SourceTrackerAnalysis to find contribution of ASVs from reagent controls

We performed 16S rRNA gene sequencing to assess treatment effects on the mouse gut microbiome. H. pylori infection reduced Shannon diversity (Figure 5A), while standard care of control antibiotic (amoxicillin (1)+clarithromycin (10)+omeprazole (10) (mg/Kg)) treatment (AB) showed a trend of increased diversity, though still lower overall. A triple therapy of AZ (AZPA) treatment significantly increased bacterial richness and evenness (p<0.05) and DISPA also increased Shannon diversity compared to AB (p<0.05), indicating that antibiotics reduce diversity, but drug combinations with AB enhance it. Untreated H. pylori infection also reduced Shannon diversity (Figure 5A). PCoA analysis showed that H. pylori-infected mice clustered separately, while treatment groups exhibited similar microbiome profiles due to antibiotics (Figure 5B). The microbiome of DIS triple therapy (DISPA) resembled AB-treated mice, suggesting modulation by antibiotics and PPI (Figure 5C). AZ treatment also altered the microbiome, with AZPA-driven changes likely due to both antibiotics and AZ (Figure 5D).

In this study, employing a culture-dependent approach, we found that dauers harvested from 10 different natural-like microbially diverse environments and 2 synthetic microbial communities are largely devoid of gut bacteria. Furthermore, through targeted sequencing method demonstrate that only 0.38± 0.24% of bacterial signal in Dauer’s gut suggesting lack of bonafide gut microbiome. Our result suggest that host gut-microbiome interactions in C. elegans do not persist continuously across successive generation.