Table 3.
Taxa in the gastric microbiomea associated with gastric intestinal metaplasia
| Taxon (class; order; family; genus; species) | Mean relative abundance, % | ORb (95% CI) | P c | |
|---|---|---|---|---|
|
| ||||
| Cases | Controls | |||
|
| ||||
| Actinobacteria | ||||
| Actinobacteria; Actinomycetales; Actinomycetaceae; Actinomyces; Actinomyces sp. oral taxon 448 (species) | 0.11 | 0.10 | 1.42 (1.02–1.99) | 0.040 |
| Bacteroidetes | ||||
| Bacteroidia; Bacteroidales; Prevotellaceae; Prevotella; Prevotella baroniae (species) | 0.20 | 0.09 | 1.61 (1.03–2.51) | 0.037 |
| Firmicutes | ||||
| Bacilli; Lactobacillales; Lactobacillaceae; Lactobacillus; Lactobacillus gasseri (species) | 0.02 | 0.04 | 0.75 (0.56–0.99) | 0.046 |
| Bacilli; Lactobacillales; Streptococcaceae; Streptococcus; Streptococcus mutans (species) | 0.03 | 0.03 | 0.61 (0.39–0.94) | 0.024 |
| Clostridia; Clostridiales; Peptostreptococcaceae; Filifactor (genus) | 0.12 | 0.05 | 1.47 (1.03–2.11) | 0.036 |
| Clostridia; Clostridiales; Peptostreptococcaceae; Filifactor; Filifactor alocis (species) | 0.11 | 0.04 | 1.43 (1.03–2.01) | 0.035 |
| Negativicutes; Veillonellales; Veillonellaceae; Veillonella; Veillonella sp. oral taxon 780 (species) | 0.05 | 0.02 | 1.53 (1.09–2.16) | 0.015 |
| Fusobacteria | ||||
| Fusobacteriia; Fusobacteriales; Leptotrichiaceae; Pseudoleptotrichia; Leptotrichia goodfellowii (species) | 0.01 | 0.01 | 1.67 (1.09–2.57) | 0.019 |
| Proteobacteria | ||||
| Deltaproteobacteria; Desulfovibrionales; Desulfomicrobiaceae (family) | 0.02 | 0.01 | 1.50 (1.04–2.17) | 0.031 |
Taxa relative abundances were normalized with the clr transformation. All taxa (phyla, classes, orders, families, genera, species) and covariates (age and race) were selected using conditional logistic regression with elastic-net penalties; leave-one-out cross-validation was conducted using the “cv.clogitL1” function in the clogitL1 R package. Taxa selected by the penalized model and with a nominal P < 0.05 based on standard conditional logistic regression models were shown in the table.
ORs were calculated using standard logistic regression models conditional on matching factors including sex, recruitment site (Bellevue Hospital, Private clinic, Ambulatory Care Center), age categories (<35, 35–49, 50–64, 65+ years), and recruitment year (± 3 years), adjusting for age (continuous) and race (White, African American, Hispanic, Asian).
P values from conditional logistic regression models.