Table S1
Sample ID (Sample Site and Body
Number)
Cad1 (Mouth 006)
Cad2 (Sm. Intestine 006)
Cad3 (Transverse Colon 006)
Cad4 (Body Cavity 006)
Cad5 (Body Cavity 006)
Cad6 (Mouth 016)
Cad7 (Body Cavity 016)
Cad8 (Transverse Colon 016)
Cad9 (Mouth 006)
Cad10 (Fecal 006)
Cad11 (Mouth 006)
Cad12 (Sigmoidal Colon 006)
Cad13 (Mouth 016)
Cad14 (Fecal 016)
Cad15 (Fecal 016)
Cad16 (Stomach 016)
Cad17 (Mouth 016)
Cad18 (Sm. Intestine 016)
Number of Sequences
Post-Trimming
7814
4503
11046
0
8019
10146
0
10163
8266
6565
5567
10634
7392
8126
7483
3199
3957
1770
Number of Sequences After
Singleton Removal
7762
4492
10897
0
7960
10060
0
9997
8258
6550
5505
10433
7308
7732
7205
3184
3933
1747
STAFS 2011- 006
Mouth pre-bloat swab
Mouth pre-bloat scrape
Genus
Abundance
Genus
Abundance
Staphylococcus (Firmicutes)
57.0%
Pseudomonas (Proteobacteria)
90.6%
Peptoniphilus (Firmicutes)
18.8%
Clostridium (Firmicutes)
8.83%
Lactobacillus (Firmicutes)
Ignatzschineria (Proteobacteria)
Unclassified, Family
Staphylococcaceae
Unclassified, Class Bacilli
5.40%
1.37%
1.06%
Streptococcus (Firmicutes)
0.618%
1.04%
Unclassified, Family
0.570%
Peptostreptococcaceae
Unclassified, Family
0.490%
Carnobacteriaceae
Mouth end bloat scrape
Peptoniphilus (Firmicutes)
41.9%
Clostridium (Firmicutes)
22.5%
Unclassified, Family
12.1%
Clostridiaceae
Lactobacillus (Firmicutes)
4.70%
Staphylococcus (Firmicutes)
4.58%
Unclassified, Family
Clostridiaceae
Unclassified, Family
Carnobacteriaceae
Peptostreptococcus (Firmicutes)
4.32%
Unclassified, Family
Peptostreptococcaceae
Sphingomonas (Proteobacteria)
Transverse colon swab
Lactobacillus (Firmicutes)
Clostridium (Firmicutes)
Unclassified, Family
Peptostreptococcaceae
Escherichia (Proteobacteria)
0.944%
1.74%
1.18%
0.727%
25.3%
20.1%
11.8%
11.7%
Eggerthella (Firmicutes)
Bacteroides (Bacteroidetes)
7.75%
4.26%
Akkermansia (Verrucomicrobia)
Unclassified, Family
Enterobacteriaceae
3.62%
2.61%
Unclassified, Family
Pseudomonadaceae
Unclassified Genus, Class
Gammaproteobacteria
Lactobacillus (Firmicutes)
Atopobium (Firmicutes)
Streptococcus (Firmicutes)
6.36%
1.62%
0.560%
0.411%
0.230%
Propionibacterium
(Actinobacteria)
Unclassified, Family
Clostridiaceae
Sphingomonas (Proteobacteria)
0.048%
Unclassified, Family Bacillaceae
0.024%
0.048%
0.048%
Small intestine end bloat swab
Clostridium (Firmicutes)
59.8%
Lactobacillus (Firmicutes)
28.9%
Sphingomonas (Proteobacteria)
1.49%
Unclassified
Unclassified, Family
Comamonadaceae
Unclassified, Family
Peptostreptococcaceae
Unclassified Bacteria
1.27%
1.18%
Unclassified, Family
Clostridiaceae
Eggerthella (Firmicutes)
0.801%
Unclassified, Order Rickettsiales
Sigmoidal colon swab
Bacteroides (Bacteroidetes)
Clostridium (Firmicutes)
Lactobacillus (Firmicutes)
Unclassified, Family
Rikenellaceae
Escherichia (Proteobacteria)
Unclassified, Family
Ruminococcaceae
Eggerthella (Firmicutes)
Eubacterium (Firmicutes)
1.16%
1.14%
0.712%
0.490%
42.0%
17.3%
5.12%
4.51%
3.98%
3.43%
2.96%
2.16%
Unclassified, Family
Lachnospiraceae
Eubacterium (Firmicutes)
Fecal scrape
Pseudomonas (Proteobacteria)
Unclassified, Family
Pseudomonadaceae
Psychrobacter (Proteobacteria)
Unclassified, Class
Gammaproteobacteria
Unclassified, Family
Moraxellaceae
Dorea (Firmicutes)
Peptoniphilus (Firmicutes)
Bacteroides (Bacteroidetes)
Streptococcus (Firmicutes)
Unclassified Bacteria
1.87%
1.10%
85.0%
7.98%
Unclassified, Family
Peptostreptococcaceae
Unclassified, Family
Lachnospiraceae
Body cavity end bloat swab
Escherichia (Proteobacteria)
Eubacterium (Firmicutes)
1.85%
1.29%
24.6%
13.2%
3.11%
2.0%
Erwinia (Proteobacteria)
Clostridium (Firmicutes)
13.1%
10.9%
0.687%
Lactobacillus (Firmicutes)
6.11%
0.153%
0.137%
0.122%
Collinsella (Firmicutes)
Ruminococcus (Firmicutes)
Unclassified Genus, Family
Enterobacteriaceae
Bacteroides (Bacteroidetes)
Eggerthella (Firmicutes)
5.98%
5.87%
4.75%
0.122%
0.076%
2.90%
1.68%
Supplementary Table 2: Relative abundances of the top ten genera present in each sample from
body 006.
STAFS 2011- 016
Mouth pre-bloat swab
Genus
Abundance
Streptococcus (Firmicutes)
32.5%
Prevotella (Bacteroidetes)
11.2%
Veillonella (Firmicutes)
9.74%
Unclassified, Family Gemellaceae
5.83%
Atopobium (Firmicutes)
4.50%
Unclassified, Family
3.96%
Clostridiaceae
Unclassified, Family
2.78%
Carnobacteriaceae
Megasphaera (Firmicutes)
2.71%
Dialister (Firmicutes)
1.88%
Actinomyces (Actinobacteria)
1.60%
Mouth end bloat scrape
Unclassified, Family
Planococcaceae
Ignatzschineria (Proteobacteria)
Unclassified, Family
Clostridiaceae
Unclassified, Order Bacillales
Unclassified, Family
Clostridiaceae
Unclassified, Family
Carnobacteriaceae
Erysipelothrix (Firmicutes)
Unclassified, Phylum Firmicutes
31.8%
Fecal scrape
Unclassified, Family
Ruminococcaceae
Megasphaera (Firmicutes)
Fusobacterium (Fusobacteria)
Unclassified, Family
Clostridiaceae
Stomach end bloat scrape
Morganella (Proteobacteria)
1.79%
1.63%
1.46%
85.8%
26.0%
11.1%
Unclassified
Unclassified Bacteria
6.98%
2.30%
8.64%
4.86%
Eggerthella (Firmicutes)
Unclassified, Family
Carnobacteriaceae
Sphingomonas (Proteobacteria)
1.32%
0.911%
4.32%
2.92%
2.39%
Vagococcus (Firmicutes)
1.93%
Unclassified, Order Bacilli
1.30%
Small intestine end bloat scrape
Unclassified
37.1%
Unclassified, Family
Clostridiaceae
Unclassified Bacteria
Unclassified, Family
Peptostreptococcaceae
Faecalibacterium (Firmicutes)
Klebsiella (Proteobacteria)
Collinsella (Firmicutes)
Unclassified, Family
Ruminococcaceae
Clostridium (Firmicutes)
Streptococcus (Firmicutes)
Mouth pre-bloat scrape
Genus
Abundance
Microbacterium (Actinobacteria)
35.1%
Streptococcus (Firmicutes)
13.8%
Prevotella (Bacteroidetes)
9.34%
Unclassified
9.21%
Veillonella (Firmicutes)
5.61%
Unclassified, Order
3.71%
Actinomycetales
Unclassified Bacteria
2.94%
26.3%
0.597
Unclassified, Family
0.440%
Coprobacillaceae
Propionibacterium
0.314%
(Actinobacteria)
Vagococcus (Firmicutes)
0.251%
Unclassified, Order Rickettsiales
0.220%
Transverse colon end bloat swab
Unclassified, Family
24.5%
Coprobacillaceae
Unclassified
22.8%
13.1%
6.30%
Eggerthella (Firmicutes)
Eubacterium (Firmicutes)
20.2%
3.27%
4.30%
2.29%
1.15%
0.973%
Escherichia (Proteobacteria)
Parabacteroides (Bacteroidetes)
Ruminococcus (Firmicutes)
Bifidobacterium (Actinobacteria)
3.03%
2.07%
1.87%
1.71%
0.801%
0.744%
Enterococcus (Firmicutes)
Unclassified, Family
Ruminococcaceae
Fecal Scrape
Unclassified, Family
Peptostreptococcaceae
1.59%
1.47%
23.9%
22.4%
Faecalibacterium (Firmicutes)
12.6%
Unclassified, Ruminococcaceae
12.3%
10.0%
Eubacterium (Firmicutes)
Collinsella (Firmicutes)
Ruminococcus (Firmicutes)
Ruminococcus (Firmicutes)
Unclassified, Family
Peptostreptococcaceae
Unclassified, Family
Lachnospiraceae
Unclassified, Class Clostridia
6.74%
4.44%
3.74%
2.99%
2.83%
2.73%
Unclassified, Family
Ruminococcaceae
Collinsella (Firmicutes)
Klebsiella (Proteobacteria)
9.81%
Faecalibacterium (Firmicutes)
Turicibacter (Firmicutes)
Megasphaera (Firmicutes)
Unclassified, Family
Ruminococcaceae
Eubacterium (Firmicutes)
4.57%
4.47%
4.22%
4.09%
Unclassified, Family
Clostridiaceae
2.96%
7.18%
6.51%
3.18%
Supplementary Table 3: Relative abundances of the top ten genera present in each sample from
body 016.