Table 3.
Differentially abundant OTUs in the family Bacteroidaceae/ Lachnospiraceae/ Bifidobacteriaceae between total and live bacteria in the LM.
| Family | Taxonomic annotation | Similarity (%) | Relative abundance (%) | padj | log2FC |
|---|---|---|---|---|---|
| Bacteroidaceae | Bacteroides vulgatus | 100 | 6.21 | 0.0014 | 1.0 |
| Bacteroides dorei | 100 | 5.08 | 0.00058 | 1.5 | |
| Bacteroides uniformis | 100 | 4.61 | 1.3e−06 | 1.8 | |
| Bacteroides ovatus | 99.4 | 2.54 | 4.2e−05 | 1.9 | |
| Bacteroides xylanisolvens | 100 | 1.67 | 4.2e−05 | 1.5 | |
| Bacteroides ovatus | 99 | 0.75 | 0.0057 | 1.4 | |
| Bacteroides thetaiotaomicron | 99.1 | 0.43 | 0.00040 | 1.6 | |
| Lachnospiraceae | Anaerostipes hadrus | 100 | 2.30 | 0.0024 | − 1.8 |
| Fusicatenibacter saccharivorans | 99.7 | 1.70 | 4.2e−05 | − 1.6 | |
| [Ruminococcus] gnavus | 100 | 1.13 | 0.00024 | − 1.3 | |
| Anaerostipes hadrus | 99.7 | 0.72 | 0.00038 | − 1.9 | |
| Fusicatenibacter saccharivorans | 96.3 | 0.65 | 0.0065 | − 1.6 | |
| [Clostridium] indolis | 94.5 | 0.19 | 0.0024 | − 2.5 | |
| Bifidobacteriaceae | Bifidobacterium longum infantis | 99.4 | 3.49 | 0.0097 | 0.9 |
The LM samples (n = 80; ten subjects, total/live over four gut sites) were used in DESeq2 analysis with full model of ~ subject + gut_sites + live and reduced model of ~ subject + gut_sites, where "live" means live or total bacteria.
Criteria for inclusion: padj < 0.01.
Relative abundance; mean on relative abundance of normalized counts for subset samples.
padj: the Benjamini–Hochberg adjusted P value.
log2FC: log2(live/total).
LM luminal microbiota, OTU operational taxonomic unit.