Table 2.
Bacteria Discriminative for Respiratory Tract Infection Groups as Identified by metagenomeSeq and Random Forest
| Operational Taxonomic Unit | Log Fold Change | P Value | Adjusted P Value | Methoda |
|---|---|---|---|---|
| Associated with disease (RTI) | ||||
| Bacillus (25) | −1.13 | .0001 | .0006 | Both |
| Klebsiella (7) | −5.48 | <.0001 | <.0001 | MGS |
| Anoxybacillus (33) | −2.25 | <.0001 | <.0001 | MGS |
| Thermus thermophilus (26) | −1.43 | .0003 | .0017 | MGS |
| Arthrobacter (12) | −1.41 | .0104 | .0359 | MGS |
| Xanthobacteraceae (97) | −1.40 | .0000 | <.0001 | MGS |
| Actinomyces (57) | −1.18 | .0001 | .0007 | MGS |
| Associated with health (absence of RTI) | ||||
| Caulobacteraceae (18) | 4.58 | <.0001 | <.0001 | Both |
| Schlegelella (40) | 3.99 | <.0001 | <.0001 | Both |
| Pseudomonas putida (49) | 1.10 | <.0001 | .0001 | Both |
| Corynebacterium (91) | 3.30 | <.0001 | <.0001 | MGS |
| Acinetobacter (10) | 2.82 | <.0001 | .0001 | MGS |
| Acinetobacter (47) | 2.38 | <.0001 | <.0001 | MGS |
| Acinetobacter soli (41) | 1.78 | .0001 | .0007 | MGS |
| Stenotrophomonas maltophilia (58) | 1.40 | <.0001 | <.0001 | MGS |
| Pseudomonas (23) | 1.25 | .0007 | .0034 | MGS |
| Acinetobacter (11) | 1.15 | <.0001 | <.0001 | MGS |
| Wautersiella (61) | 1.09 | .0001 | .0005 | MGS |
| Corynebacterium propinquum (2) | 0.50 | .2937 | .4581 | RFb |
| Pseudomonas syringae (27) | 0.12 | .5946 | .7027 | RF |
P values have been adjusted using Benjamini-Hochberg correction for multiple testing.
Abbreviation: MGS, metagenomeSeq; RF, random forest; RTI, respiratory tract infection; VSURF, variable selection using random forests.
aBoth methods adjusted for age.
bVariable selection by VSURF.