalue0.580245
6030Longimicrobiavalue0.614556
6031MB-A2-108value0.605956
6032Nitriliruptoriavalue0.577517
6033Nitrospiravalue0.599818
6034Oxyphotobacteriavalue0.545485
6035Phycisphaeraevalue0.577386
6036Planctomycetaciavalue0.619704
6037Rubrobacteriavalue0.601583
6038S0134value0.598523
6039Saccharimonadiavalue0.49659
6040Subgroupvalue0.580671
6041TK10value0.61698
6042Thermoanaerobaculiavalue0.582521
6043Thermoleophiliavalue0.589915
6044Unclassifiedvalue0.503933
6045Verrucomicrobiaevalue0.532096
6046unculturedvalue0.61627
6047Low abundancevalue11.6263
\n", "

6048 rows × 3 columns

\n", "
" ], "text/plain": [ " index variable value\n", "0 0319-7L14 level_0 0\n", "1 Acidimicrobiia level_0 1\n", "2 Acidobacteriia level_0 2\n", "3 Actinobacteria level_0 3\n", "4 Alphaproteobacteria level_0 4\n", "5 Anaerolineae level_0 5\n", "6 BD2-11 level_0 6\n", "7 Bacilli level_0 7\n", "8 Bacteroidia level_0 8\n", "9 Blastocatellia level_0 9\n", "10 Chloroflexia level_0 10\n", "11 Dehalococcoidia level_0 11\n", "12 Deinococci level_0 12\n", "13 Deltaproteobacteria level_0 13\n", "14 Entotheonellia level_0 14\n", "15 Fibrobacteria level_0 15\n", "16 Fimbriimonadia level_0 16\n", "17 Gammaproteobacteria level_0 17\n", "18 Gemmatimonadetes level_0 18\n", "19 Gitt-GS-136 level_0 19\n", "20 Holophagae level_0 20\n", "21 JG30-KF-CM66 level_0 21\n", "22 KD4-96 level_0 22\n", "23 Ktedonobacteria level_0 23\n", "24 Longimicrobia level_0 24\n", "25 MB-A2-108 level_0 25\n", "26 Nitriliruptoria level_0 26\n", "27 Nitrospira level_0 27\n", "28 Oxyphotobacteria level_0 28\n", "29 Phycisphaerae level_0 29\n", "... ... ... ...\n", "6018 Deinococci value 0.564073\n", "6019 Deltaproteobacteria value 0.565658\n", "6020 Entotheonellia value 0.575045\n", "6021 Fibrobacteria value 0.553822\n", "6022 Fimbriimonadia value 0.541226\n", "6023 Gammaproteobacteria value 0.545745\n", "6024 Gemmatimonadetes value 0.628619\n", "6025 Gitt-GS-136 value 0.560207\n", "6026 Holophagae value 0.568013\n", "6027 JG30-KF-CM66 value 0.597318\n", "6028 KD4-96 value 0.568869\n", "6029 Ktedonobacteria value 0.580245\n", "6030 Longimicrobia value 0.614556\n", "6031 MB-A2-108 value 0.605956\n", "6032 Nitriliruptoria value 0.577517\n", "6033 Nitrospira value 0.599818\n", "6034 Oxyphotobacteria value 0.545485\n", "6035 Phycisphaerae value 0.577386\n", "6036 Planctomycetacia value 0.619704\n", "6037 Rubrobacteria value 0.601583\n", "6038 S0134 value 0.598523\n", "6039 Saccharimonadia value 0.49659\n", "6040 Subgroup value 0.580671\n", "6041 TK10 value 0.61698\n", "6042 Thermoanaerobaculia value 0.582521\n", "6043 Thermoleophilia value 0.589915\n", "6044 Unclassified value 0.503933\n", "6045 Verrucomicrobiae value 0.532096\n", "6046 uncultured value 0.61627\n", "6047 Low abundance value 11.6263\n", "\n", "[6048 rows x 3 columns]" ] }, "execution_count": 55, "metadata": {}, "output_type": "execute_result" } ], "source": [ "df3" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "# Simplifying a multi index into just one index \n", "idx = pd.IndexSlice\n", "\n", "df1 = data.data.copy()\n", "\n", "df1 = df1.sum(level=\"Enzyme\", axis=1)\n", "\n", "df1 = df1.reset_index()\n", "\n", "df1 = df1.iloc[:,1:]\n", "\n", "df1 = df1.iloc[:,[1,5,6,7,8,9,10]]" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "df1.index = df1.OTU\n", "\n", "df1 = df1.drop(\"OTU\", axis=1)" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "colNames = list(df1.columns.get_level_values(\"Enzyme\"))\n", "colNames[1] = \"GC\"\n", "colNames\n", "\n", "df1.columns = colNames\n", "\n", "del df1.index.name" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "df1melted = df1.melt(id_vars=[\"Class\", \"GC\"])\n", "df1melted" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "colSum = df1melted.groupby(\"variable\").sum()[\"value\"]\n", "\n", "colSum[\"Promega42\"]\n", "\n", "newValue = []\n", "# Dividing each row value by an appropriate total sum of the category (enzyme)\n", "for row in df1melted.iterrows():\n", " newValue.append(row[1].value/colSum[row[1].variable])\n", " \n", "df1melted[\"value\"] = newValue" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "df1sum = df1melted.groupby([\"Class\", \"variable\"]).sum()" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "df1melted.groupby([\"Class\", \"variable\"]).mean()" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "for row in df1melted.iterrows():\n", " # For a future convenience\n", " row=row[1]\n", " classval = row.Class\n", " enzyme = row.variable\n", " print(classval, enzyme)\n", " break" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "idx = pd.IndexSlice\n", "df1sum.loc[idx[classval, enzyme],idx[\"value\"]]" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "df1sum.loc[idx[classval, enzyme],:]" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "df1.to_csv(\"data_for_gc_plot.csv\")" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "|Enzyme |TGIRT |SuperScriptIV|Promega42 |Promega55|\n", "|:-------------|:-----:|:-----------:|:---------:|:-------:|\n", "|TGIRT | x | TvS | Tv42 | Tv55 | \n", "|SuperScriptIV | TvS | x | Sv42 | Sv55 |\n", "|Promega42 | Tv42 | Sv42 | x | P42v55 |\n", "|Promega55 | Tv55 | Sv55 | P42v55 | x |" ] } ], "metadata": { "kernelspec": { "display_name": "Python 3", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.6.8" } }, "nbformat": 4, "nbformat_minor": 1 }