MicrobeDB Database Analysis for Microbial Diversity

 
12. Jun. 2017
進捗報告
 
 
MicrobeDB.jp
のメタゲノム情報を利用した環境に由来した遺伝
子の検出とその応用
 
瀧原 速仁
 
Dechloromonas
Methanoculleus *
Leptothrix
Verminephrobacter
Comamonas
Nitrosomonas
Rhodoferax
Niastella
Runella
Marinobacter
Acidovorax
Polaromonas
Delftia
Acetomicrobium
Haloarcula *
Ketogulonicigenium
Nostoc
Alcanivorax
Flavobacterium
Gamma proteobacterium
Variovorax
Borrelia
Methylotenera
Oceanimonas
Legionella
Methanosphaerula *
Halobacteriovorax
Oenococcus
Thermodesulfobacterium
Veillonella
*:Archaea
 
Genus                             Family                           Phylum                    Wilcoxon_P-value    Bio – Pla abundance
 
0.0727272727272727
0.104984533136531
0.109090909090909
0.109090909090909
0.109090909090909
0.163636363636364
0.163636363636364
0.163636363636364
0.163636363636364
0.163636363636364
0.163636363636364
0.163636363636364
0.163636363636364
0.215084048647664
0.218253353455316
0.23030303030303
0.23030303030303
0.23030303030303
0.23030303030303
0.23030303030303
0.23030303030303
0.23030303030303
0.23030303030303
0.23030303030303
0.23030303030303
0.287391141675814
0.294186288800238
0.294186288800238
0.297517091364237
0.315151515151515
 
Rhodocyclaceae
Methanomicrobiaceae
Burkholderiales
Comamonadaceae
Comamonadaceae
Nitrosomonadaceae
Comamonadaceae
Chitinophagaceae
Cytophagaceae
Alteromonadaceae
Comamonadaceae
Comamonadaceae
Comamonadaceae
Synergistaceae
Haloarculaceae
Rhodobacteraceae
Nostocaceae
Alcanivoracaceae
Flavobacteriaceae
-
Comamonadaceae
Borreliaceae
Methylophilaceae
Aeromonadaceae
Legionellaceae
Methanoregulaceae
Halobacteriovoraceae
Leuconostocaceae
Thermodesulfobacteriaceae
Veillonellaceae
 
Proteobacteria
Euryarchaeota
Proteobacteria
Proteobacteria
Proteobacteria
Proteobacteria
Proteobacteria
Bacteroidetes
Bacteroidetes
Proteobacteria
Proteobacteria
Proteobacteria
Proteobacteria
Synergistetes
Euryarchaeota
Proteobacteria
Cyanobacteria
Proteobacteria
Bacteroidetes
Proteobacteria
Proteobacteria
Spirochaetes
Proteobacteria
Proteobacteria
Proteobacteria
Euryarchaeota
Proteobacteria
Firmicutes
Thermodesulfobacteria
Firmicutes
 
-1.107110373
0.731165913
-0.835147277
-0.782962845
-0.759719236
-0.72715939
-0.799247961
-1.272785119
-1.134469589
-0.877247817
-0.737605993
-0.832885774
-0.773168569
-0.590426255
-1.178457194
-0.618396351
-1.232093037
-1.047552249
-0.93423204
-1.206114006
-1.162830868
-0.977969917
-0.551805721
-0.027911397
-0.309593169
-0.643086887
-0.802827733
-0.728746771
-0.774661106
-0.668095291
 
Bio – Pla
が小さいから
Pla
の方が一部が
majority
を保有している
 
Pla
Bio
 
何を目的にしているか
/
何が予想されるか
大目的と小目的を見失わない
再度、全体の流れを説明
何が得られる
?
新発見や知見の強化、
Fisher
matrix
の向き、
odds
は何を示しているか
 
仮説、理想の結果、現実、問題点の洗い出し
生態学者としての視点、何がしたいのか
Wilcoxon
補正は根本的解決ではない
 
どうしたいのかが抜けてる
/
何が正しいのか
,
予想と同じか違うか
正解じゃなく、主張したいことが大事
何がわかったらゴールなのかを列記
/
それぞれの項目の計算方法を明記
 
Bio
Pla
でエンリッチする遺伝子、微生物種
 
 
そこから機構を予測
1
メタゲノム中の存在量の平均で
Wilcoxon 
 Pla
に偏りすぎ
 
 1
メタゲノムあたりの種数が
Pla
が少ない
・属のメタゲノム数で
Fisher 
 Pla
に偏りすぎ
 
 ?
 
・ただメタゲノム数が多い
/
値が大きい
 
 
どこにでもいる
Bio
でエンリッチを抜き出す
 
 Bio count
が大きいのは土壌系が多い
Pla
でエンリッチを抜き出す
 
 Pla abundance
が大きいのは海洋系が多い
・予測される機構
 
 Biofilm
構造の中心となるコア微生物種が一定数いる属構成であると予測
Pla
は充足率が高い、
bio
は充足率が低い
B:104/224,P:258/272
 
 Pla
は同じ構成、
Bio
は異なりやることが同じ
 
DB
、岩淵メタゲノムで
Pla count
のエビデンス
・値を
Cutoff
して各メタゲノムの上位しか見ないことでいるかいないか死んでるかの微妙な属や外れ値を捨てる
値を普通の
t
検定
 
 
相対値は比べられるが、
Pla
は薄い、
Bio
は濃い種構成だから比較は難しい
 
内容
 
MicrobeDB.jp
のメタゲノム情報を用いて、微生物が
Biofilm
型と
Planktonic
型を示す環
境でエンリッチする遺伝子、微生物種を抜粋する。
 それぞれの環境で相関する遺伝子や微生物種が環境に由来するゲノム構成かどうか
を検討する
 
Biofilm cell
 
Planktonic
 cell
 
biofilm cells environment
Biofilm,sediment,rock sand and
soil,animal associated,plant
associated,geographic feature and biome
 
planktonic cells environment
Water,aerobic environment,aquatic feature
and biome,ice,
 
?
Waste treatment,food,artificial natural environment,fungi associated,large-scale artifact
 
目的
 微生物の生息の方法として
Planktonic
型と
Biofilm
型が存在しており、接着因子や細
胞の安定性などに差異があることが予想される。また、それらを優占化する傾向にあ
ると予想される
 差異がある遺伝子、または微生物種を推測することで環境に優先的に働く因子や
集団の安定性をはかる微生物種を予想する
 
手法
 
Biofilm
型と
Planktonic
型に分類したメタゲノムデータを用いて、遺伝子の検出量から
Wilcoxon
の順位和検定
:
両者で差異のある値を持つ因子を抜き出す
 
Fisher
の正確検定
:
各因子の環境間での独立性をみる
 
・抜粋
KO
を用いたクラスタリング
:
環境に相関した
KO
が抜粋されているかどうか
 
予想
 
Biofilm
型は細胞表面が担体に接触しているので、表層の接着因子や脂肪酸に差
異があることが予想される
 
前回の指摘
 
Biofilm
型と
Planktonic
型の環境の
1
メタゲノムあたりの種数を算出する
 
 
Nostoc
Gamma proteobacterium
Legionella
Leadbetterella
Yersinia
Flavobacterium
Aeromonas
Ferrimonas
Dechloromonas
Fluviicola
Zymomonas
Nitrosomonas
Ketogulonicigenium
Neisseria
Runella
Eubacterium
Acidothermus
Haliscomenobacter
Halomonas
Niastella
Actinobacillus
Flexibacter
Methylophaga
Pusillimonas
Oceanimonas
Methanoculleus (Archaea)
Oenococcus
Synechocystis
Jonesia
Pseudopedobacter
 
Genus                              Family                               Phylum                             Wilcoxon_P-value
 
0.00606060606060606
0.00606060606060606
0.00606060606060606
0.00606060606060606
0.00606060606060606
0.00606060606060606
0.0121212121212121
0.0242424242424242
0.0242424242424242
0.0242424242424242
0.0242424242424242
0.0242424242424242
0.0242424242424242
0.0242424242424242
0.0242424242424242
0.0424242424242424
0.0424242424242424
0.0424242424242424
0.0424242424242424
0.0424242424242424
0.0424242424242424
0.0424242424242424
0.0424242424242424
0.0424242424242424
0.0424242424242424
0.0452199741787572
0.0700049832291192
0.0727272727272727
0.0727272727272727
0.0727272727272727
 
Nostocaceae
-
Legionellaceae
Cytophagaceae
Yersiniaceae
Flavobacteriaceae
Aeromonadaceae
Ferrimonadaceae
Rhodocyclaceae
Crocinitomicaceae
Sphingomonadaceae
Nitrosomonadaceae
Rhodobacteraceae
Chitinophagaceae
Cytophagaceae
Eubacteriaceae
Acidothermaceae
Haliscomenobacteraceae
Halomonadaceae
Chitinophagaceae
Pasteurellaceae
Cytophagaceae
Piscirickettsiaceae
Alcaligenaceae
Aeromonadaceae
Methanomicrobiaceae
Leuconostocaceae
Merismopediaceae
Jonesiaceae
Sphingobacteriaceae
 
Cyanobacteria
Proteobacteria
Proteobacteria
Bacteroidetes
Proteobacteria
Bacteroidetes
Proteobacteria
Proteobacteria
Proteobacteria
Bacteroidetes
Proteobacteria
Proteobacteria
Proteobacteria
Bacteroidetes
Bacteroidetes
Firmicutes
Actinobacteria
Bacteroidetes
Proteobacteria
Bacteroidetes
Proteobacteria
Bacteroidetes
Proteobacteria
Proteobacteria
Proteobacteria
Euryarchaeota
Firmicutes
Cyanobacteria
Actinobacteria
Bacteroidetes
 
微生物が検出されたメタゲノム数
 (Bio:224
個、
Pla:272
)
 
Acaryochloris   88      240     136     32
Acetobacter     93      242     131     30
Acetobacterium  86      215     138     57
Acetohalobium   86      216     138     56
Acholeplasma    87      238     137     34
Achromobacter   102     257     122     15
Acidaminococcus 88      237     136     35
Acidianus       40      205     184     67
Acidilobus      64      203     160     69
Acidimicrobium  96      240     128     32
Acidiphilium    96      253     128     19
 
Pseudomonas     102     258     122     14
Leptospira      14      196     210     76
Escherichia     103     258     121     14
Fervidicoccus   28      210     196     62
Coprothermobacter       58      238     166     34
Marinomonas     97      258     127     14
 
Genus         Bio      Pla
 
微生物が検出されたメタゲノム数
 (Bio:224
個、
Pla:272
)
 
Leptospira
Fervidicoccus (Archaea)
Coprothermobacter
Halogeometricum (Archaea)
Flavobacteriaceae
Trichodesmium
Leuconostoc
Ferroglobus (Archaea)
Thermobaculum
Pelagibacterium
Methanocella (Archaea)
Staphylothermus (Archaea)
Methylomonas
Roseobacter
Bdellovibrio
Magnetococcus
Halorubrum (Archaea)
Parvularcula
Parachlamydia
Methanoregula (Archaea)
Marinomonas
Pseudoalteromonas
Acidianus (Archaea)
Prochlorococcus
 
1.84984756776945e-55
1.30666651736405e-50
1.2144453370268e-46
1.04875444172146e-45
7.15629803877711e-45
1.11039259592354e-44
2.57279815069165e-44
1.40508206857176e-43
2.25857826588668e-43
1.26051550425212e-42
9.15759027518411e-42
1.08395647986535e-41
1.35143151367562e-41
1.65228419787129e-41
2.85058161779399e-41
3.08721857119471e-41
1.53852388750522e-40
2.66173620735992e-40
4.17021551646017e-40
7.2097712066611e-40
1.34108714945582e-39
2.16569106567114e-39
2.77041615534659e-39
3.38487702676658e-39
 
0.02585034013605442
0.04217687074829932
0.049913941480206545
0.05505505505505505
0.04014096140080392
0.04556894243641232
0.040922701563712985
0.06021335641724165
0.05178947368421053
0.04583053878828527
0.061016949152542375
0.06471989230609919
0.04197761194029851
0.05131637661758144
0.04395061728395062
0.052725250278086756
0.06677157094151587
0.05772594752186589
0.0600712569392659
0.07013943699026572
0.041445400720258804
0.055421686746987955
0.07104984093319193
0.04732824427480916
 
Genus
 
P-value (Fisher’s test)
 
Odds ratio(
Bio > 1,Pla < 1
)
 
Spirochaetes
 
Phylum
 
2
 
Bone    580
Colon   33
Gut     38
Lung    558
Midgut  142
Tooth   556
acid mine drainage      117
activated sludge        79
aerobic 392
animal-associated habitat       108
aquaculture     302
aquarium        55
aquatic biome   30
beach sand      191
biofilm 81
bioreactor      166
biotic mesoscopic physical object       16
brine   118
cave    545
coast   17
coastal water   39
compost 425
coral reef      34
fresh water     39
freshwater biome        140
freshwater habitat      12
frost flowers   199
fungi associated        103
 
hot spring      37
hot water       167
hydrothermal vent       313
ice     426
insecta-associated habitat      231
kimchi  16
lake    140
lake sediment   9
lake water      14
large-scale artifact    110
mammalia-associated habitat     105
man-made structure      83
marine biome    16
marine channel  29
marine coral reef biome 50
marine habitat  4
marine reef     80
marine sediment 26
microbial mat   144
mine drainage   566
national park   37
ocean   36
ocean biome     41
oil contaminated soil   141
pasture soil    508
permafrost      289
phyllosphere    375
pond    59
 
rhizosphere soil        0
rumen   17
salt field      68
sea     111
sea floor       80
sea ice 73
sea water       2
seafood product 210
soil    82
solar saltern   131
spring sediment 9
strait  28
stream  167
surface water   4
thermophilic sediment   9
waste water     130
wastewater treatment plant      119
water   47
water column    38
wetland 223
 
B
B
B
B
B
B
P
B
P
B
P
B
P
B
B
B
B
P
B
P
P
 
P
P
P
P
P
 
P
P
P
P
B
 
P
B
P
B
B
B
P
P
P
P
P
 
B
B
 
P
P
B
B
B
B
B
 
B
B
 
P
P
P
P
 
B
 
 
 
 
P
B
 
 
P
P
B
 
各環境の
1
メタゲノムあたりの種数
 
Biofilm
Ave
: 203
Med: 126
 
Planktonic
Ave: 94
Med: 39
 
animal associated       582
rock,sand and soil      583
biofilm 584
geographic feature and biome    550
plant associated        377
sediment        572
large-scale artifact    519
 
water   583
aerobic environment     394
aquatic feature and biome       584
ice     437
 
waste treatment 562
food    424
artificial natural environment  547
organic feature and biome       0
fungi associated        314
human activity association      584
hydrosphere     584
organism association    584
 
Biofilm
 
 
 
 
 
Planktonic
 
 
その他
 
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix msv: <http://purl.jp/bio/11/msv/> .
@prefix srs: <http://www.ncbi.nlm.nih.gov/sra/> .
@prefix ncbi_refseq: <http://www.ncbi.nlm.nih.gov/nuccore/> .
@prefix ko: <http://www.genome.jp/dbget-bin/www_bget?> .
@prefix path: <http://www.genome.jp/dbget-bin/www_bget?> .
 
srs:DRS000009   msv:containedKO [
        msv:assignedKO  ko:K04033;
        msv:KOCount     "2.21645157258498e-05"^^xsd:float;
].
 
srs:DRS000009   msv:containedKO [
        msv:assignedKO  ko:K00937;
        msv:KOCount     "2.41630257974925e-05"^^xsd:float;
].
 
srs:DRS000009   msv:containedKO [
        msv:assignedKO  ko:K07735;
        msv:KOCount     "1.38171967047323e-05"^^xsd:float;
].
 
K01610  phosphoenolpyruvate carboxykinase (ATP) [EC:4.1.1.49]
K03761  MFS transporter, MHS family, alpha-ketoglutarate permease
K03577  TetR/AcrR family transcriptional regulator, acrAB operon repressor
K12538  outer membrane protein HasF
K03651  Icc protein
K01040  glutaconate CoA-transferase, subunit B [EC:2.8.3.12]
K11896  type VI secretion system protein ImpG
K03923  modulator of drug activity B
K10539  L-arabinose transport system ATP-binding protein [EC:3.6.3.17]
K01745  histidine ammonia-lyase [EC:4.3.1.3]
K02168  choline/glycine/proline betaine transport protein
K00322  NAD(P) transhydrogenase [EC:1.6.1.1]
K01246  DNA-3-methyladenine glycosylase I [EC:3.2.2.20]
K01426  amidase [EC:3.5.1.4]
K11734  aromatic amino acid transport protein AroP
K17215  inositol transport system ATP-binding protein
K02403  flagellar transcriptional activator FlhD
K16011  mannose-1-phosphate guanylyltransferase / mannose-6-phosphate isomerase [EC:2.7.7.13 5.3.1.8]
K00171  pyruvate ferredoxin oxidoreductase, delta subunit [EC:1.2.7.1]
K00355  NAD(P)H dehydrogenase (quinone) [EC:1.6.5.2]
K17320  putative aldouronate transport system permease protein
K14519  NADP-dependent aldehyde dehydrogenase [EC:1.2.1.4]
K17214  inositol transport system permease protein
K03119  taurine dioxygenase [EC:1.14.11.17]
K08195  MFS transporter, AAHS family, 4-hydroxybenzoate transporter
K07098
K03272  D-beta-D-heptose 7-phosphate kinase / D-beta-D-heptose 1-phosphate adenosyltransferase [EC:2.7.1.167 2.7.7.70]
K00849  galactokinase [EC:2.7.1.6]
K08224  MFS transporter, YNFM family, putative membrane transport protein
K10979  DNA end-binding protein Ku
K10117  raffinose/stachyose/melibiose transport system substrate-binding protein
K02108  F-type H+-transporting ATPase subunit a [EC:3.6.3.14]
K03704  cold shock protein (beta-ribbon, CspA family)
K10237  trehalose/maltose transport system permease protein
K10531  L-ornithine N5-oxygenase [EC:1.13.12.-]
K10015  histidine transport system permease protein
K03773  FKBP-type peptidyl-prolyl cis-trans isomerase FklB [EC:5.2.1.8]
K10543  D-xylose transport system substrate-binding protein
K03736  ethanolamine ammonia-lyase small subunit [EC:4.3.1.7]
K07407  alpha-galactosidase [EC:3.2.1.22]
 
Wilcoxon
順位和検定により抜粋した
KO
p
 < 0.05 (336
)
 
(1/5)
 
Wilcoxon
によって抜粋した
KO
によるクラスタリング
 
Bio
Bio
Pla
Pla
Bio
Bio
Bio
Bio
Bio
Pla
Pla
 
R
によるフィッシャー検定について
 
Genus              
 
 Biofilm             Planktonic
 
Escherichia
あり
              103                        258
 
Escherichia
なし
              121                          14
 
Escherichia
 = matrix(c(
103,258,2,0
), ncol = 2 )
Escherichia
    
    [
Bio
]
 
 
   
[
Pla
]
[
+
]  
 103     
 
  258
[
-
]  
  121      
  
  14
f
isher.test(a)
 
Fisher's Exact Test for Count Data
data:  
Escherichia
 
p-value = 
2.041e-36
alternative hypothesis: true odds ratio is not equal to 1
95 percent confidence interval:
1.497846 2.569146
sample estimates:
odds ratio 
[(103/258) / (121/14)]
0.046191
 
現在の進捗状況
 
問題点
 
Fisher
用の
matrix
を確認した結果、大半の微生物種が
Planktonic
の環境で
総数の大半を占めており、想定した環境を反映していない
 
food    5.565130795835259
fungi associated        6.055905711563868
plant associated        6.642378771462215
biofilm 6.950432001122053
aerobic environment     7.681887098090524
ice     8.122683417915658
large-scale artifact    8.377015366930495
artificial natural environment  8.717709878783833
geographic feature and biome    8.880730867862294
waste treatment 9.93970104147625
animal associated       10.319644405818543
sediment        10.385325333127858
rock,sand and soil      11.586005173411566
water   12.313033474340926
aquatic feature and biome       12.373408565130129
 
Shannon index
= 
-
Σ(
value
/s
um
)*log2(
value
/s
um
)
 
DRS000009       MEO_0000437     MEO_0000137     K00937:2.41630257974925e-05     K07735:1.38171967047323e-05     K03117:2.
DRS000201       MEO_0000437     MEO_0000137     MEO_0000437     MEO_0000416     MEO_0000437     MEO_0000026     K08590:2.
DRS000406       MEO_0000437     MEO_0000718     K02224:3.31285985940223e-06     K07749:1.98771591564134e-05     K00163:1.
DRS000407       MEO_0000437     MEO_0000718     K02793:9.26535036922421e-06     K03076:9.26535036922421e-06     K00384:9.
ERS000029       MEO_0000437     MEO_0000658     MEO_0000439     MEO_0000439     MEO_0000439     K03086:0.333333333333333
ERS007239       MEO_0000437     MEO_0000056     K07735:0.000704225352112676     K03117:0.00727663895057533      K00954:0.
ERS007241       MEO_0000437     MEO_0000056     K01952:0.00181833182080686      K07749:0.000869565217391304     K00163:0.
ERS015567       MEO_0000437     MEO_0000024     MEO_0000437     MEO_0000027     MEO_0000437     MEO_0000038     K06999:0.
ERS015568       MEO_0000437     MEO_0000038     K02777:0.00294985250737463      K02703:0.0206489675516224       K04077:0.
ERS016117       MEO_0000437     MEO_0000449     MEO_0000439     K03117:0.000471119694989063     K00954:0.0087782623731457
ERS016118       MEO_0000437     MEO_0000458     MEO_0000439     K00954:0.000635002877817424     K02224:9.98980764944161e-
ERS033180       MEO_0000437     MEO_0000704     K00549:0.000175100682892663     K13639:8.75503414463316e-05     K00163:0.
SRS000238       MEO_0000437     MEO_0000122     K07084:0.00202839756592292      K01825:0.00101419878296146      K06969:0.
SRS000239       MEO_0000437     MEO_0000122     K02275:0.00079428117553614      K03076:0.0039714058776807       K04046:0.
SRS000240       MEO_0000437     MEO_0000122     K03616:0.00272108843537415      K04748:0.00136054421768707      K07180:0.
SRS000241       MEO_0000437     MEO_0000122     K02224:0.00150037509377344      K01012:0.000750187546886722     K13482:0.
SRS000242       MEO_0000437     MEO_0000122     K00163:0.00207900207900208      K06181:0.00207900207900208      K01956:0.
 
環境名
(76
)
Bone
Colon
Gut
Lung
Midgut
Tooth
acid mine drainage
activated sludge
aerobic
animal-associated habitat
aquaculture
aquarium
aquatic biome
beach sand
biofilm
bioreactor
biotic mesoscopic physical object
brine
cave
coast
coastal water
compost
coral reef
fresh water
freshwater biome
freshwater habitat
frost flowers
fungi associated
hot spring
hot water
 
KO
4967
3825
3595
211
3703
2602
2175
3486
2087
2819
1057
268
3231
2593
2588
3490
1782
470
1752
6
1870
1988
233
4034
3148
132
742
4270
2489
2724
 
検出
KO
K01467  K03046  K03043  K04077  K02358  K03070  K04043  K03701  K02355  K03086  K01955  K03695  K03544  K09014  K03798  K
K03046  K03043  K02355  K02358  K01610  K03737  K02886  K02945  K00239  K03070  K00962  K04043  K04077  K05349  K01955  K
K01534  K01995  K05786  K03703  K00981  K03483  K00666  K03046  K06919  K03043  K01999  K06147  K02674  K02358  K03406  K
K00351  K03043  K04043  K02016  K06180  K03701  K12257  K03286  K06942  K00243  K03046  K03320  K02952  K07270  K02520  K
K03043  K03046  K03893  K02355  K02014  K07119  K03296  K00116  K00383  K01681  K00525  K04753  K00265  K06207  K02111  K
K03046  K03043  K03086  K02358  K01955  K02355  K03147  K04077  K00525  K03070  K02274  K03701  K04043  K03544  K02112  K
K07496  K02014  K01153  K09822  K07267  K07399  K01533  K07646  K00382  K03043  K02274  K02358  K03046  K01601  K00412  K
K03046  K02358  K04077  K03043  K02355  K04043  K02112  K01955  K00962  K01937  K02111  K03701  K03798  K03086  K01915  K
K03701  K03046  K03043  K02358  K01955  K00666  K00525  K02470  K03070  K00548  K01869  K02355  K04077  K02112  K00265  K
K03046  K03043  K04077  K03696  K07637  K02945  K02274  K00239  K03086  K01681  K02355  K09687  K01955  K03596  K02470  K
K08151  K00879  K15269  K03406  K02358  K03046  K03596  K04077  K04043  K01915  K02355  K03296  K02337  K01999  K03043  K
K02112  K02689  K01467  K03149  K03438  K00209  K06940  K01915  K02004  K02274  K00658  K06207  K02276  K04096  K03076  K
K07637  K07660  K07319  K07496  K01494  K06926  K03465  K07491  K02355  K01190  K02358  K03043  K02112  K03046  K00383  K
K03046  K02358  K04077  K03043  K03086  K03070  K01955  K03695  K02112  K03798  K03701  K03782  K02355  K04043  K01681  K
K06895  K03545  K01868  K00574  K01951  K13935  K00626  K02575  K07798  K03406  K03070  K00799  K01712  K00426  K06158  K
K02358  K03046  K02355  K03737  K03043  K03701  K06147  K01873  K01153  K02004  K03702  K01872  K03070  K03040  K01870  K
K06147  K02004  K03657  K03046  K16787  K03701  K01421  K16786  K07024  K03316  K02529  K00383  K01533  K03294  K03763  K
K00558  K01955  K03046  K00090  K02111  K01681  K03086  K03406  K02470  K04077  K01873  K03701  K02343  K02621  K00059  K
K03046  K03043  K02358  K04077  K03070  K04043  K03086  K02355  K01955  K03696  K03701  K03596  K03695  K02945  K02111  K
K00548  K01915  K00342  K04043  K17321  K05559
K03043  K03046  K02014  K02358  K02945  K02355  K03406  K06207  K02111  K11384  K04077  K02886  K04043  K02112  K01955  K
K03046  K03043  K02358  K02355  K04077  K02274  K04043  K01915  K03070  K00525  K03701  K01955  K01681  K03702  K09014  K
K08884  K02112  K01467  K01711  K06200  K04567  K06160  K02689  K02044  K01638  K02470  K07124  K07237  K09686  K01474  K
K00558  K04077  K08151  K04043  K02703  K01711  K03695  K02358  K15269  K01681  K02314  K02040  K03797  K00432  K00525  K
K00558  K03111  K02357  K07496  K02835  K01999  K11942  K01653  K02757  K02756  K02755  K02355  K04094  K01966  K06168  K
K00558  K03111  K02357  K01999  K07496  K02835  K01653  K11942  K02757  K02755  K02756  K04043  K04094  K02355  K01966  K
K03046  K03043  K02358  K00548  K00525  K03296  K01687  K02355  K01955  K00265  K04077  K02198  K01952  K03522  K01915  K
K02014  K03296  K00656  K03046  K00123  K01652  K03043  K02761  K00370  K01223  K00688  K00615  K00265  K05802  K00525  K
K07637  K07660  K07319  K07496  K01494  K06926  K03465  K07491  K02355  K02358  K03043  K00383  K03046  K02112  K03305  K
K03497  K00638  K01190  K00860  K03702  K00833  K01992  K00652  K06890  K03296  K06132  K03147  K01935  K03639  K07347  K
 
K00001  -10.311816354878324     -8.104774922411162      -9.12536274284216       -9.630882031115686      -10.446304307863649     -9.444659766985191
K00002  -13.141335312924086     -16     -12.704600872109006     -14.043777560434304     -12.665170969217156     -10.390757105237586
K00003  -7.121752898407186      -8.413313412355846      -7.382105014212423      -8.475435715319305      -8.852086421482788      -7.445159144381894
K00004  -13.213722194807316     -16     -12.412278655972163     -16     -16     -11.493048389416982
K00005  -9.96363701697749       -8.407649758618964      -12.14236250205763      -10.414517054242882     -16     -11.493048389416982
K00007  -10.596788922173955     -9.329282052339648      -12.918984333818889     -16     -16     -9.409468928010325
K00008  -11.584457072149807     -13.31394247457744      -10.254085944514278     -12.176686333973533     -16     -10.095757399493332
K00009  -11.006367458916358     -8.16761864984201       -12.4902708126153       -11.03250817989423      -16     -11.482051760613226
K00010  -9.264325381071723      -9.186300492329945      -9.45947148340929       -9.3754727463094        -10.469939085997646     -9.88140145587432
K00011  -16     -16     -15.131461775818128     -16     -16     -16
K00012  -7.106372296508517      -6.98777647385517       -7.183819812492088      -7.964181219197697      -6.947145554622075      -6.859389052643327
K00013  -7.7918148582413504     -8.211241559923812      -7.816358527328419      -7.338291834838282      -10.451770159980867     -7.902794931405587
K00014  -9.277120817347368      -8.54307527927404       -8.46073500012144       -8.684299576853675      -10.469939085997646     -8.544543938241562
K00015  -10.73818076223137      -14.628162042310528     -8.362338719924006      -9.334936622441244      -8.002924975011636      -8.778385710633545
K00016  -10.129216802977284     -7.4845566904656415     -10.051986464809646     -11.063919929388838     -16     -11.493048389416982
K00018  -13.225287537775754     -12.25656699684002      -10.968406047051388     -13.672214004001823     -8.843329333909496      -9.183850818741712
K00019  -9.625883141561934      -9.755969817231259      -8.47209897699472       -9.645816479474618      -8.30933106575223       -7.773560661928158
K00020  -9.315047048838318      -9.92986455302942       -8.044325803389565      -9.261050917282379      -9.544127635689426      -7.384846155199226
K00021  -16.245565046960508     -9.061901547084124      -12.748580411992254     -13.246077759947227     -10.446304307863649     -11.482051760613226
K00023  -8.702620832331586      -9.834925987742565      -7.746683551255264      -8.53001839575091       -9.203602442460852      -7.990860797863764
K00024  -6.574629532570801      -7.580959967649561      -5.292461661964257      -7.523288272986434      -7.8223424865027535     -6.844201977115136
K00027  -6.679113848508194      -7.299539418709296      -7.41204210776536       -8.079553675448148      -8.480051144947907      -9.287260449470113
K00028  -16     -13.239973934562654     -16     -16     -16     -16
K00029  -6.88173249202305       -8.052890251183237      -6.470484779211342      -6.858808198174476      -6.8971375085262006     -5.863457907014847
K00030  -9.996294929960587      -9.996499401331711      -9.241982940346352      -8.841324475788843      -10.968721679793427     -9.2945959757397
K00031  -5.604052648376666      -7.0236236350845065     -5.736622818699684      -6.02264419242527       -5.888872580320814      -5.9616659039450965
K00032  -14.554995368110623     -16     -11.621793774892419     -14.554603184200294     -10.968721679793427     -16
K00033  -6.783449648079597      -7.386708390371603      -6.756252671315078      -7.606976602999303      -6.9025269661364295     -7.022195787939136
K00034  -11.068633989656037     -16     -12.067132542569965     -10.063455860550718     -16     -9.08913996971469
K00035  -15.532192564464934     -16     -12.057015551
 
KO       
メタゲノムの存在量の対数
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In June 2017, data from MicrobeDB.jp was analyzed, revealing microbial diversity in various phyla and families. The study included Wilcoxon P-values and abundances of different microbial genera. The analysis indicated the presence of various bacterial and archaeal species in different environments, including biofilms, planktonic cells, and waste treatment systems. The findings provide insights into the composition and distribution of microbes in natural and artificial environments.

  • Microbial Diversity
  • MicrobeDB Analysis
  • Wilcoxon P-values
  • Bacterial Species
  • Archaeal Species

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  1. 12. Jun. 2017 MicrobeDB.jp

  2. Genus Family Phylum Wilcoxon_P-value Bio Pla abundance Rhodocyclaceae Methanomicrobiaceae Burkholderiales Comamonadaceae Comamonadaceae Nitrosomonadaceae Comamonadaceae Chitinophagaceae Cytophagaceae Alteromonadaceae Comamonadaceae Comamonadaceae Comamonadaceae Synergistaceae Haloarculaceae Rhodobacteraceae Nostocaceae Alcanivoracaceae Flavobacteriaceae - Comamonadaceae Borreliaceae Methylophilaceae Aeromonadaceae Legionellaceae Methanoregulaceae Halobacteriovoraceae Leuconostocaceae Thermodesulfobacteriaceae Veillonellaceae Firmicutes Dechloromonas Methanoculleus * Leptothrix Verminephrobacter Comamonas Nitrosomonas Rhodoferax Niastella Runella Marinobacter Acidovorax Polaromonas Delftia Acetomicrobium Haloarcula * Ketogulonicigenium Nostoc Alcanivorax Flavobacterium Gamma proteobacterium Variovorax Borrelia Methylotenera Oceanimonas Legionella Methanosphaerula * Halobacteriovorax Oenococcus Thermodesulfobacterium Veillonella *:Archaea Proteobacteria Euryarchaeota Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Bacteroidetes Bacteroidetes Proteobacteria Proteobacteria Proteobacteria Proteobacteria Synergistetes Euryarchaeota Proteobacteria Cyanobacteria Proteobacteria Bacteroidetes Proteobacteria Proteobacteria Spirochaetes Proteobacteria Proteobacteria Proteobacteria Euryarchaeota Proteobacteria Firmicutes Thermodesulfobacteria 0.0727272727272727 0.104984533136531 0.109090909090909 0.109090909090909 0.109090909090909 0.163636363636364 0.163636363636364 0.163636363636364 0.163636363636364 0.163636363636364 0.163636363636364 0.163636363636364 0.163636363636364 0.215084048647664 0.218253353455316 0.23030303030303 0.23030303030303 0.23030303030303 0.23030303030303 0.23030303030303 0.23030303030303 0.23030303030303 0.23030303030303 0.23030303030303 0.23030303030303 0.287391141675814 0.294186288800238 0.294186288800238 0.297517091364237 0.315151515151515 -1.107110373 0.731165913 -0.835147277 -0.782962845 -0.759719236 -0.72715939 -0.799247961 -1.272785119 -1.134469589 -0.877247817 -0.737605993 -0.832885774 -0.773168569 -0.590426255 -1.178457194 -0.618396351 -1.232093037 -1.047552249 -0.93423204 -1.206114006 -1.162830868 -0.977969917 -0.551805721 -0.027911397 -0.309593169 -0.643086887 -0.802827733 -0.728746771 -0.774661106 -0.668095291 Bio Pla Pla majority Pla Bio

  3. Wilcoxon / , / Bio Pla 1 Wilcoxon Pla 1 Pla Fisher Pla ? / Bio Bio count Pla Pla abundance Biofilm Pla bio B:104/224,P:258/272 Pla Bio DB Pla count Cutoff t Pla Bio / ? Fisher matrix odds

  4. MicrobeDB.jp Biofilm Planktonic ? Waste treatment,food,artificial natural environment,fungi associated,large-scale artifact biofilm cells environment Biofilm,sediment,rock sand and soil,animal associated,plant associated,geographic feature and biome planktonic cells environment Water,aerobic environment,aquatic feature and biome,ice, Biofilm cell Planktonic cell

  5. Planktonic Biofilm Biofilm Planktonic Wilcoxon : Fisher : KO : KO Biofilm

  6. Biofilm Planktonic 1

  7. Genus Family Phylum Wilcoxon_P-value Nostocaceae - Legionellaceae Cytophagaceae Yersiniaceae Flavobacteriaceae Aeromonadaceae Ferrimonadaceae Rhodocyclaceae Crocinitomicaceae Sphingomonadaceae Nitrosomonadaceae Rhodobacteraceae Chitinophagaceae Cytophagaceae Eubacteriaceae Acidothermaceae Haliscomenobacteraceae Halomonadaceae Chitinophagaceae Pasteurellaceae Cytophagaceae Piscirickettsiaceae Alcaligenaceae Aeromonadaceae Methanomicrobiaceae Leuconostocaceae Merismopediaceae Jonesiaceae Sphingobacteriaceae Nostoc Gamma proteobacterium Legionella Leadbetterella Yersinia Flavobacterium Aeromonas Ferrimonas Dechloromonas Fluviicola Zymomonas Nitrosomonas Ketogulonicigenium Neisseria Runella Eubacterium Acidothermus Haliscomenobacter Halomonas Niastella Actinobacillus Flexibacter Methylophaga Pusillimonas Oceanimonas Methanoculleus (Archaea) Oenococcus Synechocystis Jonesia Pseudopedobacter Cyanobacteria Proteobacteria Proteobacteria Bacteroidetes Proteobacteria Bacteroidetes Proteobacteria Proteobacteria Proteobacteria Bacteroidetes Proteobacteria Proteobacteria Proteobacteria Bacteroidetes Bacteroidetes Firmicutes Actinobacteria Bacteroidetes Proteobacteria Bacteroidetes Proteobacteria Bacteroidetes Proteobacteria Proteobacteria Proteobacteria Euryarchaeota Firmicutes Cyanobacteria Actinobacteria Bacteroidetes 0.00606060606060606 0.00606060606060606 0.00606060606060606 0.00606060606060606 0.00606060606060606 0.00606060606060606 0.0121212121212121 0.0242424242424242 0.0242424242424242 0.0242424242424242 0.0242424242424242 0.0242424242424242 0.0242424242424242 0.0242424242424242 0.0242424242424242 0.0424242424242424 0.0424242424242424 0.0424242424242424 0.0424242424242424 0.0424242424242424 0.0424242424242424 0.0424242424242424 0.0424242424242424 0.0424242424242424 0.0424242424242424 0.0452199741787572 0.0700049832291192 0.0727272727272727 0.0727272727272727 0.0727272727272727

  8. (Bio:224Pla:272) Genus Bio Pla Acaryochloris 88 240 136 32 Acetobacter 93 242 131 30 Acetobacterium 86 215 138 57 Acetohalobium 86 216 138 56 Acholeplasma 87 238 137 34 Achromobacter 102 257 122 15 Acidaminococcus 88 237 136 35 Acidianus 40 205 184 67 Acidilobus 64 203 160 69 Acidimicrobium 96 240 128 32 Acidiphilium 96 253 128 19 Pseudomonas Leptospira Escherichia 103 258 121 14 Fervidicoccus 28 210 196 62 Coprothermobacter Marinomonas 97 258 127 14 102 258 122 14 14 196 210 76 58 238 166 34

  9. (Bio:224Pla:272) 2 Phylum Genus P-value (Fisher s test) Odds ratio(Bio > 1,Pla < 1) Spirochaetes Leptospira Fervidicoccus (Archaea) Coprothermobacter Halogeometricum (Archaea) Flavobacteriaceae Trichodesmium Leuconostoc Ferroglobus (Archaea) Thermobaculum Pelagibacterium Methanocella (Archaea) Staphylothermus (Archaea) Methylomonas Roseobacter Bdellovibrio Magnetococcus Halorubrum (Archaea) Parvularcula Parachlamydia Methanoregula (Archaea) Marinomonas Pseudoalteromonas Acidianus (Archaea) Prochlorococcus 1.84984756776945e-55 1.30666651736405e-50 1.2144453370268e-46 1.04875444172146e-45 7.15629803877711e-45 1.11039259592354e-44 2.57279815069165e-44 1.40508206857176e-43 2.25857826588668e-43 1.26051550425212e-42 9.15759027518411e-42 1.08395647986535e-41 1.35143151367562e-41 1.65228419787129e-41 2.85058161779399e-41 3.08721857119471e-41 1.53852388750522e-40 2.66173620735992e-40 4.17021551646017e-40 7.2097712066611e-40 1.34108714945582e-39 2.16569106567114e-39 2.77041615534659e-39 3.38487702676658e-39 0.02585034013605442 0.04217687074829932 0.049913941480206545 0.05505505505505505 0.04014096140080392 0.04556894243641232 0.040922701563712985 0.06021335641724165 0.05178947368421053 0.04583053878828527 0.061016949152542375 0.06471989230609919 0.04197761194029851 0.05131637661758144 0.04395061728395062 0.052725250278086756 0.06677157094151587 0.05772594752186589 0.0600712569392659 0.07013943699026572 0.041445400720258804 0.055421686746987955 0.07104984093319193 0.04732824427480916

  10. 1 B B B B B B P B P B P B P B B B B P B P P Bone 580 Colon 33 Gut Lung 558 Midgut 142 Tooth 556 acid mine drainage 117 activated sludge 79 aerobic 392 animal-associated habitat 108 aquaculture 302 aquarium 55 aquatic biome 30 beach sand 191 biofilm 81 bioreactor 166 biotic mesoscopic physical object brine 118 cave 545 coast 17 coastal water 39 compost 425 coral reef 34 fresh water 39 freshwater biome freshwater habitat 12 frost flowers 199 fungi associated P P P P B hot spring 37 hot water 167 hydrothermal vent 313 ice 426 insecta-associated habitat 231 kimchi 16 lake 140 lake sediment 9 lake water 14 large-scale artifact 110 mammalia-associated habitat 105 man-made structure marine biome 16 marine channel 29 marine coral reef biome 50 marine habitat 4 marine reef 80 marine sediment 26 microbial mat 144 mine drainage 566 national park 37 ocean 36 ocean biome 41 oil contaminated soil 141 pasture soil 508 permafrost 289 phyllosphere 375 pond 59 B B rhizosphere soil 0 rumen 17 salt field 68 sea 111 sea floor 80 sea ice 73 sea water 2 seafood product 210 soil 82 solar saltern 131 spring sediment 9 strait 28 stream 167 surface water 4 thermophilic sediment 9 waste water 130 wastewater treatment plant 119 water 47 water column 38 wetland 223 38 P P P P P B P B B B P P P P P B 83 P B 16 P P B B B P P B B B B B Biofilm Ave: 203 Med: 126 Planktonic Ave: 94 Med: 39 P P P P P 140 103

  11. animal associated 582 rock,sand and soil biofilm 584 geographic feature and biome plant associated 377 sediment 572 large-scale artifact 583 Biofilm 550 519 water 583 aerobic environment 394 aquatic feature and biome ice 437 Planktonic 584 waste treatment 562 food 424 artificial natural environment 547 organic feature and biome fungi associated human activity association hydrosphere 584 organism association 584 0 314 584

  12. @prefix xsd: <http://www.w3.org/2001/XMLSchema#> . @prefix msv: <http://purl.jp/bio/11/msv/> . @prefix srs: <http://www.ncbi.nlm.nih.gov/sra/> . @prefix ncbi_refseq: <http://www.ncbi.nlm.nih.gov/nuccore/> . @prefix ko: <http://www.genome.jp/dbget-bin/www_bget?> . @prefix path: <http://www.genome.jp/dbget-bin/www_bget?> . srs:DRS000009 msv:containedKO [ msv:assignedKO ko:K04033; msv:KOCount ]. "2.21645157258498e-05"^^xsd:float; srs:DRS000009 msv:containedKO [ msv:assignedKO ko:K00937; msv:KOCount ]. "2.41630257974925e-05"^^xsd:float; srs:DRS000009 msv:containedKO [ msv:assignedKO ko:K07735; msv:KOCount ]. "1.38171967047323e-05"^^xsd:float;

  13. WilcoxonKO p < 0.05 (336 ) K01610 phosphoenolpyruvatecarboxykinase(ATP) [EC:4.1.1.49] K03761 MFS transporter, MHS family, alpha-ketoglutarate permease K03577 TetR/AcrR family transcriptional regulator, acrAB operon repressor K12538 outer membrane protein HasF K03651 Icc protein K01040 glutaconateCoA-transferase, subunit B [EC:2.8.3.12] K11896 type VI secretion system protein ImpG K03923 modulator of drug activity B K10539 L-arabinose transport system ATP-binding protein [EC:3.6.3.17] K01745 histidine ammonia-lyase[EC:4.3.1.3] K02168 choline/glycine/prolinebetaine transport protein K00322 NAD(P) transhydrogenase[EC:1.6.1.1] K01246 DNA-3-methyladenine glycosylaseI [EC:3.2.2.20] K01426 amidase [EC:3.5.1.4] K11734 aromaticamino acid transportprotein AroP K17215 inositoltransportsystem ATP-binding protein K02403 flagellar transcriptionalactivatorFlhD K16011 mannose-1-phosphate guanylyltransferase/ mannose-6-phosphate isomerase [EC:2.7.7.13 5.3.1.8] K00171 pyruvate ferredoxin oxidoreductase, delta subunit [EC:1.2.7.1] K00355 NAD(P)H dehydrogenase(quinone) [EC:1.6.5.2] K17320 putative aldouronatetransportsystem permease protein K14519 NADP-dependentaldehyde dehydrogenase [EC:1.2.1.4] K17214 inositoltransportsystem permease protein K03119 taurine dioxygenase [EC:1.14.11.17] K08195 MFS transporter, AAHS family, 4-hydroxybenzoate transporter K07098 K03272 D-beta-D-heptose7-phosphate kinase / D-beta-D-heptose1-phosphate adenosyltransferase [EC:2.7.1.167 2.7.7.70] K00849 galactokinase [EC:2.7.1.6] K08224 MFS transporter, YNFM family, putative membrane transport protein K10979 DNA end-binding protein Ku K10117 raffinose/stachyose/melibiosetransport system substrate-binding protein K02108 F-type H+-transporting ATPase subunit a [EC:3.6.3.14] K03704 cold shock protein (beta-ribbon, CspA family) K10237 trehalose/maltose transport system permease protein K10531 L-ornithine N5-oxygenase [EC:1.13.12.-] K10015 histidine transport system permease protein K03773 FKBP-type peptidyl-prolylcis-trans isomerase FklB [EC:5.2.1.8] K10543 D-xylose transport system substrate-binding protein K03736 ethanolamine ammonia-lyasesmall subunit [EC:4.3.1.7] K07407 alpha-galactosidase[EC:3.2.1.22] (1/5)

  14. WilcoxonKOWilcoxonKO Bio Bio Pla Pla Bio Bio Bio Bio Bio Pla Pla

  15. R Genus Biofilm Planktonic Escherichia Escherichia 103 258 121 14 Escherichia = matrix(c(103,258,2,0), ncol = 2 ) Escherichia [Bio] [Pla] [+] 103 258 [-] 121 14 fisher.test(a) Fisher's Exact Test for Count Data data: Escherichia p-value = 2.041e-36 alternative hypothesis: true odds ratio is not equal to 1 95 percent confidence interval: 1.497846 2.569146 sample estimates: odds ratio [(103/258) / (121/14)] 0.046191

  16. Fisher matrix Planktonic

  17. Shannon index= -(value/sum)*log2(value/sum) food 5.565130795835259 fungi associated 6.055905711563868 plant associated 6.642378771462215 biofilm 6.950432001122053 aerobic environment 7.681887098090524 ice 8.122683417915658 large-scale artifact 8.377015366930495 artificial natural environment 8.717709878783833 geographic feature and biome 8.880730867862294 waste treatment 9.93970104147625 animal associated 10.319644405818543 sediment 10.385325333127858 rock,sand and soil 11.586005173411566 water 12.313033474340926 aquatic feature and biome 12.373408565130129

  18. DRS000009 MEO_0000437 MEO_0000137 K00937:2.41630257974925e-05 K07735:1.38171967047323e-05 K03117:2. DRS000201 MEO_0000437 MEO_0000137 MEO_0000437 MEO_0000416 MEO_0000437 MEO_0000026 K08590:2. DRS000406 MEO_0000437 MEO_0000718 K02224:3.31285985940223e-06 K07749:1.98771591564134e-05 K00163:1. DRS000407 MEO_0000437 MEO_0000718 K02793:9.26535036922421e-06 K03076:9.26535036922421e-06 K00384:9. ERS000029 MEO_0000437 MEO_0000658 MEO_0000439 MEO_0000439 MEO_0000439 K03086:0.333333333333333 ERS007239 MEO_0000437 MEO_0000056 K07735:0.000704225352112676 K03117:0.00727663895057533 K00954:0. ERS007241 MEO_0000437 MEO_0000056 K01952:0.00181833182080686 K07749:0.000869565217391304 K00163:0. ERS015567 MEO_0000437 MEO_0000024 MEO_0000437 MEO_0000027 MEO_0000437 MEO_0000038 K06999:0. ERS015568 MEO_0000437 MEO_0000038 K02777:0.00294985250737463 K02703:0.0206489675516224 K04077:0. ERS016117 MEO_0000437 MEO_0000449 MEO_0000439 K03117:0.000471119694989063 K00954:0.0087782623731457 ERS016118 MEO_0000437 MEO_0000458 MEO_0000439 K00954:0.000635002877817424 K02224:9.98980764944161e ERS033180 MEO_0000437 MEO_0000704 K00549:0.000175100682892663 K13639:8.75503414463316e-05 K00163:0. SRS000238 MEO_0000437 MEO_0000122 K07084:0.00202839756592292 K01825:0.00101419878296146 K06969:0. SRS000239 MEO_0000437 MEO_0000122 K02275:0.00079428117553614 K03076:0.0039714058776807 K04046:0. SRS000240 MEO_0000437 MEO_0000122 K03616:0.00272108843537415 K04748:0.00136054421768707 K07180:0. SRS000241 MEO_0000437 MEO_0000122 K02224:0.00150037509377344 K01012:0.000750187546886722 K13482:0. SRS000242 MEO_0000437 MEO_0000122 K00163:0.00207900207900208 K06181:0.00207900207900208 K01956:0.

  19. (76) Bone Colon Gut Lung Midgut Tooth acid mine drainage activated sludge aerobic animal-associated habitat aquaculture aquarium aquatic biome beach sand biofilm bioreactor biotic mesoscopic physical object brine cave coast coastal water compost coral reef fresh water freshwater biome freshwater habitat frost flowers fungi associated hot spring hot water KO 4967 3825 3595 211 3703 2602 2175 3486 2087 2819 1057 268 3231 2593 2588 3490 1782 470 1752 6 1870 1988 233 4034 3148 132 742 4270 2489 2724 KO K01467 K03046 K03043 K04077 K02358 K03070 K04043 K03701 K02355 K03086 K01955 K03695 K03544 K09014 K03798 K K03046 K03043 K02355 K02358 K01610 K03737 K02886 K02945 K00239 K03070 K00962 K04043 K04077 K05349 K01955 K K01534 K01995 K05786 K03703 K00981 K03483 K00666 K03046 K06919 K03043 K01999 K06147 K02674 K02358 K03406 K K00351 K03043 K04043 K02016 K06180 K03701 K12257 K03286 K06942 K00243 K03046 K03320 K02952 K07270 K02520 K K03043 K03046 K03893 K02355 K02014 K07119 K03296 K00116 K00383 K01681 K00525 K04753 K00265 K06207 K02111 K K03046 K03043 K03086 K02358 K01955 K02355 K03147 K04077 K00525 K03070 K02274 K03701 K04043 K03544 K02112 K K07496 K02014 K01153 K09822 K07267 K07399 K01533 K07646 K00382 K03043 K02274 K02358 K03046 K01601 K00412 K K03046 K02358 K04077 K03043 K02355 K04043 K02112 K01955 K00962 K01937 K02111 K03701 K03798 K03086 K01915 K K03701 K03046 K03043 K02358 K01955 K00666 K00525 K02470 K03070 K00548 K01869 K02355 K04077 K02112 K00265 K K03046 K03043 K04077 K03696 K07637 K02945 K02274 K00239 K03086 K01681 K02355 K09687 K01955 K03596 K02470 K K08151 K00879 K15269 K03406 K02358 K03046 K03596 K04077 K04043 K01915 K02355 K03296 K02337 K01999 K03043 K K02112 K02689 K01467 K03149 K03438 K00209 K06940 K01915 K02004 K02274 K00658 K06207 K02276 K04096 K03076 K K07637 K07660 K07319 K07496 K01494 K06926 K03465 K07491 K02355 K01190 K02358 K03043 K02112 K03046 K00383 K K03046 K02358 K04077 K03043 K03086 K03070 K01955 K03695 K02112 K03798 K03701 K03782 K02355 K04043 K01681 K K06895 K03545 K01868 K00574 K01951 K13935 K00626 K02575 K07798 K03406 K03070 K00799 K01712 K00426 K06158 K K02358 K03046 K02355 K03737 K03043 K03701 K06147 K01873 K01153 K02004 K03702 K01872 K03070 K03040 K01870 K K06147 K02004 K03657 K03046 K16787 K03701 K01421 K16786 K07024 K03316 K02529 K00383 K01533 K03294 K03763 K K00558 K01955 K03046 K00090 K02111 K01681 K03086 K03406 K02470 K04077 K01873 K03701 K02343 K02621 K00059 K K03046 K03043 K02358 K04077 K03070 K04043 K03086 K02355 K01955 K03696 K03701 K03596 K03695 K02945 K02111 K K00548 K01915 K00342 K04043 K17321 K05559 K03043 K03046 K02014 K02358 K02945 K02355 K03406 K06207 K02111 K11384 K04077 K02886 K04043 K02112 K01955 K K03046 K03043 K02358 K02355 K04077 K02274 K04043 K01915 K03070 K00525 K03701 K01955 K01681 K03702 K09014 K K08884 K02112 K01467 K01711 K06200 K04567 K06160 K02689 K02044 K01638 K02470 K07124 K07237 K09686 K01474 K K00558 K04077 K08151 K04043 K02703 K01711 K03695 K02358 K15269 K01681 K02314 K02040 K03797 K00432 K00525 K K00558 K03111 K02357 K07496 K02835 K01999 K11942 K01653 K02757 K02756 K02755 K02355 K04094 K01966 K06168 K K00558 K03111 K02357 K01999 K07496 K02835 K01653 K11942 K02757 K02755 K02756 K04043 K04094 K02355 K01966 K K03046 K03043 K02358 K00548 K00525 K03296 K01687 K02355 K01955 K00265 K04077 K02198 K01952 K03522 K01915 K K02014 K03296 K00656 K03046 K00123 K01652 K03043 K02761 K00370 K01223 K00688 K00615 K00265 K05802 K00525 K K07637 K07660 K07319 K07496 K01494 K06926 K03465 K07491 K02355 K02358 K03043 K00383 K03046 K02112 K03305 K K03497 K00638 K01190 K00860 K03702 K00833 K01992 K00652 K06890 K03296 K06132 K03147 K01935 K03639 K07347 K

  20. KO K00001 -10.311816354878324 -8.104774922411162 -9.12536274284216 -9.630882031115686 -10.446304307863649 -9.444659766985191 K00002 -13.141335312924086 -16 -12.704600872109006 -14.043777560434304 -12.665170969217156 -10.390757105237586 K00003 -7.121752898407186 -8.413313412355846 -7.382105014212423 -8.475435715319305 -8.852086421482788 -7.445159144381894 K00004 -13.213722194807316 -16 -12.412278655972163 -16 -16 -11.493048389416982 K00005 -9.96363701697749 -8.407649758618964 -12.14236250205763 -10.414517054242882 -16 -11.493048389416982 K00007 -10.596788922173955 -9.329282052339648 -12.918984333818889 -16 -16 -9.409468928010325 K00008 -11.584457072149807 -13.31394247457744 -10.254085944514278 -12.176686333973533 -16 -10.095757399493332 K00009 -11.006367458916358 -8.16761864984201 -12.4902708126153 -11.03250817989423 -16 -11.482051760613226 K00010 -9.264325381071723 -9.186300492329945 -9.45947148340929 -9.3754727463094 -10.469939085997646 -9.88140145587432 K00011 -16 -16 -15.131461775818128 -16 -16 -16 K00012 -7.106372296508517 -6.98777647385517 -7.183819812492088 -7.964181219197697 -6.947145554622075 -6.859389052643327 K00013 -7.7918148582413504 -8.211241559923812 -7.816358527328419 -7.338291834838282 -10.451770159980867 -7.902794931405587 K00014 -9.277120817347368 -8.54307527927404 -8.46073500012144 -8.684299576853675 -10.469939085997646 -8.544543938241562 K00015 -10.73818076223137 -14.628162042310528 -8.362338719924006 -9.334936622441244 -8.002924975011636 -8.778385710633545 K00016 -10.129216802977284 -7.4845566904656415 -10.051986464809646 -11.063919929388838 -16 -11.493048389416982 K00018 -13.225287537775754 -12.25656699684002 -10.968406047051388 -13.672214004001823 -8.843329333909496 -9.183850818741712 K00019 -9.625883141561934 -9.755969817231259 -8.47209897699472 -9.645816479474618 -8.30933106575223 -7.773560661928158 K00020 -9.315047048838318 -9.92986455302942 -8.044325803389565 -9.261050917282379 -9.544127635689426 -7.384846155199226 K00021 -16.245565046960508 -9.061901547084124 -12.748580411992254 -13.246077759947227 -10.446304307863649 -11.482051760613226 K00023 -8.702620832331586 -9.834925987742565 -7.746683551255264 -8.53001839575091 -9.203602442460852 -7.990860797863764 K00024 -6.574629532570801 -7.580959967649561 -5.292461661964257 -7.523288272986434 -7.8223424865027535 -6.844201977115136 K00027 -6.679113848508194 -7.299539418709296 -7.41204210776536 -8.079553675448148 -8.480051144947907 -9.287260449470113 K00028 -16 -13.239973934562654 -16 -16 -16 -16 K00029 -6.88173249202305 -8.052890251183237 -6.470484779211342 -6.858808198174476 -6.8971375085262006 -5.863457907014847 K00030 -9.996294929960587 -9.996499401331711 -9.241982940346352 -8.841324475788843 -10.968721679793427 -9.2945959757397 K00031 -5.604052648376666 -7.0236236350845065 -5.736622818699684 -6.02264419242527 -5.888872580320814 -5.9616659039450965 K00032 -14.554995368110623 -16 -11.621793774892419 -14.554603184200294 -10.968721679793427 -16 K00033 -6.783449648079597 -7.386708390371603 -6.756252671315078 -7.606976602999303 -6.9025269661364295 -7.022195787939136 K00034 -11.068633989656037 -16 -12.067132542569965 -10.063455860550718 -16 -9.08913996971469 K00035 -15.532192564464934 -16 -12.057015551

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