Close social contact helps define the adult microbiome

Infants are born without microbial passengers and acquire them early in life. Researchers know that particular microbial species transmitted during childbirth and nursing seed an infant’s microbiome, but that microbiome becomes more complex as that infant grows into an adult. “One of the open questions is, ‘Why do we get the strains that we get?’” says microbial evolutionary biologist Nandita Garud of the University of California, Los Angeles. In a new study, researchers led by Nicola Segata at the University of Trento find that the people we are closest to may provide the answer. Close social contact is an important predictor of which bacterial strains within species get shared between people (Nature 2023, DOI: 10.1038/s41586-022-05620-1).

Working with oral and gut microbiome DNA sequences from more than 9,700 people around the world, Segata and colleagues used evolutionary relationships between genes unique to each bacterial species to identify strains shared between individuals. When two people shared closely related bacteria, the researchers could infer that one person must have passed the strain to another. The data set is unusually large and encompasses more types of social relationships than prior studies, says Garud, who was not involved in the work.

The researchers found that the parental microbiome’s impact wanes over time. Adults share about as many bacterial strains with members of their household as with parents they live apart from, and the proportion of strains shared within a household increases with time spent living together. Members of the same small community also share more strains among themselves than with the wider population.

In recent years, researchers have proposed that social transmission of microbes could influence conditions such as diabetes and cardiovascular disease that have long been considered noncommunicable but are affected by the microbiome. Study authors Mireia Valles Colomer and Aitor Blanco Míguez of the University of Trento say in an email that their next step will be to ask how the most transmissible microbes they observed correlate with human health and whether those microbes might be risk factors for disease.