Interspecies systems biology links bacterial metabolic pathways to nematode gene expression, chemotaxis behavior, and...

All animals live in tight association with complex microbial communities, yet studying the effects of individual bacteria remains challenging. Bacterial feeding nematodes are powerful systems to study host-microbe interactions as worms can be grown on monoxenic cultures. Here, we present three different types of resources that may assist future research of cross-species interactions in the nematode Pristionchus pacificus and also in other organisms. First, by sequencing the genomes of 84 Pristionchus-associated bacteria, we establish a genomic basis to study host-microbe interactions, and we demonstrate its utility in identifying candidate pathways in the bacteria affecting chemotaxis behavior and survival in the nematodes. Second, we generate nematode transcriptomes of P. pacificus nematodes on 38 bacterial diets and characterize 60 coexpression modules with differential responses to environmental microbiota. Third, we link the microbial genome and host transcriptome data by predicting a global map of more than 2800 metabolic interactions. These interactions represent statistical associations between variation in bacterial metabolic potential and differential transcriptomic responses of coexpression modules in the nematode. Analysis of the interactome identifies several intestinal modules as the primary response layer to diverse microbiota and reveals a number of broadly conserved metabolic interactions. In summary, our study establishes a multiomic framework for future mechanistic studies in P. pacificus, and may also be conceptually transferred and reimplemented in other organisms in order to investigate the evolution of the host-microbe interactomes.