TABLE 1.
Bacterial taxa differentially represented under different treatment conditionsa
| Lineageb | No. of OTUs | Mean count (SD) |
RFc importance score | |||||
|---|---|---|---|---|---|---|---|---|
| Control |
FNR |
Prebiotics |
||||||
| Unchallenged | Challenged | Unchallenged | Challenged | Unchallenged | Challenged | |||
| Bacteroidetes, Bacteroidia, Bacteroidales, Rikenellaceae | 10 | 2.88 (8.1) | 0.15 (0.4) | 86.01 (247.4) | 91.91 (263.2) | 0.24 (0.7) | 0.22 (0.6) | 0.06 |
| Firmicutes, Clostridia, Clostridiales, Christensenellaceae | 4 | 0.02 (0.02) | 0.06 (0.1) | 0.01 (0.02) | 0.00 (0.0) | 2.25 (2.1) | 4.48 (2.9) | 0.06 |
| Tenericutes, Mollicutes, RF39 | 4 | 8.99 (15.0) | 12.29 (21.9) | 0.01 (0.02) | 0.13 (0.2) | 0.66 (1.3) | 5.46 (10.9) | 0.03 |
| Firmicutes, Clostridia, Clostridiales, Ruminococcaceae, Faecalibacterium | 6 | 94.54 (117.0) | 209.77 (282.2) | 15.79 (16.4) | 29.71 (27.9) | 43.89 (46.3) | 147.97 (133.5) | 0.02 |
| Firmicutes, Clostridia, Clostridiales, Ruminococcaceae | 52 | 13.02 (37.7) | 27.34 (86.5) | 4.75 (14.8) | 4.51 (12.6) | 10.96 (31.8) | 19.25 (69.4) | 0.01 |
| Firmicutes, Clostridia, Clostridiales, Ruminococcaceae, Anaerotruncus | 1 | 11.46 | 15.50 | 7.32 | 5.89 | 4.68 | 2.79 | 0.01 |
| Firmicutes, Clostridia, Clostridiales | 61 | 18.16 (38.3) | 20.63 (42.9) | 29.77 (76.0) | 22.04 (64.0) | 35.32 (90.5) | 23.41 (45.3) | 0.01 |
| Firmicutes, Erysipelotrichi, Erysipelotrichales, Erysipelotrichaceae | 3 | 5.69 (3.8) | 7.87 (2.9) | 6.08 (4.6) | 7.35 (9.1) | 5.99 (6.2) | 26.70 (39.9) | 0.01 |
| Firmicutes, Clostridia, Clostridiales, Lachnospiraceae, Dorea | 3 | 1.45 (1.7) | 1.74 (0.9) | 0.10 (0.2) | 0.14 (0.2) | 0.51 (0.9) | 4.48 (4.8) | 0.01 |
| Firmicutes, Clostridia, Clostridiales, Lachnospiraceae, Blautia | 1 | 8.61 | 1.82 | 0.21 | 0.39 | 0.04 | 0.43 | 0.01 |
| Firmicutes, Clostridia, Clostridiales, Ruminococcaceae, Oscillospira | 10 | 21.76 (34.4) | 24.28 (35.2) | 7.80 (13.3) | 9.02 (11.4) | 12.18 (18.7) | 19.48 (26.7) | 0.01 |
| Firmicutes, Clostridia, Clostridiales, Lachnospiraceae, Coprococcus | 5 | 10.04 (17.9) | 18.12 (35.6) | 11.08 (16.9) | 11.26 (13.9) | 11.99 (14.3) | 36.88 (59.6) | 0.01 |
a
Differential representation determined by Kruskal-Wallis tests with Bonferroni's correction (P < 0.05). Only lineages considered to be highly discriminative by random forest analysis (importance score ≥0.01) are included in the table.
b
Listed by phylum, class, order, family (if available), and genus (if available).
c
RF, random forest.