Table 3 Population subspecies profiles.
Species | N° strains matched | Strains with single hit | Strain richness | Richness (if present) | Richness (all) | Prevalence | ||||
|---|---|---|---|---|---|---|---|---|---|---|
1× | 2× | 3× | 4× | 5× | ||||||
Healthy-ICST | ||||||||||
Bacteroides fragilis | 157 | 13 | 24.7% | 6.6% | 0.3% | 0.0% | 0.0% | 1.2 | 0.39 | 31.7% |
Bacteroides uniformis | 174 | 32 | 19.1% | 4.6% | 0.3% | 0.0% | 0.0% | 1.2 | 0.29 | 24.0% |
Bifidobacterium bifidum | 163 | 12 | 29.8% | 13.2% | 0.4% | 0.0% | 0.0% | 1.3 | 0.58 | 43.4% |
Bifidobacterium breve | 150 | 34 | 24.5% | 7.6% | 0.4% | 0.0% | 0.0% | 1.3 | 0.41 | 32.5% |
Bifidobacterium longum | 388 | 90 | 22.1% | 34.7% | 13.2% | 1.5% | 0.1% | 1.9 | 1.37 | 71.5% |
Bifidobacterium pseudocatenulatum | 137 | 27 | 27.4% | 4.4% | 0.2% | 0.0% | 0.0% | 1.2 | 0.37 | 32.0% |
Blautia wexlerae | 160 | 24 | 21.5% | 6.9% | 0.9% | 0.1% | 0.0% | 1.3 | 0.38 | 29.4% |
Enterobacter hormaechei | 72 | 30 | 5.5% | 1.0% | 0.2% | 0.1% | 0.0% | 1.2 | 0.08 | 6.8% |
Enterococcus faecalis | 114 | 43 | 11.8% | 3.4% | 1.1% | 0.3% | 0.0% | 1.4 | 0.23 | 16.6% |
Escherichia coli | 1059 | 482 | 35.2% | 19.5% | 6.7% | 1.3% | 0.2% | 1.6 | 1.00 | 62.8% |
Klebsiella michiganensis | 76 | 38 | 5.2% | 0.6% | 0.0% | 0.0% | 0.0% | 1.1 | 0.06 | 5.7% |
Klebsiella pneumoniae | 233 | 107 | 10.3% | 3.6% | 0.6% | 0.1% | 0.0% | 1.4 | 0.20 | 14.5% |
Prevotella copri | 96 | 8 | 7.5% | 7.0% | 6.3% | 4.0% | 2.4% | 2.5 | 0.69 | 27.2% |
Prevotella unknown species | 59 | 1 | 3.0% | 4.4% | 5.9% | 3.7% | 2.4% | 2.9 | 0.57 | 19.5% |
Ruminococcus gnavus | 176 | 31 | 22.7% | 11.3% | 2.0% | 0.3% | 0.0% | 1.4 | 0.52 | 36.2% |
Staphylococcus epidermidis | 87 | 36 | 3.6% | 2.1% | 0.7% | 0.4% | 0.1% | 1.7 | 0.12 | 6.8% |
Veillonella parvula | 86 | 12 | 12.9% | 4.4% | 0.4% | 0.0% | 0.0% | 1.3 | 0.23 | 17.7% |
Mixed-ICST | ||||||||||
Bacteroides fragilis | 67 | 37 | 7.3% | 2.2% | 0.1% | 0.0% | 0.0% | 1.2 | 0.12 | 9.6% |
Bacteroides uniformis | 57 | 36 | 8.5% | 0.4% | 0.0% | 0.0% | 0.0% | 1.0 | 0.09 | 8.9% |
Bifidobacterium bifidum | 123 | 42 | 16.5% | 11.4% | 0.1% | 0.0% | 0.0% | 1.4 | 0.40 | 28.1% |
Bifidobacterium breve | 134 | 27 | 26.3% | 19.8% | 4.9% | 0.2% | 0.0% | 1.6 | 0.81 | 51.2% |
Bifidobacterium longum | 204 | 98 | 14.7% | 15.6% | 3.1% | 0.2% | 0.0% | 1.7 | 0.56 | 33.7% |
Bifidobacterium pseudocatenulatum | 57 | 22 | 8.1% | 2.4% | 0.7% | 0.2% | 0.0% | 1.4 | 0.16 | 11.4% |
Blautia wexlerae | 59 | 31 | 8.6% | 1.6% | 0.2% | 0.0% | 0.0% | 1.2 | 0.12 | 10.3% |
Enterobacter hormaechei | 94 | 23 | 32.8% | 10.0% | 0.9% | 0.7% | 0.0% | 1.3 | 0.58 | 44.3% |
Enterococcus faecalis | 95 | 36 | 33.5% | 11.7% | 2.1% | 0.2% | 0.1% | 1.4 | 0.64 | 47.5% |
Escherichia coli | 291 | 175 | 25.5% | 14.7% | 3.0% | 0.6% | 0.2% | 1.5 | 0.67 | 44.0% |
Klebsiella michiganensis | 36 | 14 | 8.5% | 1.6% | 0.0% | 0.0% | 0.0% | 1.2 | 0.12 | 10.0% |
Klebsiella pneumoniae | 119 | 55 | 18.0% | 5.9% | 0.5% | 0.0% | 0.1% | 1.3 | 0.32 | 24.5% |
Prevotella copri | 18 | 13 | 1.3% | 0.5% | 0.1% | 0.1% | 0.0% | 1.5 | 0.03 | 2.0% |
Prevotella unknown species | 13 | 13 | 0.2% | 0.3% | 0.1% | 0.0% | 0.0% | 1.9 | 0.01 | 0.6% |
Ruminococcus gnavus | 89 | 33 | 9.9% | 7.2% | 1.2% | 0.0% | 0.0% | 1.5 | 0.28 | 18.4% |
Staphylococcus epidermidis | 73 | 23 | 17.5% | 6.6% | 3.0% | 3.0% | 0.8% | 1.8 | 0.56 | 30.9% |
Veillonella parvula | 77 | 14 | 19.8% | 5.0% | 0.7% | 0.0% | 0.0% | 1.3 | 0.32 | 25.6% |
Unhealthy-ICST | ||||||||||
Bacteroides fragilis | 65 | 38 | 2.3% | 0.3% | 0.0% | 0.0% | 0.0% | 1.1 | 0.03 | 2.6% |
Bacteroides uniformis | 72 | 42 | 3.2% | 0.2% | 0.0% | 0.0% | 0.0% | 1.1 | 0.04 | 3.4% |
Bifidobacterium bifidum | 76 | 29 | 2.6% | 0.9% | 0.0% | 0.0% | 0.0% | 1.3 | 0.04 | 3.5% |
Bifidobacterium breve | 91 | 33 | 4.2% | 1.8% | 0.1% | 0.0% | 0.0% | 1.3 | 0.08 | 6.1% |
Bifidobacterium longum | 198 | 77 | 4.2% | 4.4% | 1.0% | 0.1% | 0.0% | 1.7 | 0.17 | 9.8% |
Bifidobacterium pseudocatenulatum | 37 | 19 | 1.8% | 0.3% | 0.0% | 0.0% | 0.0% | 1.1 | 0.02 | 2.1% |
Blautia wexlerae | 44 | 19 | 1.9% | 0.3% | 0.0% | 0.0% | 0.0% | 1.1 | 0.02 | 2.1% |
Enterobacter hormaechei | 92 | 27 | 10.0% | 1.3% | 0.0% | 0.0% | 0.0% | 1.1 | 0.13 | 11.4% |
Enterococcus faecalis | 158 | 45 | 33.6% | 12.4% | 3.0% | 0.4% | 0.0% | 1.4 | 0.69 | 49.4% |
Escherichia coli | 576 | 310 | 30.4% | 9.3% | 2.2% | 0.5% | 0.1% | 1.4 | 0.59 | 42.7% |
Klebsiella michiganensis | 92 | 18 | 15.2% | 2.4% | 0.1% | 0.0% | 0.0% | 1.2 | 0.20 | 17.7% |
Klebsiella pneumoniae | 257 | 78 | 19.7% | 8.1% | 1.9% | 0.6% | 0.0% | 1.5 | 0.44 | 30.2% |
Prevotella copri | 21 | 14 | 0.6% | 0.0% | 0.0% | 0.0% | 0.0% | 1.1 | 0.01 | 0.6% |
Prevotella unknown species | 15 | 9 | 0.2% | 0.1% | 0.0% | 0.0% | 0.0% | 1.4 | 0.00 | 0.3% |
Ruminococcus gnavus | 78 | 25 | 2.5% | 1.5% | 0.1% | 0.0% | 0.0% | 1.4 | 0.06 | 4.2% |
Staphylococcus epidermidis | 133 | 27 | 21.5% | 11.8% | 6.1% | 2.4% | 2.0% | 1.9 | 0.83 | 43.7% |
Veillonella parvula | 93 | 11 | 12.8% | 5.2% | 1.3% | 0.1% | 0.0% | 1.4 | 0.28 | 19.5% |
