Table 3. Sample Species Compositions.
Species information for each of the tested samples. HM-782D (20 species), and all 48G (45 species), samples have known DNA quantities added for each of the species. The species composition of fecal microbiota samples recovered from gnotobiotic mice was determined by short read shotgun sequencing of community DNA and mapping the results reads to the genomes of members of the consortium of cultured human gut bacterial strains that had been introduced into the animals. The COPRO-Seq percent relative abundance of each species is given as the mean for all 92 gnotobiotic samples plus or minus the standard deviation.
| HM-782D (20-taxa consortium) | 48G 45-taxa consortium | Gnotobiotic Mice 68-taxa consortium | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Known Species | Known Species | Stg1 Rel. % | Stg2 Rel. % | Stg3 Rel. % | Known Species | COPRO-Seq Rel. % | |||||||
| Acinetobacter baumannii | Akkermansia muciniphila | 4.2 | 0.3 | 4.2 | Akkermansia muciniphila | 3.5E+01 ± 6.8E+00 | |||||||
| Actinomyces odontolyticus | Alistipes indistinctus | 0.1 | 0.5 | 4.2 | Anaerotruncus colihominis | 2.7E-01 ± 1.3E-01 | |||||||
| Bacillus cereus | Anaerococcus hydrogenalis | 0.3 | 4.2 | 8.4 | Bacteroides WH2 | 7.9E+00 ± 2.4E+00 | |||||||
| Bacteroides vulgatus | Anaerotruncus colihominis | 8.4 | 1.1 | 0.1 | Bacteroides caccae | 1.6E+01 ± 2.7E+00 | |||||||
| Clostridium beijerinckii | Bacteroides cellulosilyticus | 0.3 | 0.5 | 0.1 | Bacteroides cellulosilyticus | 3.0E-01 ± 6.4E-01 | |||||||
| Deinococcus radiodurans | Bacteroides dorei | 8.4 | 2.1 | 1.1 | Bacteroides coprophilus | 4.2E-04 ± 6.0E-04 | |||||||
| Enterococcus faecalis | Bacteroides eggerthii | 1.1 | 8.4 | 0.3 | Bacteroides dorei | 5.3E+00 ± 4.9E+00 | |||||||
| Escherichia coli | Bacteroides finegoldii | 0.1 | 0.1 | 0.5 | Bacteroides eggerthii | 1.8E+00 ± 8.3E-01 | |||||||
| Helicobacter pylori | Bacteroides intestinalis | 1.1 | 4.2 | 1.1 | Bacteroides finegoldii | 1.5E-01 ± 1.0E-01 | |||||||
| Lactobacillus gasseri | Bacteroides ovatus | 8.4 | 1.1 | 0.1 | Bacteroides intestinalis | 1.2E-01 ± 1.4E-01 | |||||||
| Listeria monocytogenes | Bact. thetaiotaomicron | 1.1 | 17.3 | 5.4 | Bacteroides ovatus | 1.5E-01 ± 1.7E-01 | |||||||
| Neisseria meningitidis | Bacteroides uniformis | 2.1 | 0.3 | 4.2 | Bacteroides plebeius | 6.1E-04 ± 6.6E-04 | |||||||
| Propionibacterium acnes | Bacteroides vulgatus | 1.1 | 0.1 | 0.3 | Bact, thetaiotaomicron | 6.9E+00 ± 1.3E+00 | |||||||
| Pseudomonas aeruginosa | Bacteroides xylanisolvens | 0.1 | 2.1 | 0.5 | Bacteroides uniformis | 8.3E-01 ± 2.3E-01 | |||||||
| Rhodobacter sphaeroides | Bifidobacterium bifidum | 0.3 | 0.3 | 2.1 | Bacteroides vulgatus | 4.3E+00 ± 2.6E+00 | |||||||
| Staphylococcus aureus | Bifid. pseudocatenulatum | 0.1 | 4.2 | 8.4 | Bacteroides xylanisolvens | 1.2E-01 ± 5.8E-02 | |||||||
| Staph. epidermidis | Blautia hansenii | 8.4 | 0.3 | 0.1 | Bifidobacterium adolescentis | 1.7E-02 ± 7.9E-03 | |||||||
| Streptococcus agalactiae | Blautia luti | 2.1 | 1.1 | 2.1 | Bifidobacterium bifidum | 1.5E-05 ± 1.0E-04 | |||||||
| Streptococcus mutans | Clostridium asparagiforme | 0.1 | 0.5 | 8.4 | Bifid. pseudocatenulatum | 3.6E-04 ± 8.2E-04 | |||||||
| Strep. pneumoniae | Clostridium hathewayi | 0.3 | 0.3 | 0.1 | Blautia hansenii | 6.7E-01 ± 2.3E-01 | |||||||
| Clostridium leptum | 0.5 | 0.1 | 2.1 | Blautia hydrogenotrophica | 9.8E-06 ± 9.6E-05 | ||||||||
| Clostridium nexile | 4.7 | 2.2 | 0.5 | Blautia luti | 2.5E-04 ± 5.2E-04 | ||||||||
| Clost. saccharolyticum | 8.4 | 0.1 | 4.2 | Citrobacter youngae | 4.9E-02 ± 5.8E-02 | ||||||||
| Clostridium sporogenes | 2.1 | 2.1 | 0.5 | Clostridium asparagiforme | 1.2E-01 ± 6.0E-02 | ||||||||
| Collinsella intestinalis | 1.1 | 2.1 | 1.1 | Clostridium bartlettii | 5.7E-06 ± 5.6E-05 | ||||||||
| Coprococcus comes | 4.2 | 1.1 | 0.5 | Clostridium bolteae | 1.1E+00 ± 2.6E-01 | ||||||||
| Dorea formicigenerans | 4.2 | 1.1 | 0.1 | Clostridium hathewayi | 3.6E+00 ± 1.3E+00 | ||||||||
| Dorea longicatena | 0.1 | 0.5 | 8.4 | Clostridium hylemonae | 5.2E-02 ± 7.1E-02 | ||||||||
| Edwardsiella tarda | 0.1 | 8.4 | 0.1 | Clostridium leptum | 3.0E-02 ± 1.3E-02 | ||||||||
| Enterobacter cancerogenus | 1.1 | 0.1 | 0.5 | Clostridium nexile | 2.0E-01 ± 1.6E-01 | ||||||||
| Escherichia coli | 0.1 | 0.1 | 8.4 | Clostridium ramosum | 5.6E-01 ± 2.6E-01 | ||||||||
| Escherichia fergusonii | 1.1 | 0.5 | 0.1 | Clostridium scindens | 4.2E-01 ± 1.4E-01 | ||||||||
| Eubacterium biforme | 2.1 | 8.4 | 2.1 | Clostridium spM62 1 | 4.5E-05 ± 2.0E-04 | ||||||||
| Eubacterium eligens | 0.3 | 4.2 | 0.5 | Clostridium sporogenes | 1.1E-02 ± 9.6E-03 | ||||||||
| Eubacterium ventriosum | 0.3 | 0.1 | 2.1 | Clostridium symbiosum | 5.1E-01 ± 1.6E-01 | ||||||||
| Faecalibacterium prausnitzii | 4.2 | 0.1 | 0.3 | Collinsella aerofaciens | 9.6E-01 ± 6.6E-01 | ||||||||
| Parabacteroides johnsonii | 0.1 | 0.1 | 8.4 | Collinsella intestinalis | 4.3E-01 ± 2.7E-01 | ||||||||
| Proteus penneri | 4.2 | 0.1 | 0.1 | Collinsella stercoris | 8.6E-01 ± 6.2E-01 | ||||||||
| Providencia alcalifaciens | 2.1 | 0.1 | 4.2 | Coprococcus comes | 2.9E-02 ± 2.4E-02 | ||||||||
| Roseburia intestinalis | 8.4 | 1.1 | 0.3 | Desulfovibrio piger | 3.1E+00 ± 7.6E-01 | ||||||||
| Ruminococcus gnavus | 0.5 | 4.2 | 1.1 | Dorea formicigenerans | 2.5E-03 ± 5.7E-03 | ||||||||
| Ruminococcus lactaris | 0.5 | 4.2 | 0.1 | Dorea longicatena | 2.4E-04 ± 5.2E-04 | ||||||||
| Ruminococcus torques | 2.1 | 2.1 | 1.1 | Edwardsiella tarda | 2.5E-01 ± 2.0E-01 | ||||||||
| Streptococcus infantarius | 0.1 | 0.3 | 0.1 | Enterobacter cancerogenus | 3.8E-02 ± 9.0E-02 | ||||||||
| Subdoligranulum variabile | 0.1 | 8.4 | 2.1 | Escherichia coli | 1.6E-03 ± 5.8E-03 | ||||||||
| Escherichia fergusonii | 2.7E-01 ± 2.5E-01 | ||||||||||||
| Eubacterium biforme | 7.0E-04 ± 9.7E-04 | ||||||||||||
| Eubacterium cylindroides | 2.1E-03 ± 1.8E-03 | ||||||||||||
| Eubacterium dolichum | 3.5E-05 ± 1.6E-04 | ||||||||||||
| Eubacterium hallii | 2.0E-04 ± 4.6E-04 | ||||||||||||
| Eubacterium rectale | 2.2E-05 ± 1.3E-04 | ||||||||||||
| Faecalibacterium prausnitzii | 4.1E-05 ± 1.9E-04 | ||||||||||||
| Flavonifractor plautii | 1.1E-03 ± 1.2E-03 | ||||||||||||
| Fusobacterium varium | 1.7E+00 ± 6.4E-01 | ||||||||||||
| Holdemania filiformis | 3.6E-01 ± 1.0E-01 | ||||||||||||
| Lactobacillus ruminis | 4.6E-04 ± 1.2E-03 | ||||||||||||
| Marvin, formatexigens | 9.1E-06 ± 8.9E-05 | ||||||||||||
| Megamonas funiformis | 9.2E-02 ± 7.3E-02 | ||||||||||||
| Mitsuokella multacida | 1.3E-04 ± 6.6E-04 | ||||||||||||
| Parabacteroides distasonis | 2.2E-02 ± 5.2E-03 | ||||||||||||
| Parabacteroides johnsonii | 3.8E+00 ± 1.2E+00 | ||||||||||||
| Parabacteroides merdae | 3.4E-01 ± 4.2E-01 | ||||||||||||
| Proteus penneri | 2.7E-02 ± 4.9E-02 | ||||||||||||
| Providencia stuartii | 1.9E-04 ± 4.3E-04 | ||||||||||||
| Ruminococcus gnavus | 4.7E-01 ± 2.1E-01 | ||||||||||||
| Ruminococcus lactaris | 7.5E-05 ± 2.4E-04 | ||||||||||||
| Ruminococcus torques | 7.2E-01 ± 8.5E-01 | ||||||||||||
| Subdoligranulum variabile | 4.0E-01 ± 1.2E-01 | ||||||||||||