Caenorhabditis elegans microbiome members have combinatorial effects on host survival and fitness

Microbiomes are a fundamental part of eukaryotic life and play a role in both host health and fitness. Although microbes are often associated with health and positive effects on the host, certain microbiome compositions are associated with disease. Some disease-associated microbiome compositions are correlated with a change in abundance of a member that is part of the healthy microbiome. We used Caenorhabditis elegans and its experimental microbiome, CeMbio, to explore the interactions that individual microbiome members have with the host, and how the entire microbiome community interacts with the host. We compared the effects of individual microbiome members on host survival to those of the standard C. elegans laboratory diet of E. coli OP50 as well as to the experimental microbiome. We found that while all microbiome members and the whole experimental microbiome are detrimental to C. elegans survival when compared to E. coli, the survival effects of the individual members show more variation when compared to the experimental microbiome. We also measured effects on host fitness by measuring fecundity and development time across the same comparisons. We found consistent effects on fecundity, but development time was more variable when compared to E. coli, but consistently slower when compared to the experimental microbiome. We found that comparisons of the individual microbiome members' effects on host survival and fitness to the effects of the experimental microbiome suggests that the members act in combination with one another. These combinatorial interactions result in specific effects of the microbiome that are different from those of the individual microbiome members that in some cases may be complementary. This further suggests there are potentially different mechanisms resulting in the observed differences in how host survival and fitness respond to individual microbiome members, as well as the whole microbiome. Elucidation of the mechanisms involved in these combinatorial microbe-microbe and host-microbe interactions will lead to greater understanding of the nature of the host-microbiome and host-microbe relationships.