Strain-level ecological interactions in human gut microbiomes

Gut microbial community composition varies from one person to another. Potentially, this means the ecological interactions experienced by individual strains or species also vary among microbiomes of different people. However, testing this directly in human microbiomes and identifying associated ecological drivers is challenging. Here, we use replicated anaerobic microcosms to quantify variability of population growth for a key commensal species among microbiome samples from different individuals, and to identify underlying intra- and interspecific interactions. In a reciprocal transplant experiment, both absolute and relative growth perfomance of different Escherichia coli strains varied among gut microbiome samples from different healthy individuals. This was partly explained by intraspecific competition: ecological success of individual E. coli strains was associated with displacement of resident conspecifics. However, the determinants of E. coli growth varied among samples from different individuals. In one microbiome sample with a distinctive taxonomic composition, culture acidification by resident microbes impaired growth of all E. coli strains. These results suggest inter-individual microbiome variation is a key driver of susceptibility to colonisation by incoming bacteria, impacting the relative success of different strains and thereby helping to explain the structure and diversity of human microbiomes.