TABLE 2.
Metagenomic comparisons between TBI and control subjects.
| Target | TBI | Control | TBI FD | BKY p-value | W p-value | FE p-value | Match 2015 FC | ||||
| Genus and species | Count | Avg | SD | Count | Avg | SD | |||||
| Akkermansia spp. | 5 | 2.7E+05 | 5.1E+05 | 3 | 6.7E+04 | 1.1E+05 | 4.01 | 0.36 | 0.34 | 0.44 | Y |
| Alistipes spp. | 5 | 6.9E+05 | 1.3E+06 | 5 | 1.1E+05 | 1.9E+05 | 6.32 | 0.36 | 0.39 | 1 | NR |
| Alistipes onderdonkii | 4 | 7.8E+05 | 1.5E+06 | 5 | 9.1E+04 | 1.9E+05 | 8.56 | 0.35 | 0.34 | 1 | Y |
| Alistipes putredinis | 5 | 6.3E+04 | 9.2E+04 | 5 | 1.5E+04 | 3.2E+04 | 4.15 | 0.36 | 0.34 | 1 | NR |
| Anaerotruncus colihominis | 5 | 2.3E+03 | 4.6E+03 | 5 | 1.3E+02 | 1.3E+02 | 17.98 | 0.12 | 0.10 | 1 | Y |
| Bacteroides spp. | 5 | 1.7E+05 | 3.2E+05 | 5 | 2.7E+05 | 2.2E+05 | 0.64 | 0.73 | 0.60 | 1 | NR |
| Bacteroides caccae | 2 | 5.4E+02 | 7.6E+02 | 4 | 1.2E+04 | 9.9E+03 | 0.04 | 0.23 | 0.08 | 0.52 | Y |
| Bacteroides cellulosilyticus | 1 | 3.4E+03 | N/A | 2 | 4.3E−03 | 4.9E−03 | N/A | N/A | N/A | 1 | NT |
| Bacteroides dorei | 2 | 3.4E+01 | 4.8E+01 | 4 | 2.2E+02 | 2.3E+02 | 0.15 | 0.15 | 0.15 | 0.52 | N (1.03) |
| Bacteroides fragilis | 2 | 3.1E+03 | 3.2E+03 | 0 | N/A | N/A | N/A | N/A | N/A | 0.44 | NR |
| Bacteroides massiliensis | 1 | 1.5E+01 | N/A | 2 | 1.2E+02 | 5.3E+01 | 0.12 | N/A | N/A | 1 | Y |
| Bacteroides ovatus | 3 | 1.0E+04 | 1.5E+04 | 5 | 4.1E+03 | 4.6E+03 | 2.48 | 0.18 | 0.13 | 0.17 | NR |
| Bacteroides plebeius | 2 | 1.8E+01 | 2.6E+01 | 0 | N/A | N/A | N/A | N/A | N/A | 0.44 | NA |
| Bacteroides sartorii | 4 | 4.2E+00 | 7.3E+00 | 2 | 4.3E+00 | 2.5E+00 | 0.97 | 0.23 | 0.22 | 0.52 | N (11) |
| Bacteroides stercoris | 3 | 1.2E+03 | 9.4E+02 | 4 | 1.1E+04 | 1.2E+04 | 0.11 | 0.15 | 0.15 | 1 | N (1.56) |
| Bacteroides stercorirosoris | 3 | 3.4E+02 | 5.2E+02 | 2 | 2.6E+01 | 3.6E+01 | 12.96 | 0.39 | 0.38 | 1 | Y |
| Bacteroides thetaiotaomicron | 2 | 1.8E+04 | 2.5E+04 | 4 | 4.1E+03 | 3.6E+03 | 4.42 | 0.11 | 0.11 | 0.52 | Y |
| Bacteroides uniformis | 4 | 1.4E+05 | 2.6E+05 | 5 | 1.2E+05 | 9.4E+04 | 1.2 | 0.13 | 0.05 | 1 | Y |
| Bacteroides vulgatus | 3 | 7.2E+03 | 8.9E+03 | 5 | 2.1E+04 | 2.1E+04 | 0.34 | 0.15 | 0.07 | 0.17 | N (1.25) |
| Bifidobacterium spp. | 5 | 1.3E+04 | 2.2E+04 | 5 | 3.5E+03 | 2.7E+03 | 3.82 | 0.41 | 0.37 | 1 | NR |
| Bifidobacterium bifidum | 2 | 2.2E+04 | 1.3E+04 | 2 | 2.7E+02 | 3.8E+02 | 79.21 | 0.44 | 0.41 | 1 | N (0.39) |
| Bifidobacterium longum | 3 | 7.7E+03 | 1.2E+04 | 4 | 1.9E+03 | 1.5E+03 | 3.98 | 0.21 | 0.09 | 1 | NR |
| Blautia spp. | 5 | 2.4E+06 | 3.2E+06 | 5 | 3.4E+06 | 3.1E+06 | 0.72 | 0.03 | 0.07 | 1 | NR |
| Clostridium spp. | 5 | 4.2E+02 | 2.6E+02 | 5 | 1.1E+03 | 2.1E+03 | 0.37 | 0.45 | 0.49 | 1 | NR |
| Clostridium leptum | 5 | 3.2E+02 | 1.9E+02 | 5 | 1.1E+03 | 2.1E+03 | 0.29 | 0.32 | 0.30 | 1 | N (5.5) |
| Clostridium symbiosum | 4 | 1.3E+02 | 1.1E+02 | 5 | 2.4E+01 | 2.5E+01 | 5.14 | 0.11 | 0.10 | 1 | Y |
| Collinsella spp. | 5 | 8.1E+04 | 1.5E+05 | 5 | 2.3E+05 | 1.6E+05 | 0.35 | 0.06 | 0.03 | 1 | Y |
| Corynebacterium spp. | 5 | 7.6E+05 | 4.0E+05 | 5 | 7.1E+05 | 1.1E+06 | 1.07 | 0.64 | 0.92 | 1 | NR |
| Corynebacterium propinquum | 2 | 3.6E+00 | 3.3E+00 | 0 | N/A | N/A | N/A | N/A | N/A | 0.44 | NR |
| Desulfovibrio spp. | 4 | 3.6E+03 | 1.2E+03 | 5 | 1.6E+04 | 2.4E+04 | 0.22 | 0.22 | 0.21 | 1 | N (3.44) |
| Dialister spp. | 5 | 1.9E+04 | 2.2E+04 | 5 | 7.7E+03 | 6.4E+03 | 2.45 | 0.05 | 0.06 | 1 | NR |
| Eubacterium spp. | 4 | 1.6E+05 | 1.7E+05 | 5 | 1.2E+05 | 1.1E+05 | 1.36 | 0.71 | 0.66 | 1 | NR |
| Eubacterium rectale | 4 | 1.9E+05 | 1.7E+05 | 5 | 1.2E+05 | 1.1E+05 | 1.67 | 0.17 | 0.08 | 1 | NR |
| Eubacterium siraeum | 4 | 5.7E+03 | 7.3E+03 | 3 | 2.5E+03 | 4.3E+03 | 2.28 | 0.39 | 0.37 | 1 | NR |
| Faecalibacterium prausnitzii | 5 | 2.9E+05 | 4.6E+05 | 5 | 5.3E+05 | 2.8E+05 | 0.55 | 0.01 | 0.01 | 1 | Y |
| Lachnoclostridium spp. | 5 | 2.0E+06 | 1.4E+06 | 5 | 2.2E+06 | 1.2E+06 | 0.93 | 0.05 | 0.02 | 1 | NR |
| Lactobacillus spp. | 5 | 7.0E+03 | 1.5E+04 | 5 | 1.3E+03 | 1.1E+03 | 5.54 | 0.44 | 0.44 | 1 | NR |
| Lactobacillus fermentum | 1 | 1.1E+00 | N/A | 5 | 4.4E+02 | 9.7E+02 | 0.002 | N/A | N/A | 0.048 | N (15.6) |
| Lactobacillus reuteri | 0 | N/A | N/A | 0 | N/A | N/A | N/A | N/A | N/A | 1 | NA |
| Lactobacillus rhamnosus | 5 | 2.1E+01 | 3.2E+01 | 2 | 3.8E+00 | 5.2E+00 | 5.42 | 0.39 | 0.37 | 0.17 | NR |
| Lactobacillus salivarius | 0 | N/A | N/A | 0 | N/A | N/A | N/A | N/A | N/A | 1 | NA |
| Megasphaera massiliensis | 0 | N/A | N/A | 2 | 3.0E+03 | 4.0E+03 | N/A | N/A | N/A | 0.44 | NA |
| Odoribacter spp. | 4 | 1.5E+04 | 1.6E+04 | 4 | 9.7E+03 | 4.9E+03 | 1.59 | 0.03 | 0.05 | 1 | Y |
| Parabacteroides spp. | 5 | 5.5E+03 | 8.3E+03 | 5 | 9.5E+03 | 5.2E+03 | 0.59 | 0.76 | 0.41 | 1 | NR |
| Parabacteroides distasonis | 3 | 1.9E+03 | 2.4E+03 | 5 | 1.8E+03 | 3.2E+03 | 1.11 | 0.30 | 0.28 | 0.17 | Y |
| Parabacteroides goldsteinii | 1 | 2.0E+04 | N/A | 5 | 3.3E+02 | 5.0E+02 | 60.32 | N/A | N/A | 0.048 | NR |
| Parabacteroides merdae | 3 | 6.0E+02 | 1.0E+03 | 5 | 7.4E+03 | 6.1E+03 | 0.08 | 0.13 | 0.05 | 0.17 | Y |
| Prevotella spp. | 5 | 1.7E+05 | 3.8E+05 | 5 | 2.2E+06 | 3.3E+06 | 0.08 | 0.24 | 0.24 | 1 | Y |
| Prevotella copri | 1 | 1.5E+04 | N/A | 3 | 6.0E+04 | 1.0E+05 | 0.25 | N/A | N/A | 0.52 | Y |
| Prevotella stercorea | 0 | N/A | N/A | 1 | 5.4E+02 | N/A | N/A | N/A | N/A | 1 | NA |
| Propionibacterium acnes | 1 | 1.1E+01 | N/A | 2 | 9.6E−01 | 1.1E−01 | 11.14 | N/A | N/A | 1 | NR |
| Ralstonia pickettii | 4 | 2.9E+03 | 3.2E+03 | 1 | N/A | N/A | N/A | N/A | N/A | 0.048 | NR |
| Ruminococcus spp. | 4 | 1.51E+04 | 1.21E+04 | 5 | 5.5E+04 | 6.2E+04 | 0.27 | 0.27 | 0.22 | 1 | NR |
| Ruminococcus bromii | 2 | 2.3E+03 | 1.3E+03 | 4 | 3.4E+03 | 5.5E+03 | 0.68 | 0.31 | 0.29 | 0.52 | Y |
| Streptococcus spp. | 5 | 1.1E+04 | 1.4E+04 | 5 | 3.1E+04 | 4.4E+04 | 0.34 | 0.19 | 0.19 | 1 | Y |
| Streptococcus salivarius | 2 | 1.4E+04 | 1.8E+04 | 4 | 3.3E+02 | 3.1E+02 | 42.29 | 0.16 | 0.14 | 0.52 | Y |
| Subdoligranulum spp. | 4 | 2.9E+04 | 3.1E+04 | 4 | 1.3E+04 | 9.3E+03 | 2.27 | 0.07 | 0.08 | 1 | NR |
| Sutterella spp. | 5 | 8.6E+04 | 1.5E+05 | 5 | 4.3E+04 | 3.1E+04 | 1.99 | 0.07 | 0.03 | 1 | N (0.37) |
| Veillonella spp. | 5 | 2.2E+02 | 2.8E+02 | 5 | 9.8E+02 | 1.8E+03 | 0.23 | 0.35 | 0.28 | 1 | NR |
Results for the TBI cohort are displayed in columns 2, 3 and 4. The Control results are shown in columns 5, 6 and 7. The count column shows the number of detections for each target out of the five samples in each cohort. The average genomic abundance (avg column; by qPCR) and standard deviation (SD column) for each cohort is shown. The fold difference (FD) between abundance of specified qPCR targets in the average TBI FMB compared to control FMBs is shown. Because of the complexity of these comparisons, several methods of statistical comparisons were performed as depicted. BKY, paired t-test with Benjamini, Krieger, and Yekutieli correction for false discovery; W, Mann–Whitney test; FE, Fischer’s exact test for detection differences. The results for the 2020 comparison were compared to those of the 2015 comparison with the original control group to determine if the fold change (FC) was not previously reported (NR) or matched [yes (Y) or no (N)] the prior data, discordances are shown as a numerical value.