Strain dropouts reveal interactions that govern the metabolic output of the gut microbiome

The gut microbiome is complex, raising questions about the role of individual strains in the community. Here, we address this question by constructing variants of a complex defined community in which we eliminate strains that occupy the bile acid 7a-dehydroxylation niche. Omitting Clostridium scindens (Cs) and Clostridium hylemonae (Ch) eliminates secondary bile acid production and reshapes the community in a highly specific manner: eight strains change in relative abundance by >100-fold. In single-strain dropout communities, Cs and Ch reach the same relative abundance and dehydroxylate bile acids to a similar extent. However, Clostridium sporogenes increases >1,000-fold in the DCs but not DCh dropout, reshaping the pool of microbiome-derived phenylalanine metabolites. Thus, strains that are functionally redundant within a niche can have widely varying impacts outside the niche, and a strain swap can ripple through the community in an unpredictable manner, resulting in a large impact on an unrelated community-level phenotype.

Automated summary

By constructing variant communities of a complex defined microbial community, we found that removing specific strains occupying the bile acid 7a-dehydroxylation niche resulted in significant changes in the community composition and function. Strains that are functionally redundant within a niche can have differential impacts outside the niche, leading to unpredictable effects on unrelated community-level phenotypes. This study highlights the complexity of the gut microbiome and the importance of understanding individual strain dynamics in the context of the entire community.