Nematodes represent one of the most abundant and ecologically significant taxonomic groups on earth, playing diverse roles in the cycling of organic matter. However, little is known about their effects on their microbial environment. To explore such effects, we took advantage of the bacteriovore free-living nematode C. elegans, which has been shown to assemble a characteristic gut microbiome from different microbial environments. Worm populations (initially germ-free) were raised in several microbially-distinct natural-like environments emulating the environment from which C. elegans are often isolated, allowing worms to go through four generations encompassing the typical boom-to-bust population growth cycle. Samples from worms, their environments and from control environments without worms, were analyzed using next-generation 16S rRNA gene sequencing. Data analysis showed that microbial diversity increased in the environment, either when worms were present or not, but that trajectories of change were different depending on the presence of worms. Importantly, the presence of worms led with time to convergence in the composition of their microbial environments, particularly affecting the abundance of members of bacterial families which are part of the C. elegans gut microbiome. Our findings reveal that C. elegans not only responds to environmental microbial changes but also shapes them, suggesting new roles for nematodes in modulating environmental microbial diversity and ecosystems.

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.