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Abstract:
Unraveling the multifaceted and bidirectional interactions between microbiota and host represents scientific challenges. Nematodes, with their biological simplicity and genetic tractability, serve as robust models for host-microbiota studies. However, the innate complexity and dynamics of natural microbiota add another layer of difficulty, and as such, how these factors affect the interactions between microbiota and nematodes remains unclear. Employing Pristionchus pacificus, nematodes that feed on microbes derived from insect carcasses, we created a semi-artificial microcosm to simulate natural microbiota succession. Through shotgun metagenomics, we identified 89 and 233 metagenome-assembled genomes at nutrient-rich and nutrient-poor stages of decomposition, respectively. Nematode foraging increased the beta diversity of bacteria, and bacteria of smaller genomes became the dominant species at the nutrient-poor stage. On the nematode side, we found that P. pacificus preferred to consume bacteria capable of producing vitamins and in response to the natural microbiota, nematodes allocated lipids from storage to utilization. Additionally, we showed that horizontally acquired cellulases could assist P. pacificus’ foraging more efficiently and extend the reproductive phase. Lastly, expression levels of Pristionchus species-specific genes are more responsive to the natural microbiota compared to conserved genes, suggesting that species-specific genes might assist the nematodes to adapt to their ecological niche.
