Table 2.
Effect of cRG-I on microbial composition (25 most abundant OTUs across all samples) in the lumen (log cells/mL as estimated via multiplying total cell counts (cells/mL) with 16S rRNA gene profiling (%)) and mucus (%) of the simulated proximal (PC) and distal colon (DC) of the quad-M-SHIME. Values presented are the averages of the differences at the end of the treatment period (Day 35) versus those at the end of the control period (Day 14) across the four human adult donors tested (n = 4). As a result, positive values indicate that a given OTU is increased upon cRG-I treatment. Statistical differences are indicated in bold.
| Phylum | Family | OTU | Related Species | Lumen | Mucus | ||
|---|---|---|---|---|---|---|---|
| PC | DC | PC | DC | ||||
| Actinobacteria | Bifidobacteriaceae | 1 | Bifidobacterium adolescentis | 0.26 | −0.01 | −1.03% | 6.64% |
| 8 | Bifidobacterium bifidum | −0.56 | −0.84 | −9.28% | −5.96% | ||
| 10 | Bifidobacterium longum | 1.32 | 1.05 | 4.13% | 3.23% | ||
| Coriobacteriaceae | 12 | Collinsella aerofaciens | 0.23 | −0.02 | 2.16% | −0.41% | |
| Bacteroidetes | Bacteroidaceae | 6 | Bacteroides dorei | 0.83 | 0.73 | 5.22% | −0.14% |
| 16 | Bacteroides ovatus | −0.38 | 0.03 | −0.22% | 0.04% | ||
| 28 | Bacteroides fragilis | −0.58 | −0.80 | −0.29% | −2.09% | ||
| 17 | Bacteroides massiliensis | −0.25 | −0.57 | −1.12% | −1.25% | ||
| 13 | Bacteroides intestinalis | −0.19 | 0.02 | −0.17% | 0.20% | ||
| Prevotellaceae | 2 | Prevotella sp. | 0.52 | 0.69 | 7.55% | 1.85% | |
| Firmicutes | Acidaminococcaceae | 11 | Phascolarctobacterium faecium | 0.47 | 0.39 | 0.46% | 0.16% |
| Clostridiaceae | 32 | Clostridium butyricum | 0.00 | 0.00 | −0.01% | −0.98% | |
| Lachnospiraceae | 5 | Clostridium clostridioforme/bolteae | 0.04 | 0.15 | −3.74% | 2.27% | |
| 9 | Lachnoclostridium sp. | 0.57 | 0.16 | −2.16% | −0.09% | ||
| 14 | Eubacterium contortum | 0.00 | 0.04 | 0.00% | −1.44% | ||
| 25 | Clostridium sp. | 0.34 | 0.32 | 0.10% | 0.11% | ||
| Ruminococcaceae | 19 | Gemmiger formicilis | 0.36 | −0.05 | 0.06% | −0.74% | |
| 42 | Faecalibacterium prausnitzii | 0.00 | 0.00 | 0.00% | −0.10% | ||
| Veillonellaceae | 3 | Megamonas funiformis | 0.05 | −0.01 | −1.70% | 0.52% | |
| 4 | Megamonas funiformis | 0.06 | 0.01 | −0.26% | 1.21% | ||
| 18 | Megasphaera sp. | −0.05 | −0.13 | −1.78% | −0.02% | ||
| 26 | Anaeroglobus geminatus | −0.01 | −0.24 | −1.49% | −0.21% | ||
| Proteobacteria | Pseudomonadaceae | 15 | Pseudomonas aeruginosa | 0.31 | −0.06 | 0.04% | −1.88% |
| Synergistetes | Synergistaceae | 7 | Cloacibacillus sp. | 0.54 | −0.09 | 3.36% | 0.04% |
| Verrucomicrobia | Akkermansiaceae | 20 | Akkermansia muciniphila | 0.00 | −0.09 | 0.00% | −0.01% |