SI Appendix - PNAS taxonomic assignment of four ... 95%HCI 1.16 2.017 0.945 1.695 1.793 2.392 1.252...

SI Appendix

Tables S1-S8

Table S1. The microbial flora of wild and captive pandas.

Table S2. The comparison of OTUs (97% threshold) related to Clostridium group I

and XIVa in this study with previous studies.

Table S3. Summary of Illumina GA reads.

Table S4. Summary of de novo assembly results.

Table S5. ORF prediction in all samples.

Table S6. Number of genes classified.

Table S7. The taxonomic assignment of four enzymes.

Table S8. The putative GH profiles targeting plant structural polysaccharides in

metagenomes of herbivorous carnivores, herbivores and omnivores.

Figures S1-S6

Figure S1. The gut microbial diversity in giant pandas.

Figure S2. The neighbor-joining tree of all OTUs with the related published

sequences.

Figure S3. Phylogenetic tree showing relationships of 16S rRNA genes from

Clostridium clusters.

Figure S4. The starch metabolism pathway in gut microbiomes of three wild giant

pandas (A, W1; B, W2; C, W5).

Figure S5. The KEGG pathway classification in gut microbiomes of three wild giant

pandas (A, W1; B, W2; C, W5).

Figure S6. Metabolic clustering of giant panda, wallaby, termite, cow and human

gastrointestinal or rumen metagenomes.

Table S1. The microbial flora of wild and captive pandas.

Sample size W1 W2 W3 W4 W5 W6 W7 C1 C2 C3 C4 C5 C6 C7 C8

Sequences 811 187 385 339 821 285 533 244 349 396 290 292 193 145 252

No. OTUs 13 16 12 16 22 25 6 13 13 15 16 8 4 7 16

Unique OTUs 0 4 1 3 8 9 1 2 4 3 3 2 1 2 10

Species

richness 1.073 1.883 0.835 1.600 1.714 2.256 1.189 1.652 1.449 1.761 1.719 0.579 0.609 1.112 1.602

95%LCI 0.985 1.748 0.724 1.505 1.635 2.121 1.126 1.508 1.328 1.657 1.582 0.442 0.494 0.973 1.462

95%HCI 1.16 2.017 0.945 1.695 1.793 2.392 1.252 1.796 1.569 1.865 1.856 0.716 0.724 1.252 1.743 Seqs AC Phylum MI

Closest full length

neighbor Description

OTU1 1 35 36 JF920308 Proteobacteria 97% EU461088 Uncultured bacterium clone

OTU2 1 1 JF920309 Proteobacteria 97% AY554143 Campylobacter sp.

OTU3 4 84 3 9 100 JF920310 Proteobacteria 99% AY792271 Uncultured bacterium clone

OTU4 7 7 JF920311 Proteobacteria 99% AB244470 Hafnia alvei

OTU5 16 3 116 191 133 66 4 152 18 18 717 JF920312 Proteobacteria 99% JF018002 Uncultured bacterium clone

OTU6 1 1 JF920313 Proteobacteria 96% HQ728209 Uncultured bacterium clone

OTU7 2 2 JF920314 Proteobacteria 97% AF024528 Bisgaard Taxon

OTU8 2 2 JF920315 Proteobacteria 99% AF371853 Uncultured bacterium clone

OTU9 1 1 JF920316 Proteobacteria 99% EU540172 Uncultured bacterium clone

OTU10 2 2 JF920317 Proteobacteria 99% HQ652575 Ochrobactrum sp.

OTU11 1 1 JF920318 Proteobacteria 98% JF214577 Uncultured bacterium clone

OTU12 1 1 JF920319 Proteobacteria 98% JF117025 Uncultured bacterium clone

OTU13 30 24 65 96 61 44 3 9 14 7 353 JF920320 Firmicutes-Bacilli 99% EU775570 Uncultured bacterium clone

OTU14 1 1 JF920321 Firmicutes-Bacilli 96% EU474085 Uncultured bacterium clone

OTU15 1 1 JF920322 Firmicutes-Bacilli 90% JF180284 Uncultured bacterium clone

OTU16 2 3 4 9 JF920323 Firmicutes-Bacilli 99% EU181438 Uncultured bacterium clone

OTU17 1 3 4 JF920324 Firmicutes-Bacilli 99% EU075064 Streptococcus orisratti strain

OTU18 1 1 JF920325 Firmicutes-Bacilli 99% AB501126 Streptococcus ursoris

OTU19 15 61 12 15 10 79 192 JF920326 Firmicutes-Bacilli 99% HQ716560 Uncultured bacterium clone

OTU20 1 1 JF920327 Firmicutes-Bacilli 99% JF010987 Uncultured bacterium clone

OTU21 2 2 JF920328 Firmicutes-Bacilli 99% EU483236 Streptococcus criceti

OTU22 5 5 JF920329 Firmicutes-Bacilli 99% AB469559 Streptococcus sp.


OTU24 1 5 1 7 JF920331 Firmicutes-Bacilli 100% JF235874 Uncultured bacterium clone

OTU25 2 2 JF920332 Firmicutes-Bacilli 99% HQ407256 Lactococcus garvieae strain

OTU26 1 2 2 5 JF920333 Firmicutes-Bacilli 100% GQ337029 Enterococcus hirae strain

OTU27 1 1 JF920334 Firmicutes-Bacilli 100% CP002621 Enterococcus faecalis

OTU28 1 1 JF920335 Firmicutes-Bacilli 97% FJ675223 Uncultured bacterium clone

OTU29 70 70 JF920336 Firmicutes-Bacilli 99% AJ871178 Lactobacillus apodemi

OTU30 3 43 46 JF920337 Firmicutes-Bacilli 99% FJ881005 Uncultured bacterium clone


OTU32 118 118 JF920339 Firmicutes-Bacilli 96% AB559623 Uncultured bacterium


OTU34 281 3 3 5 4 36 332 JF920341 Firmicutes-Bacilli 99% HM058633 Leuconostoc lactis

OTU35 2 8 1 4 1 16 JF920342 Firmicutes-Bacilli 99% AB596944 Weissella confusa

OTU36 27 1 1 5 6 29 4 73

JF920343

Firmicutes-Bacilli 98% HM109883

Uncultured Bacilli bacterium

clone

OTU37 4 2 1 7 JF920344 Firmicutes-Bacilli 95% HM035089 Bacillus sp.

OTU38 2 1 13 16 JF920345 Firmicutes-Bacilli 99% DQ129500 Uncultured bacterium clone

OTU39 1 1 2 JF920346 Firmicutes-Bacilli 97% EU466454 Uncultured bacterium clone

OTU40 1 1 2 JF920347 Firmicutes-Bacilli 98% JF085461 Uncultured bacterium clone

OTU41 1 1 JF920348 Firmicutes-Bacilli 97% AB362824 Paenibacillus sp.

OTU42 572 58 259 149 185 47 1 1271 JF920349 Firmicutes-Clostridia 98% EU869238 Clostridium sp.

OTU43 10 2 22 17 66 3 10 130 JF920350 Firmicutes-Clostridia 99% EU869238 Clostridium sp.

OTU44 12 43 1 9 4 3 72 JF920351 Firmicutes-Clostridia 98% EF590059 Uncultured bacterium clone

OTU45 1 1 JF920352 Firmicutes-Clostridia 97% GU085093 Clostridium sp.

OTU46 1 8 3 2 14 JF920353 Firmicutes-Clostridia 97% EU869238 Clostridium sp.

OTU47 5 12 2 13 138 46 30 32 134 255 2 24 693 JF920354 Firmicutes-Clostridia 99% EU474117 Uncultured bacterium clone

OTU48 109 1 10 14 30 8 1 173 JF920355 Firmicutes-Clostridia 98% EU474132 Uncultured bacterium clone

OTU49 1 1 1 3 JF920356 Firmicutes-Clostridia 96% EU775597 Uncultured bacterium clone

OTU50 1 1 JF920357 Firmicutes-Clostridia 94% EF434348 Uncultured bacterium clone

OTU51 12 12 JF920358 Firmicutes-Clostridia 96% CP000721 Clostridium beijerinckii

OTU52 3 2 5 JF920359 Firmicutes-Clostridia 98% AB298770 Clostridiaceae bacterium

OTU53 2 5 5 12 JF920360 Firmicutes-Clostridia 97% EU471033 Uncultured bacterium clone

OTU54 33 25 1 5 359 10 48 3 484 JF920361 Firmicutes-Clostridia 98% EU471033 Uncultured bacterium clone

OTU55 2 2 JF920362 Firmicutes-Clostridia 97% EU471033 Uncultured bacterium clone

OTU56 2 1 3 JF920363 Firmicutes-Clostridia 99% EF399333 Uncultured bacterium clone

OTU57 1 1 JF920364 Firmicutes-Clostridia 99% FJ506694 Uncultured bacterium clone


OTU59 4 8 37 73 3 8 13 146 JF920366 Firmicutes-Clostridia 95% JF129924 Uncultured bacterium clone

OTU60 1 1 JF920367 Firmicutes-Clostridia 92% DQ113748 Uncultured bacterium clone

OTU61 2 2 JF920368 Firmicutes-Clostridia 95% CP002582 Clostridium lentocellum



OTU64 2 2 JF920371 Firmicutes-Clostridia 97% JF171802 Uncultured bacterium clone

OTU65 3 7 10 JF920372 Firmicutes-Clostridia 93% DQ352806 Uncultured bacterium clone

OTU66 124 124 JF920373 Firmicutes-Clostridia 99% HQ452857 Clostridiales bacterium

OTU67 1 1 JF920374 Firmicutes-Clostridia 99% AY534872 Anaerosporobacter mobilis

OTU68 60 60 JF920375 Firmicutes-Clostridia 97% EF399560 Uncultured bacterium clone

OTU69 40 38 20 13 111 JF920376 Firmicutes-Clostridia 99% FJ506990 Uncultured bacterium clone


OTU71 2 1 3 JF920378 Firmicutes-Clostridia 98% JF214889 Uncultured bacterium clone

OTU72 13 13 JF920379 Firmicutes-Clostridia 99% GQ479981 Uncultured bacterium clone


OTU74 1 1 JF920381 Firmicutes-Clostridia 99% AB506376 Uncultured bacterium clone

OTU75 1 1 JF920382 Cyanobacteria 97% FJ625336 Uncultured bacterium clone

OTU76 2 2 JF920383 Acidobacteria 95% HM186654 Uncultured bacterium clone

OTU77 1 1 JF920384 Acidobacteria 98% DQ906050 Uncultured bacterium clone

OTU78 3 3 JF920385 Actinobacteria 99% NR_025310 Rothia nasimurium

OTU79 1 1 JF920386 Actinobacteria 99% JF235534 Uncultured bacterium clone

OTU80 2 2 JF920387 Actinobacteria 100% GQ897303 Uncultured bacterium clone

OTU81 1 1 JF920388 Actinobacteria 95% FJ507109 Uncultured bacterium clone

OTU82 1 1 JF920389 Actinobacteria 99% FJ367859 Uncultured bacterium clone

OTU83 1 1 JF920390 Actinobacteria 94% EU772911 Uncultured bacterium clone

OTU84 4 4 JF920391 Cyanobacteria 99% GQ104078.1 Uncultured bacterium clone

OTU85 1 1 JF920392 Bacteroidetes 96% FJ825548 Uncultured bacterium clone

Abbreviations: W: Wild panda; C: Captive panda. Species richness is the Shannon-Weaver diversity indices. 95%LCI and 95%HCI represent the low 95% confidence interval and high 95% confidence interval of

species richness respectively. Seq. denotes the number of sequences. AC represents the accession number of NCBI for each OTU in our study. MI represents the maximum identity.

Table S2. The comparison of OTUs (97% threshold) related to Clostridium group I and XIVa in this study with previous studies

The different colors represent the proportion in total sequences.

N indicates no identical OTUs and the black dot represents the existence of identical OTUs between species; * indicates data cited from ref. 2.; # indicates data of Bos frontalis cited from ref. 19 (PopSet: 110333543 in GenBank); & indicates data cited from ref. 20; ‡ indicates data cited from ref. 21.

Giant panda:This study

Carnivora*: Giant panda_GP

Carnivora* (Herbivores): Red panda_RP,RPSD

Carnivora*(Non-herbivores):Cheetah_CE2, Bushdog-_bdog1, Polar bear_PB1, Spotted Hyena_HY1

Artiodactyla: Cowes#

Artiodactyla*: Argali Sheep_AS1,2,3, Bighorn Sheep_BH1,2,BHSD

Artiodactyla*: Banteng_ BG, Takin_ TAK, Speke's Gazelle_ SP2

Perissodactyla*: Horses_Horsem, Horsej

Rodentia*: Naked Molerat_ molerat, Capybara_ CAP

Diprotodontia: Red Kangaroo*_KO1,2 Tammar wallaby&_T1, T2

Primate: Goeldi's Marmoset*_CAL, Gorilla*_GOR, Monkey*_ SPIM, Saki*_ SAKI, Lemur*_ML, Human‡_HUM7,8

Sample size

15 1 2 4 6 6 3 2 2 4 7

No. Seqs compared

5522 564 1145 682 231 1159 469 509 477 570 3322

Isolation source

Feces Feces Feces Feces Rumen fluid Feces Feces Feces Feces Feces Foregut contents

Feces

OTU44 N N N N N N N N N N

OTU47 N N N N N N N OTU48 N N N N N N N N N N



OTU53 N N N N N N N N N




Group I

OTU57 N N N N N N N N N Group XIVa




10-20% 5-10% 1-5% 0.1-1% <0.1%

Table S3. Summary of Illumina GA reads Sample ID Raw reads High quality reads Host removed reads % of host contaminant

W1 32,477,661 31,960,609 24,481,312 23.40%

W2 13,333,336 13,252,380 12,124,580 8.51%

W5 38,733,359 38,225,343 24,481,312 35.95%

Table S4. Summary of de novo assembly results

Map to own contig Sample Kmer

Contig

number

Contig

length(bp) N50(bp) N90(bp) Max(bp) Min(bp)

PE SE %

W1 K53 3,972 6,880,931 2,810 670 131,085 500 10,213,362 1,478,917 47.76

W1 K55 3,840 6,855,931 2,915 679 105,750 500 10,455,106 1,507,026 48.86

W1 K57 4,122 6,069,446 2,003 633 105,746 500 8,432,992 1,354,569 39.98

W2 K21 8,810 9,101,146 1,115 579 11,352 500 1,343,148 869,119 18.25%

W2 K23 9,039 10,218,444 1,267 595 11,403 500 1,859,134 1,061,991 24.09%

W2 K25 8,860 10,871,934 1,453 610 13,251 500 2,343,980 1,193,682 29.18%

W2 K27 8,324 11,523,323 1,772 631 23,915 500 3,098,028 1,339,085 36.59%

W2 K31 7,297 12,127,743 2,512 663 63,798 500 4,779,200 1,509,415 51.87%

W5 K51 14,476 19,229,889 1,628 605 60,029 500 4,747,444 1655,810 26.16

W5 K53 13,881 18,437,535 1,631 604 117,989 500 4,954,548 1,673,535 27.07

W5 K55 13,440 17,675,862 1,589 604 76,687 500 5,041,874 1,661,584 27,38

Table S5. ORF prediction in all samples

Gene set Sample ORFs

Total

length

Average

length

Complete

ORFs

Fragmented

ORFs PE SE % of total

W1 8,583 5,845,722 681 4,415 4,168 7,955,424 1,781,577 39.77

W2 15,704 10,192,248 649 7,157 8,547 2,809,902 2,179,657 41.16

W5 25,557 15,966,270 625 10,351 15,206 3,790,164 1,629,862 22.14

Table S6. Number of genes classified. The predicted genes were aligned to the known microbial

genes, the genes in KEGG orthology database and in COG database. BLASTP software was used

to align genes with E-value <10-5, and the best hit was selected. LCA-based algorithm was used

to assign gene sequences to taxa. When a gene was conserved in many species, it was assigned to

the lowest common ancestor (LCA). However, if the LCA is at phylum-level or below, it was

considered to be “Classified” all the same. If not, it was treated as “Unclassified”.

Sample W1 W2 W5

Total ORF number 8583 15704 25557

Phylotype Unknow 13.91% 13.09% 18.59%

Unclassified 2.70% 3.44% 4.76%

Classified 83.39% 83.47% 76.65%

eggNOG Unannotated 26.53% 27.02% 33.08%

Annotated 73.47% 72.98% 66.92%

COG Orthology Unannotated 38.23% 38.01% 43.58%

Annotated 61.77% 61.99% 56.42%

KEGG Pathway Unannotated 75.48% 76.73% 86.92%

Annotated 24.42% 23.27% 13.08%

Table S8. The putative GH profiles targeting plant structural polysaccharides in metagenomes of

herbivorous carnivores, herbivores and omnivores.

CAZy family Panda Wallaby Termite Cow Human

Cellulases, endohemicellulases

GH5 3 10 56 8 155

GH6 0 0 0 0 0

GH7 0 0 0 0 0

GH8 2 1 5 4 48

GH9 0 0 9 6 1

GH10 2 11 46 7 86

GH11 0 0 14 1 0

GH12 0 0 0 0 0

GH26 0 5 15 5 104

GH28 1 2 6 5 10

GH44 0 0 6 0 0

GH45 0 0 4 0 0

GH48 0 0 0 0 0

GH53 0 9 12 17 0

Total 8 (2) 38 (7) 173 (25) 53 (6) 404 (7)

Debranching enzymes

GH51 5 12 18 64 0

GH54 0 0 0 1 0

GH62 0 0 0 0 0

GH67 2 5 10 0 60

GH78 2 25 0 34 0

Total 9 (2) 42 (8) 28 (4) 99 (10) 60 (1)

Oligosaccharide-degrading enzymes

GH1 101 61 22 10 229

GH2 1 24 23 186 94

GH3 18 72 69 176 1102

GH29 1 2 0 74 386

GH35 4 3 3 12 97

GH38 10 3 11 17 222

GH39 9 1 3 2 39

GH42 18 8 24 11 135

GH43 0 10 16 61 0

GH52 0 0 3 0 0

Total 162 (36) 184 (33) 174 (25) 549 (57) 2304 (37)

Data are presented using the format described in ref. 20, with the GHs grouped according to their major functional roles in

the degradation of plant fiber. The numbers in parentheses represent the percentages of these groups relative to the total

number of GH’s identified in the metagenomic datasets [448 genes for giant panda, 557 for wallaby (ref.20), 704 for termite

(ref.25), 957 for cow (ref. 6) and 6188 for human (ref.7, from 6 random healthy humans)].

Enterococcus hirae FJ751788

Enterococcus faecium EU789396

Enterococcus durans AY902461

OTU26

Enterococcus sanguinicola FJ378705

OTU27

Enterococcus faecalis AB534553

OTU28

Lactococcus lactis GQ871743

OTU32

Lactobacillus salivarius FJ751787

OTU33

OTU31

OTU29

OTU30

Lactobacillus animalis AB326350

OTU34

Leuconostoc lactis GQ476981

Leuconostoc citreum GQ392137

Weissella cibaria FJ429986

OTU35

Weissella confusa FJ429978

OTU25

Lactococcus garvieae FJ215671

OTU24

OTU20

Streptococcus sanguinis GQ995675

OTU23

Streptococcus gallinaceus NR 025453

Streptococcus suis FM252032

OTU21

Streptococcus criceti EU483243

OTU17

Streptococcus orisratti EU075064

OTU22

Streptococcus caballi EF364098

OTU18

Streptococcus ratti NR 025516

OTU16

Streptococcus lutetiensis EU163503

OTU19

Streptococcus alactolyticus EU728776

Paenibacillus provencensis EF212893

Paenibacillus urinalis EF212893

OTU40

OTU41

Paenibacillus granivorans NR 025085

Staphylococcus epidermidis AF397060

OTU36

1 0 0

1 0 0

1 0 0

1 0 0

1 0 0

1 0 0

1 0 0

1 0 0

1 0 0

1 0 0

1 0 0

1 0 0

1 0 0

9 4

1 0 0

1 0 0

8 0

8 5

1 0 0

9 6

8 3

1 0 0

1 0 0

1 0 0

5 9

8 0

1 0 0

7 5

1 0 0

9 9

1 0 0

1 0 0

7 0

1 0 0

1 0 0

7 4

9 9

1 0 0

5 6

7 1

7 5

6 0

7 7

7 2

7 6

8 1

OTU36

Lysinibacillus parviboronicapiens AB300598

Lysinibacillus fusiformis GU084135

OTU37

Bacillus shack letonii NR 025373

Bacillus simplex FJ544334

OTU38

OTU39

OTU15

OTU14

OTU13

Turicibacter sanguinis GQ130019

Ruminococcus lactaris NR 027579

Ruminococcus torques L76604

Ruminococcus obeum X85101

Ruminococcus productus AB196512

OTU68

Ruminococcus gnavus EU139255

OTU66

OTU67

OTU65

Clostridium piliforme D14639

OTU64

OTU63

OTU61

Clostridium lentocellum NR 026101

OTU62

OTU59

OTU60

Clostridium bifermentans FJ424479

Eubacterium tenue M59118

Clostridium lituseburense EU887828

Clostridium bartlettii NR 027573

OTU69

Clostridium glycolicum FJ384385

OTU58

OTU57

Clostridium perfringens FJ215349

OTU52

OTU54

Clostridium butyricum EU477411

OTU55

Clostridium diolis FJ947160

Clostridium puniceum NR 026105

Clostridium saccharoperbutylacetonicum U16122

OTU56

OTU53

Clostridium paraputrificum NR 026135

OTU44

Clostridium gasigenes NR 024945

1 0 0

6 4

1 0 0

1 0 0

1 0 0

9 5

7 5

1 0 0

9 9

8 6

8 7

9 7

8 6

5 4

7 0

1 0 0

9 9

1 0 0

1 0 0

9 4

6 1

1 0 0

9 6

6 5

9 1

5 4

9 9

1 0 0

9 3

1 0 0

9 0

9 4

6 4

7 3

1 0 0

1 0 0

9 1

7 0

9 7

Clostridium gasigenes NR 024945

OTU45

OTU46

OTU42

OTU47

Clostridium disporicum DQ855943

OTU48

OTU43

Clostridium sartagoforme NR 026490

Clostridium tertium AJ245413

OTU51

OTU49

OTU50

OTU71

Veillonella parvula EU728725

OTU72

Megasphaera elsdenii AF283705

OTU74

OTU73

Megamonas funiformis AB300988

Ruminococcus flavefaciens AM915271

Ruminococcus callidus X85100

Ruminococcus albus AB301912

Ruminococcus bromii EU266549

Clostridium thermocellum FN555230

Clostridium stercorarium NR 025100

Bacteroides cellulosolvens NR 025918

Clostridium papyrosolvens NR 026102

Fusobacterium nucleatum GQ496163

OTU70

Anaerococcus lactolyticus AF542233

OTU1

Campylobacter jejuni GQ479822

OTU2

Campylobacter helveticus AF550649

Helicobacter bilis AY578101

Helicobacter canis EU144019

OTU85

Chitinophaga niabensis EU714260

Flexibacter tractuosus AB078076

OTU10

Kaistia granuli AB244762

Rhodobium gokarnense AM180706

OTU11

OTU12

Bradyrhizobium elkanii FJ418701

Stella vacuolata AJ535711

Candidatus Burkholderia EU834251

Variovorax boronicumulans AB300597

OTU9

1 0 0

7 7

1 0 0

1 0 0

1 0 0

1 0 0

1 0 0

1 0 0

5 9

1 0 0

1 0 0

1 0 0

1 0 0

1 0 0

5 2

9 6

1 0 0

6 2

1 0 0

1 0 0

8 7

8 3

1 0 0

1 0 0

8 4

8 9

6 8

5 8

5 1

7 8

1 0 0

9 5

8 8

6 0

7 6

8 2

7 8

OTU9

Steroidobacter denitrificans EF605262

Natronocella acetinitrilica EF103127

Pseudomonas stutzeri GQ480478

Aeromonas hydrophila GQ403072

OTU8

Actinobacillus minor FJ435959

Actinobacillus rossii DQ211730

Actinobacillus equuli EF166060

OTU7

OTU6

Morganella morganii FJ858185

Proteus vulgaris GQ292550

OTU3

Raoultella ornithinolytica GQ979985

Citrobacter werkmanii NR 024862

Klebsiella pneumoniae AY114159

OTU4

Yersinia k ristensenii FM955884

Yersinia enterocolitica FJ641888

Salmonella enteritidis FJ465088

Shigella boydii EU554433

Shigella dysenteriae FJ937911

Shigella sonnei GQ259886

OTU5

Escherichia coli AB480753

Escherichia fergusonii FN433037

Shigella flexneri FN433018

Edaphobacter aggregans DQ528761

Edaphobacter modestus DQ528760

OTU77

Acidobacterium capsulatum D26171

Thermaerobacter marianensis NR 024672

Thermaerobacter nagasak iensis AB061441

OTU76

Byssovorax cruenta AJ833647

Haliangium tepidum AB062751

Iamia majanohamensis AB360448

OTU80

Bifidobacterium pseudocatenulatum D86187

Bifidobacterium subtile NR 029139

Propionibacterium propionicum NR 025277

OTU79

Humicoccus flavidus DQ321750

Arthrobacter humicola AB279890

OTU78

Rothia nasimurium NR 025310

OTU75

Gemmatimonas aurantiaca NR 027529

OTU84

1 0 0

1 0 0

8 6

5 3

5 7

9 7

1 0 0

9 2

8 2

9 9

5 3

5 4

6 3

1 0 0

8 8

1 0 0

7 6

6 5

6 4

1 0 0

9 0

7 0

1 0 0

6 9

1 0 0

1 0 0

9 8

1 0 0

1 0 0

8 2

9 2

1 0 0

7 4

6 4

9 6

5 9

9 6

9 5

1 0 0

8 9

7 7

6 4

7 1

OTU84

Prochlorothrix hollandica AJ007907

Singulisphaera acidiphila AM902527

Pirellula staleyi AF399914

Planctomyces limnophilus X62911

OTU83

Slack ia faecicanis AJ608686

OTU81

Collinsella stercoris NR 027527

OTU82

Collinsella aerofaciens AJ245920

Archaea

1 0 0

9 5

1 0 0

1 0 0

5 0

1 0 0

1 0 0

9 5

0.05

Clostridium favososporum X76749 I

Clostridium corinoforum X76742 I

Clostridium puniceum NR 026105 I

Clostridium caliptrosporum X77843 I

Clostridium beijerinck ii GQ375085 I

Clostridium acetobutylicum CAU16165 I

OTU55

OTU54

Clostridium butyricum AY442812 I

OTU56

OTU53

Clostridium chartatabidum NR 029239 I

Clostridium longisporum X76164 I

Clostridium paraputrificum AY442815 I

OTU57

Clostridium perfringens AB541975 I

Clostridium baratii NR 029229 I

Clostridium sardiniense AB161373 I

Clostridium absonum X77842 I

OTU51

OTU47

Clostridium celatum X77844 I

OTU48

Clostridium quinii X76745 I

OTU44

Clostridium carnis CLORR16SS I

OTU42

OTU45

OTU46

OTU49

OTU50

OTU43

Clostridium cellulovorans NR 027589 I

Clostridium cadaveris AB542932 I

Clostridium algidicarnis AF127023 I

Clostridium intestinale AM158323 I

Clostridium fallax AY208919 I

Clostridium thermopalmarium NR 026112 I

Clostridium thermobutyricum X72868 I

Clostridium novyi AB536772 I

Clostridium collagenovorans NR 029246 I

Clostridium aurantibutyricum FJ358641 I

OTU52

Clostridium subterminale GU329912 I

Clostridium tyrobutyricum GU227151 I

Clostridium ljungdahlii GU139552 I

Clostridium magnum GU129927 I

Clostridium pasteurianum EF140983 I

Clostridium estertheticum S46734 I

Clostridium botulinum EF051574 I

Clostridium sporogenes AY442816 I

Clostridium tetanomorphum DQ241819 I

Clostridium tetani NR 029260 I

Clostridium proteolyticum NR 029250 II

Clostridium limosum GQ360089 II

Clostridium histolyticum CLORR16SP II

OTU58

OTU59

OTU607 7

6 2

9 9

9 9

9 9

9 8

9 9

9 9

9 9

9 9

9 1

9 9

9 9

6 3

8 3

9 6

9 5

9 9

9 9

9 0

9 9

9 9

9 9

5 6

6 0

7 4

6 8

7 3

5 8

5 4

7 2

5 7

9 1

6 3

9 2

5 5

5 3

6 0

6 7

6 5

5 2

OTU60

OTU62

OTU63

OTU61

Clostridium lentocellum NR 026101 XIVb

OTU64

Epulopiscium sp EPURRNAC XIVb

Clostridium colinum X76748 XIVb

Clostridium piliforme CLOPILIFRG XIVb

OTU65

Clostridium neopropionicum NR 026150 XIVb

Clostridium propionicum NR 029269 XIVb

Acetomaculum ruminis AETRR16S XIVa

OTU67

Clostridium populeti NR 026103 XIVa

Clostridium polysaccharolyticum X77839 X XIVa

OTU66

Clostridium aminovalericum NR 029245 XIVa

Coprococcus eutactus COP16SRR13 XIVa

Clostridium aminophilum DQ278862 XIVa

Eubacterium cellulosolvens NR 026106 XIVa

OTU68

Roseburia cecicola GU233441 XIVa

Clostridium nexile NR 029248 XIVa

Clostridium oroticum CLORR16SB XIVa

Ruminococcus torques EUBRGOAC XIVa

Clostridium coccoides EF025906 XIVa

peptostreptococcus productus X94966 XIVa

Blautia hansenii AB534168 XIVa

Clostridium symbiosum EF025909 XIVa

Clostridium sp. DSM 6877 X76747 XIVa

Clostridium clostridioforme AY169422 XIVa

Clostridium aerotolerans X76163 XIVa

Clostridium xylanolyticum X76739 XIVa

Clostridium celerecrescens FM994938 XIVa

Clostridium sphenoides AB075772 XIVa

Clostridium aminobutyricum X76161 XI

Clostridium litorale X77845 XI

Clostridium paradoxum Z69939 XI

OTU69

Clostridium glycolicum FJ966228 XI

Clostridium difficile X73450 XI

Clostridium bifermentans AB538434 XI

Clostridium ghonii AB542933 XI

Clostridium sordellii XI

clostridium barkeri CLOBRRNA XV

Eubacterium limosum AB298910 XV

OTU70

Helcococcus kunzii NR 029237 XIII

Peptostreptococcus micros PEP16SRR8 XIII

Clostridium acidiurici CLORR16SZ XII

Clostridium purinolyticum CLORR16SAG XII

Clostridium hydroxybenzoicum CLORRSMALB XIII

Clostridium filamentosum X77847 XII

Clostridium hastiforme X80841 XII

Clostridium sp. (BN II) X75909 XII

Clostridium ramosum NR 029247 XVIII

Clostridium spiroforme NR 027592 XVIII

Lactobacillus catenaformis AJ621549 XVII

L t b ill it li AB425916 XVII

9 9

9 9

9 9

9 9

9 9

9 9

9 9

9 9

8 8

8 1

9 9

9 9

9 9

9 9

6 2

9 9

9 6

9 9

7 6

6 7

9 9

6 9

5 2

8 0

5 0

9 9

9 9

5 4

9 9

9 9

9 7

7 6

8 0

6 1

9 9

8 2

5 4

9 9

8 5

8 1

7 9

Lactobacillus vitulinus AB425916 XVII

Clostridium innocuum NR 029164 XVI

Eubacterium biforme EUBRG XVI

streptococcus pleomorphus STRRRNA XVI

Asteroleplasma anaerobium M22351

Alicyclobacillus acidocaldarius AY573796

Alicyclobacillus cycloheptanicus AB05968

OTU13

OTU14

OTU15

OTU38

OTU39

OTU37

OTU36

OTU40

OTU41

OTU16

OTU19

OTU17

OTU22

OTU18

OTU21

OTU23

OTU20

OTU24

OTU25

OTU34

OTU35

OTU26

OTU27

OTU28

OTU32

OTU33

OTU31

OTU29

OTU30

Clostridium cellobioparum NR 026104 III

Clostridium termitidis X71854 III

Clostridium cellulolyticum X71847 III

Clostridium papyrosolvens X71852 III

Clostridium aldrichii X71846 III

Clostridium thermocellum EF680276 III

Clostridium stercorarium AF266461 III

Clostridium cellulosi CLORG16SH IV

Clostridium leptum AJ305238 IV

Clostridium sporosphaeroides X66002 IV

Thermoanaerobacter ethanolicus AF542517

Thermoanaerobacter finii TEORG16SE V

Clostridium thermocopriae CLORG16SAA V

Acetogenium k ivui ACORG16S V

Desulfotomaculum australicum DSORR16S VI

Clostridium thermoaceticum CLORR16SAF VI

Clostridium thermoautotrophicum CLORG16S VI

Thermoanaerobacterium xylanolyticum TEOR L09172 VI

Clostridium thermoamylolyticum X76743 VI

Syntrophomonas wolfei DQ449034 VIII

Syntrophomonas bryantii SYBRRSA VIII

Quinella ovalis QUIRR16S IX

Phascolarctobacterium faecium NR 026111 IX

9 9

9 9

9 9

9 9

9 9

9 9

8 5

9 9

5 1

5 7

9 9

8 5

5 0

6 2

9 9

9 9

9 9

9 9

9 9

9 9

9 9

7 9

6 3

9 9

9 9

9 9

9 8

9 9

9 9

9 9

8 0

9 9

9 9

9 9

9 0

9 9

6 6

9 2

9 9

5 4

9 9

5 5

5 3

6 8

7 7

8 3

Phascolarctobacterium faecium NR 026111 IX

Acidaminococcus fermentans EF060091 IX

Sporomusa paucivorans SOORR16S IX

OTU72

Megasphaera elsdenii EU728750 IX

OTU71

OTU73

Pectinatus cerevisiiphilus AF373026 IX

Selenomonas sputingena AF373023 IX

OTU74

Selenomonas ruminantium EF112197 IX

Leptotrichia buccalis GU086178 XIX

Propionigenium modestum NR 029216 XIX

Fusobacterium nucleatum AB540989 XIX

Clostridium rectum NR 029271 XIX

OTU1

OTU2

OTU85

OTU75

OTU84

OTU10

OTU11

OTU12

OTU9

OTU7

OTU8

OTU6

OTU5

OTU3

OTU4

OTU76

OTU77

Caldicellulosiruptor saccharolyticus AF1 X

naerocellum thermophilum ANBRG16S X

Thermoanaerobacter cellulolyticus TEORG1 X

OTU80

OTU78

OTU79

OTU83

OTU81

OTU82

Archaea

9 9

9 8

9 9

9 9

5 7

9 9

9 9

9 9

9 9

9 9

9 9

9 9

9 9

9 7

9 9

9 9

8 1

7 9

7 4

6 3

9 4

9 9

9 8

9 6

8 9

9 7

9 6

7 4

9 9

6 3

8 5

6 3

6 9

0.05

A (W1)

B (W2)

C (W5)

Figure S4. The starch metabolism pathway in gut microbiomes of three wild giant

pandas (A, W1; B, W2; C, W5). The different color represent the value: (the number

of genes coding for this enzyme)×(the participating number in the metabolism

pathway of this enzyme).

A (W1)

B (W2)

C (W5)

Figure S5. The KEGG pathway classification in gut microbiomes of three wild giant pandas (A, W1; B, W2; C, W5).

Figure S6. Metabolic clustering of giant panda, wallaby, termite, cow and human

gastrointestinal or rumen metagenomes. The different color represents relative

percentage of the metabolic classes within each sample.

SI Appendix - PNAS taxonomic assignment of four ... 95%HCI 1.16 2.017 0.945 1.695 1.793 2.392 1.252...

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Transcript of SI Appendix - PNAS taxonomic assignment of four ... 95%HCI 1.16 2.017 0.945 1.695 1.793 2.392 1.252...