Table 1.
Mean microbial concentrations (± SD) as detected with applied fluorescence in situ hybridization probes (109 bacteria/mL)
| Day 0 | Day 10 | Day 31 | Day 45 | Change in % from day 0 to day 45 | P value | |
| Mean sum concentrations of all detected bacteria | 85.4 ± 25.6 | 107.4 ± 15.6 | 123.7 ± 34.1 | 126.1 ± 50.1 | ↑ 32% | < 0.001 |
| Essential all (n = 3) | 36.2 ± 14.7 | 44.0 ± 5.1 | 42.7 ± 7.7 | 42.8 ± 9.0 | ↑ 14% | < 0.01 |
| Erec (Eubacterium rectale, Clostridium coccoides group) | 11.7 ± 6.9 | 17.1 ± 2.5 | 19 ± 4 | 17.7 ± 4.8 | ↑ 30% | < 0.001 |
| Bac303 (Bacteroides) | 12.9 ± 5.3 | 12.2 ± 5.7 | 9.5 ± 4.4 | 9.9 ± 5.0 | ↓ 30% | ns |
| Fprau (Faecalibacterium prausnitzii) | 11.6 ± 5.9 | 14.7 ± 3.8 | 14 ± 3.6 | 14.7 ± 6.9 | ↑ 21% | ns |
| Individual pioneer | ||||||
| All (n = 4) | 7.8 ± 5.0 | 11.5 ± 9.3 | 9.9 ± 6.8 | 10.9 ± 8.5 | ↑ 28% | ns |
| Ebac1790 Enterobacteriaceae | 0.25 ± 0.8 | 0.6 ± 2.1 | 1.2 ± 2.3 | 1.1 ± 2.0 | ↑ 72% | ns |
| Cdif198 Clostridium difficile | 0.04 ± 0.09 | 0.01 ± 0.03 | 0.3 ± 0.93 | 0.10 ± 0.03 | ↑ 96% | ns |
| Bif153 Genus Bifidobacterium | 7.1 ± 5.5 | 9.1 ± 8.6 | 7.7 ± 5.3 | 9.7 ± 7.2 | ↑ 27% | ns |
| Clit135 Clostridium lituseburense group including C. difficile | 0.5 ± 0.86 | 0.7 ± 1.05 | 0.4 ± 1.08 | 0.4 ± 0.8 | ↔ | ns |
| Individual substantial mean > 0.1 × 109/mL | ||||||
| All (n = 28) | 41.7 ± 17.3 | 51.4 ± 14.0 | 70.4 ± 28.8 | 71.6 ± 36.8 | ↑ 41% | < 0.002 |
| ACI623 Acidaminococcaceae sp. (not the Selenomonas species) | 1.4 ± 1.9 | 0.7 ± 0.8 | 1.6 ± 2.2 | 1.2 ± 1.6 | ↔ | ns |
| AKK406 Akkermansia | 2.3 ± 3.7 | 2.8 ± 4.6 | 1.9 ± 2.9 | 2.6 ± 4.1 | ↔ | ns |
| Ato291 Atopobium cluster | 3.8 ± 2.9 | 4.9 ± 3.5 | 6.1 ± 4.5 | 6.4 ± 3.6 | ↑ 41% | 0.01 |
| Bbif186 B. bifidum | 0.3 ± 0.9 | 0.3 ± 0.6 | 0.2 ± 0.5 | 0.3 ± 0.5 | ↔ | ns |
| Blon1004 B. longum | 0.7 ± 1.2 | 0.9 ± 1.5 | 1.0 ± 1.5 | 0.6 ± 0.9 | ↔ | ns |
| Bputre698 Bacteroides putredinis | 0.8 ± 1.6 | 0.8 ± 1.3 | 1.8 ± 2.1 | 1.6 ± 1.8 | ↑ 50% | ns |
| Burkho Burkholderia spp. | 0.7 ± 0.7 | 1.4 ± 1.0 | 1.3 ± 1.4 | 1.3 ± 1.2 | ↑ 46% | 0.01 |
| Ceut705 C. eutactus, Coprococcus sp. | 3.0 ± 4.4 | 4.5 ± 5.1 | 5.6 ± 6.7 | 4.1 ± 5.2 | ↑ 32% | ns |
| Chis150 Clostridium histolyticum | 0.6 ± 1.2 | 1.4 ± 3.6 | 2.5 ± 4.5 | 1.5 ± 2.1 | ↑ 60% | ns |
| Cor653 Coriobacterium group | 0.5 ± 0.8 | 0.8 ± 1.0 | 1.2 ± 2.2 | 1.2 ± 1.5 | ↑ 42% | ns |
| Cvir1414 Clostridium viride group | 1.9 ± 2.1 | 3.4 ± 2.2 | 4.2 ± 2.5 | 4.0 ± 2.1 | ↑ 53% | < 0.001 |
| Ecyl387 Eubacterium cylindroides | 0.7 ± 0.5 | 0.7 ± 0.4 | 1.4 ± 1.1 | 1.2 ± 0.7 | ↑ 42% | 0.01 |
| Ehal1469 Eubacterium hallii | 0.6 ± 0.9 | 0.6 ± 1.1 | 0.7 ± 0.8 | 0.7 ± 0.8 | ↔ | ns |
| Eram997 Eubacterium ramulus | 0.3 ± 1.3 | 0.03 ± 0.04 | 0.7 ± 1.4 | 1.0 ± 1.5 | ↑ 70% | ns |
| Lab158 Lactobacillus sp., Enterococcus sp. | 0.1 ± 0.2 | 0.8 ± 1.1 | 1.7 ± 3.0 | 0.5 ± 0.9 | ↑ 80% | 0.02 |
| Muc1437 Akkermansia muciniphila | 2.8 ± 3.9 | 1.8 ± 3.2 | 6.5 ± 7.4 | 7.8 ± 8.9 | ↑ 64% | 0.015 |
| Myc657 Mycobacterium subdivision (mycolic acid-containing Actinomycetes) | 3.1 ± 1.5 | 2.5 ± 1.3 | 1.6 ± 1.1 | 1.9 ± 1.9 | ↓ 39% | ns |
| Phasco741 Phascolarctobacterium faecium | 0.6 ± 0.9 | 0.9 ± 0.8 | 0.8 ± 0.8 | 1.1 ± 1.1 | ↑ 45% | ns |
| Pnig657 Prevotella nigrescens | 2.2 ± 3.7 | 0.7 ± 1.3 | 2.6 ± 3.1 | 1.7 ± 2.3 | ↔ | ns |
| ProCo1264 Ruminococcus productus | 0.7 ± 2.0 | 1.5 ± 2.6 | 1.4 ± 2.3 | 1.9 ± 3.7 | ↑ 63% | ns |
| Rfla729 Ruminococcus albus | 2.2 ± 3.2 | 5.5 ± 5.0 | 4.7 ± 5.0 | 3.9 ± 4.6 | ↑ 44% | 0.02 |
| SFB1 Segmented filame(14%ntous bacteria | 2.3 ± 3.3 | 1.6 ± 2.7 | 2.3 ± 1.6 | 2.9 ± 1.9 | ↔ | ns |
| SNA Sphaerotilus natans | 4.3 ± 3.7 | 6.1 ± 5.4 | 6.8 ± 5.9 | 5.9 ± 5.8 | ↑ 27% | ns |
| Strc493 most Streptococcus spp. | 1.3 ± 3.3 | 0.5 ± 1.1 | 1.9 ± 3.9 | 3.7 ± 4.9 | ↑ 65% | ns |
| SUBU1237 Burkholderia spp., Sutterella spp. | 1.7 ± 2.6 | 3.4 ± 2.6 | 5.6 ± 4.4 | 5.6 ± 4.2 | ↑ 69% | 0.001 |
| Urobe63a Ruminococcus obeum-like | 1.6 ± 2.3 | 2.2 ± 2.3 | 2.5 ± 2.9 | 3.2 ± 2.4 | ↑ 50% | 0.05 |
| Veil223 Veilonella | 0.1 ± 0.3 | 0.1 ± 0.4 | 0.6 ± 1.4 | 0.9 ± 2.1 | ↑ 88% | ns |
| Ver620 Verrucomicrobium | 1.7 ± 3.9 | 0.5 ± 1.6 | 1.1 ± 3.2 | 1.9 ± 5.3 | ↔ | ns |
| Individual marginal or accidental mean 150 (n = 6) | ||||||
| Cperf191 Clostridium perfringens | 0.001 | 0 | 0 | 0.001 | ↔ | ns |
| Efaec Enterococcus faecalis | 0.01 ± 0.02 | 0.01 ± 0.03 | 0.01 ± 0.02 | 0.01 ± 0.03 | ↔ | ns |
| MIB724 mouse intestinal bacteria | 0.01 ± 0.06 | 0.001 ± 0.002 | 0.01 ± 0.03 | 0.07 ± 0.1 | ↔ | ns |
| Pce Burkholderia spp. | 0.09 ± 0.30 | 0.03 ± 0.10 | 0.3 ± 0.7 | 0.07 ± 0.20 | ↔ | ns |
| Rbro730 Clostridium sporosphaeroides, Ruminococcus bromii, Clostridium leptum | 0.04 ± 0.20 | 0.08 ± 0.30 | 0.8 ± 3.0 | 0.1 ± 0.5 | ↑ | ns |
| Urobe63b Ruminococcus obeum-like | 0.01 ± 0.04 | 0.0001 | 0.001 | 0.6 ± 1.1 | ↔ | ns |