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No strain, no gain: within-host bacterial microdiversity and human health | Infection and Immunity
The bacterial world is teeming with diversity, from cyanobacteria to episymbiotic Saccharibacteria to the well-studied Escherichia coli. However, even within a single species, organisms vary in their gene content and gene sequences, leading to significant functional differences across very closely related bacteria. For instance, two isolates of E. coli may share only 40% of the same gene content, allowing different strains to function as human pathogens, gut mutualists, or environmental specialists (1–4). Although this population-level diversity in bacteria has been long-recognized, recent studies have increasingly emphasized that a single person can harbor multiple genotypes of a species at the same time within a single body site. High within-host intra-species diversity can occur in the human microbiota, including in the gut, skin, oral cavity, and vagina. Furthermore, although acute infections are primarily monoclonal, chronic infections can often be polyclonal. Both in the microbiota and in chronic infections, this high intra-species diversity can occur when multiple strains colonize a site over time and when bacteria diversify through evolutionary processes.
