How our microbiome is shaped by family, friends and even neighbours

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The microbial communities living in and on our bodies evolve through our lives and are shaped by our social interactions, a study has found.Credit: Moyo Studio/E+/Getty

People living in the same household share more than just a roof (and pints of milk). Be they family or flatmate, housemates tend to have the same microbes colonizing their bodies, and the longer the cohabitation, the more similar these microbiomes become.

The conclusion — based on an 18 January study in Nature of the gut and mouth microbiomes of thousands of people from around the world1 — raises the possibility that diseases linked to microbiome dysfunction, including cancer, diabetes and obesity, could be partly transmissible.

“This study is the most comprehensive look to date at when and why microbes transmit into the gut and oral microbiomes,” says Katherine Xue, a microbiome researcher at Stanford University in California. “New microbes can continue to reshape our microbiomes throughout our lives.”

Most studies on how humans acquire their microbiomes have focused on people’s first contact with microbes: through their mums. “It’s key to providing a microbial starter kit,” says Hilary Browne, a microbiologist at the Wellcome Sanger Institute in Hinxton, UK.

Starter kit

To examine how and why this starter kit changes over a person’s life, a team led by microbiome researchers Mireia Valles-Colomer and Nicola Segata at the University of Trento, Italy, analysed DNA from nearly 10,000 stool and saliva samples from people all over the world, from rural villages in Argentina to a city in China to populations in Europe and North America. The researchers then looked for overlap in the strains of microbes found in the guts and mouths of family members, partners, housemates and other social contacts.

The analysis confirmed the strong link between the microbiomes of mothers and those of their children, particularly early in life. During an infant’s first year of life, half of the microbial strains in their guts were shared with their mothers. The extent of overlap decreased as children aged — but did not vanish. Older people, aged 50–85, still had gut microbe strains in common with their mothers.

Other family members were also an important source of gut microbes. After the age of 4, children shared similar numbers of microbe strains with their father as with their mother. And twins who moved away from each other shared fewer gut microbes the longer they had lived apart. Sharing occurred even between households in several of the rural-living groups: people from separate households in the same village tended to have more overlap in gut microbes than did people from different villages.

The maternal microbial starter kit has less of an impact on the microbes in people’s mouths, compared to those in their guts. The researchers found that people who lived together — no matter their relationship — tended to have the same microbe strains in their mouths, and the longer they lived together, the more they shared. Couples, though, tended to share strains to a greater extent than children and parents.

The researchers also found that the extent of household sharing was no less in people from Westernized cultures than it was elsewhere. Ilana Brito, a microbiome researcher at Cornell University in Ithaca, New York, was surprised by that insight. She expected that microbiome transmission would be harder to detect in Western populations, because of factors, such as better public-health infrastructure, that might impede spread.

“This is going to be a very important paper,” says Browne, because it provides a basis to study how the spread of microbes that aren’t thought of as pathogens can contribute to disease. Doing so will require linking specific microbes — and their spread — to people’s health in long-term studies, a direction that microbiome research is now heading in, Browne adds. “We’re going to be able to answer some of those questions.”

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