For Veena Taneja, an immunologist at the Mayo Clinic who was not involved in the study, one of the more surprising tidbits in the findings was that although infants born vaginally shared more strains with their mothers than infants born by C-section did, this difference vanished by three years of age. “People make a big deal out of it” that babies born via C-section might be more at risk for certain diseases, she said. But the findings suggest that maybe it “should not be a big thing.”

(That view was corroborated by a new study published this month in Cell Host & Microbe. It found that babies born via C-section received less of their mother’s microbiomes than babies born vaginally, but that they didn’t miss out because they received more microbes from breast milk.)

As we get older, a sizable portion of our microbiomes continues to come from the people we live with or near. Unsurprisingly, the study by Segata and colleagues found that spouses and other physically intimate partners shared a lot of microbes: 13% of the gut species they shared were of the same strain, as were 38% of their shared oral species.

But people who lived together platonically weren’t far behind, at 12% for shared gut species and 32% for shared oral species. That’s because, as Segata, Valles-Colomer and their team found, the single most important determinant of transmission was time spent together. People living under one roof shared the most strains, but even people living in the same village tended to have more strains in common than people separated by greater distances. The frequency of strain sharing was consistent across different societies, but the team did confirm previous findings that people in non-westernized countries tend to have more diverse microbiomes.

The researchers also found that strains held in common could be lost over time. Twins growing up together had about a 30% strain-sharing level that dropped to about 10% after 30 years of living apart.

Segata thinks it’s likely that most of the other strains of shared species also come from other people — primarily from close contacts like friends or co-workers, but maybe also from people we encounter far more briefly and casually. (Pets, however, are probably not big contributors: Segata said that animals mostly harbor microbial species that don’t typically colonize or persist in us.)

The findings are the strongest evidence to date that we share parts of our microbiomes with the people we spend the most time with. The fact that the authors were able to see this pattern of transmission across the globe, and not just in a single population, was “striking,” said Ilana Brito, an associate professor in biomedical engineering at Cornell University. These data sets are extremely noisy, with many mutations happening across these different organisms, she added. But the team successfully uncovered “the signal across the noise.”

It’s not clear how microbiome organisms spread between people. Kissing and sex explain some of it, but microbes could also be transmitted through droplets spewed by coughs and sneezes, or they could be picked up from contaminated surfaces. There’s also still a lot to learn about which microbes are more easily spread than others. Answering that question is critical for understanding the implications of the idea that microbiome organisms can spread.

Spreading Health or Disease

Now that the extent of sharing has revealed the patterns of distribution of unique microbes, we can examine what happens in disease. “In that sense, I think this work is really fundamental,” Clemente said.

Some diseases that aren’t usually considered contagious could have an overlooked communicable aspect. Studies have found that many people with diseases that don’t spread person to person have microbiomes that seem to be “screwed up,” Finlay said.

Some E. coli strains, for example, may release toxins that could increase the risk of cancer. People with certain colorectal cancers whose microbiomes contain more of a Fusobacterium species tend to have a worse prognosis and worse outcomes with treatment. Gut microbes that affect glucose and insulin levels in the body have been tied to obesity and conditions like metabolic syndrome and even Type 2 diabetes. An unbalanced gut microbiome has been linked to neurodegeneration, and it’s theorized that it might play a role in brain conditions like Alzheimer’s disease.