Table 1.
The mean of the relative abundance of dominant phyla, classes and genera in ileum, distal colon, and caecum samples obtained from mice bred in Room 1 or Room 2
| Ileum lumen | Ileum mucus | Distal colon lumen | Distal colon mucus | Caecum | ||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Room 1 | Room 2 | Room 1 | Room 2 | Room 1 | Room 2 | Room 1 | Room 2 | Room 1 | Room 2 | |
| n = 11 | n = 11 | n = 11 | n = 11 | n = 11 | n = 11 | n = 9 | n = 7 | n = 11 | n = 11 | |
| mean % (SD) | mean % (SD) | mean % (SD) | mean % (SD) | mean % (SD) | mean % (SD) | mean % (SD) | mean % (SD) | mean % (SD) | mean % (SD) | |
| Firmicutes | 88 (6) | 92 (6) | 81 (9) | 88 (9) | 80 (10) | 71 (8) | 73 (11) | 62 (24) | 85 (3) | 83 (3) |
| Bacilli | 50 (19) | 76 (15) | 50 (23) | 38 (24) | 28 (12) | 34 (19) | 15 (11) | 17 (14) | 12 (5) | 7 (4) |
| Lactobacillus | 50 (19) | 75 (15) | 50 (21) | 38 (24) | 27 (12) | 34 (19) | 15 (11) | 16 (9) | 12 (5) | 7 (4) |
| Clostridia | 2 (1) | 11 (11) | 15 (23)** | 47 (28)** | 30 (20) | 35 (22) | 50 (22) | 45 (28) | 64 (11)** | 75 (5)** |
| Unknown genus (family unknown) | < 1 | < 1 | 1 (2) | < 1 | 10 (9) | 12 (14) | 18 (10) | 16 (17) | 27 (13) | 29 (19) |
| Other | < 1 | < 1 | 2 (4) | < 1 | 10 (8) | 9 (6) | 18 (11) | 13 (14) | 21 (7) | 19 (16) |
| Ruminococcus | 0.1 (0.01)*** | 0.3 (0.2)*** | < 1 | < 1 | < 1 | < 1 | < 1 | < 1 | 0.7 (0.3)*** | 1 (1)*** |
| Candidatus arthromitus (Segmented filamentous bacteria) | 0.04 (0.12)*** | 1 (2)*** | 11 (23) | 43 (29) | 0.01 (0.02)*** | 0.2 (0.3)*** | 0.03 (0.1)*** | 1 (1)*** | < 1 | < 1 |
| Anaerostipes | 0.06 (0.05)** | –** | 0.2 (0.2)** | –** | 2 (2)** | < 1** | 0.8 (0.8)*** | –*** | 0.8 (0.6)** | –** |
| Dehalobacterium | < 1 | < 1 | < 1 | < 1 | < 1 | < 1 | < 1 | < 1 | 0.2 (0.1)** | 0.6 (0.2)** |
| Erysipelotrichi | 36 (16)* | 5 (6)* | 17 (13)** | 3 (3)** | 22 (14)* | 2 (2)* | 8 (7) | 1 (1) | 9 (7)* | 0.6 (0.7)* |
| Allobaculum | 35 (17)** | 5 (6)** | 15 (13) | 3 (3) | 22 (14)** | 2 (2)** | 7 (7) | 1 (1) | 9 (7)** | 0.4 (0.4)** |
| Other | 1 (1)** | –** | < 1 | < 1 | 0.5 (0.8)*** | 0.003 (0.01)*** | 0.2 (0.3)*** | –*** | 0.2 (0.2)** | –** |
| Bacteroidetes | 11 (6) | 6 (5) | 18 (9) | 10 (8) | 19 (10) | 27 (8) | 12 (6) | 17 (14) | 13 (4) | 13 (3) |
| Bacteroidia | 11 (5) | 6 (5) | 18 (9) | 10 (8) | 19 (10) | 27 (8) | 12 (6) | 17 (14) | 13 (4) | 13 (3) |
| Unknown genus (family S24-7) | 11 (6)** | 6 (5)** | 16 (10) | 10 (8) | 15 (9) | 14 (6) | 9 (5) | 10 (10) | 8 (2)** | 5 (1)** |
| Bacteroides | < 1 | < 1 | < 1 | < 1 | 0.4 (0.4)** | 4 (3)** | < 1 | 3 (2) | 0.4 (0.2)** | 2 (1)** |
| Parabacteroides | < 1 | < 1 | < 1 | < 1 | 0.3 (0.3)** | 4 (4)** | < 1 | 2 (2) | 0.3 (0.2)** | 2 (2)** |
| Prevotella | – | < 1 | < 1 | – | 0.01 (0.01)** | 0.3 (0.4)** | < 1 | < 1 | –** | 0.1 (0.1)** |
| Odoribacter | – | – | < 1 | – | < 1 | < 1 | < 1 | < 1 | 0.4 (0.3)** | 0.6 (0.5)** |
| Proteobacteria | 0.1 (0.1)* | 1 (1)* | < 1 | 1 (1) | < 1 | 1 (2) | 3 (3) | 10 (16) | 0.7 (0.4)*** | 2 (2)*** |
| Alphaproteobacteria | – | < 1 | < 1 | < 1 | – | < 1 | < 1 | 1 (2) | < 1 | < 1 |
| Betaproteobacteria | < 1 | < 1 | < 1 | < 1 | < 1 | < 1 | 1 (2) | 5 (8) | 0.2 (0.001)** | 0.1 (0.04)** |
| Deltaproteobacteria | 0.003 (0.01)* | 1 (1)* | 0.021 (0.028)* | 0.5 (0.5)* | < 1 | < 1 | < 1 | < 1 | < 1 | < 1 |
| Desulfovibrio | –** | 1 (1)** | 0.003 (0.006)** | 0.5 (0.5)** | –** | 0.2 (0.2)** | 0.002 (0.005)*** | 0.3 (0.2)*** | 0.002 (0.005)** | 0.6 (0.3)** |
| Epsilonproteobacteria | – | < 1 | – | < 1 | –* | 0.02 (0.1)* | < 1 | 2 (5) | –** | 2 (2)** |
| Unknown genus (family Helicobacteraceae) | – | < 1 | < 1 | < 1 | –*** | 1 (1)*** | 0.002 (0.006) | 2 (5) | –*** | 2 (2)*** |
| Gammaproteobacteria | < 1 | < 1 | < 1 | < 1 | < 1 | < 1 | < 1 | 1 (1) | < 1 | < 1 |
| Actinobacteria | < 1 | < 1 | < 1 | < 1 | < 1 | < 1 | < 1 | < 1 | 0.4 (0.2)** | 0.2 (0.1)** |
| TM7 | 0.002 (0.006)* | 0.2 (0.2)* | –** | 0.12 (0.14)** | 0.003 (0.01)* | 0.2 (0.1)* | < 1 | < 1 | 0.001 (0.003)* | 0.2 (0.1)* |
| Deferribacteres | < 1 | < 1 | < 1 | < 1 | < 1 | < 1 | 11 (11) | 9 (10) | < 1 | < 1 |
| Deferribacteres | < 1 | < 1 | < 1 | < 1 | < 1 | < 1 | 11 (11) | 9 (10) | < 1 | < 1 |
| Mucispirillum | < 1 | < 1 | < 1 | < 1 | < 1 | < 1 | 11 (11) | 9 (10) | < 1 | < 1 |
Statistical tests of over-or under-representation of bacterial lineages among sample groups (Room 1 versus Room 2) at each sample location were made at the phylum (bold), class (bold) and genus levels using Wilcoxon's rank-sum test. To correct for multiple testing, the P-values were converted to false discovery rate values (Q-values). (–) corresponds to no sequences present. For values < 1, the exact value is only given if significantly different.
*
P-value < 0.001, Q-value < 0.001,
**
P-value <0.001, Q-value < 0.01
***
P-value < 0.01, Q-value< 0.05.