Microbiota restoration: natural and supplemented recovery of human microbial communities

Key Points Many infections self-resolve, but in most cases the mechanism of this resolution is unknown. There are several theories concerning how homeostasis might be restored in the oral cavity, skin, and intestinal and urogenital tracts, the sites that collectively contain the bulk of the human microbiome. The shifts in microbial abundance and diversity are often linked with host immunity, and together these influence whether we remain healthy or become sick. By correlating changes in the microbiota with a diseased state, it should be possible to develop novel interventions that help restore health. Mechanisms that seem to be involved in the restoration of homeostasis include: bacterial co-aggregation; production of biosurfactants, antimicrobials and signalling molecules that target the host or pathogens; competitive exclusion of pathogens; immunomodulation; and factors that increase tight junction barrier function on the host epithelia. The composition of the human microbiota at various body sites can become altered following injury, infection and antibiotic treatment. In this Review, Gregor Reid and colleagues describe how a healthy microbiota can be restored, either naturally or aided by probiotic treatment, following such challenge. In a healthy host, a balance exists between members of the microbiota, such that potential pathogenic and non-pathogenic organisms can be found in apparent harmony. During infection, this balance can become disturbed, leading to often dramatic changes in the composition of the microbiota. For most bacterial infections, nonspecific antibiotics are used, killing the non-pathogenic members of the microbiota as well as the pathogens and leading to a substantial delay in the restoration of a healthy microbiota. However, in some cases, infections can self-resolve without the intervention of antibiotics. In this Review, we explore the mechanisms underlying microbiota restoration following insult (antibiotic or otherwise) to the skin, oral cavity, and gastrointestinal and urogenital tracts, highlighting recovery by natural processes and after probiotic administration.