Do behavioral choices depend on animals’ microbiota? To answer this question, we studied how different bacterial assemblies impact the life-history traits of the bacterivore nematode C. elegans using isolated bacteria found in association with wild nematodes in Chilean soil. We identified the first isolate, Iso1, as a novel species of Stenotrophomonas and isolate Iso2 as Bacillus pumilus .

Bacterivore nematodes are the most abundant animals in the biosphere, largely contributing to global biogeochemistry. The effect of environmental microbes as source of associated microbiota and natural diet on their life history traits of nematodes is likely to impact the general health of the biosphere. Caenorhabditis elegans is a unique model to study the behavioral and physiological outputs of different available microbial diets. Nonetheless, most studies are on monoaxenic cultures of laboratory bacteria while the effect of natural microbiota isolates has only recently started to be reported. Here, we quantified physiological, phenotypical and behavioral traits of worms feeding on two bacteria that co-isolated with wild nematodes and tested how combinations of these isolates with other bacteria affected the traits measured. These bacteria were identified as a putative novel species of Stenotrophomonas denominated Stenotrophomonas sp. Iso1 and a strain of Bacillus pumilus designated Iso2. The isolates induced distinctive behaviors and development patterns that changed in mixes of the two bacteria and/or the pathogen Salmonella enterica. Focusing on the degeneration rate of the touch circuit of C. elegans we show that B. pumilus alone is protective while the mix with Stenotrophomonas sp. is degenerative. The analysis of the metabolite content of each isolate and their combination identified NAD+ as potentially neuroprotective. In vivo supplementation shows that NAD+ restores neuroprotection to the mixes and also to individual non-protective bacteria. The results highlight the need to study the physiological effects of bacteria resembling native diets in a multicomponent scenario rather than using single isolates.