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Introduction: The development and metabolism of nematodes can be significantly impacted by the microbes in their environment. Adaptation to environmental stimuli may also be facilitated by the creation of new genes. About one third of genes in the nematode Pristionchus pacificus are characterized as taxonomically-restricted orphan genes, i.e. genes whose function can't be inferred from homology. Objectives: Our main goal is to gain insight on the interactions between the nematode P. pacificus and bacterial food sources by answering two questions: do novel genes contribute to environmental adaptation and which are the bacterial metabolites that modulate the environmentally responsive networks containing those novel genes. Materials & methods: To determine the functionality of novel genes, we generated transcriptome profiles of P. pacificus worms that were grown on 24 different bacteria isolated from Pristionchus-associated environments1 and clustered the genes in co-expression modules. In order to characterize the bacterial metabolic potential, we performed whole genome sequencing of 93 bacterial strains and computationally identified the metabolic pathways present or absent. This allowed us to correlate the metabolic potential of bacteria with various nematode traits including survival, chemoattraction and the response of the previously identified co-expression modules. Results: Based on the co-expression analysis, we identified 28 large modules that harbor 3,727 diplogastrid-specific orphan genes and that respond dynamically to different bacteria. These modules showed distinct regulatory architecture and differential expression patterns across development. Integrative analysis associated most coexpression modules with biological processes or tissues, which resulted in the first functional annotation for thousands of orphan genes. In addition, the presence of bacterial metabolic pathways was associated with higher indexes of chemotaxis and survival. For example, the ability of bacterial diets to supply spermidine and its derivative, spermine, vitamins of the B complex and molybdenum cofactor correlated with higher chemoattraction and survival compared to bacteria lacking those biosynthesis pathways. The only case of lower chemoattraction was associated with the production of propionic acid from the bacteria. Conclusion: We showed that new genes aid environmental adaptation in the nematode P. pacificus by exploring the transcriptomic changes after exposure to different bacteria2 . This allowed us to better understand the plastic response to diverse environmental microbiota. We are currently extending this work to include transcriptomic data on a larger number of bacterial food sources in order to improve the resolution of the co-expression network and explore how metabolic pathways in the worm are regulated by the presence/absence of metabolites.
