Cohabitating people share about a quarter of their gut and oral microbiota

People who live together share more oral and gut microbes with each other than with other people in their communities, according to a study publishing June 15 in the Cell Press journal Cell Press Blue. This was true regardless of the cohabitants’ relationships—siblings, parents, and offspring all shared similar numbers of microbial strains, and romantic partners shared even more oral (but not gut) microbes with each other, likely due to kissing. The researchers also found a link between more transmissible microbes and health, particularly type 2 diabetes. The findings could help design more targeted therapies for improving people’s microbiomes. 

“Who we decide to share our homes with can have a huge influence on our microbiomes, which has potential consequences for our health,” says first author and computational biologist Vitor Heidrich of the University of Trento, Italy. 

Previous studies have revealed how the infant microbiome is shaped, but much less is known about what impacts our microbiomes later in life. There’s also relatively little known about interactions and transmissions between microbiomes in different body sites within the same individual, such as between the oral cavity and gastrointestinal tract, for example. 

“We know that diet and other lifestyle factors can change our microbiome, but these factors are acting on the microbes that are already within us,” says senior author and computational biologist Nicola Segata of the University of Trento, Italy. “It doesn’t solve the question about where the microbes are coming from.”  

To understand how microbiomes are transmitted between individuals, the researchers analyzed metagenomic data from the oral and gut microbiomes of 430 people living in 207 households in Italy and Fiji. They identified microbial strains within each individual and then compared strains between people who lived together to see whether transmission was occurring. 

They found that cohabitants shared significantly more oral and gut strains than people from the same population who did not live together. On average, cohabiting individuals shared 19% of their gut microbiome strains and 26% of their oral microbiome strains, compared to 6% and 0%, respectively, for individuals living in different households. Romantic partners shared an average of 44% of their oral microbes with each other, likely due to kissing. 

“It was surprising to see that the oral microbiome is not much more transmissible than the gut microbiome,” says Segata. “This speaks to the fact that most of our microbes are kind of everywhere, and the microbial exchange is very high, but our microbiomes are shaped more at the level of whether our body accepts the colonization of these bacteria.” 

When they estimated the transmissibility of the different microbes, the researchers found that the most transmissible gut microbes were associated with biomarkers of type 2 diabetes and poor cardiometabolic health. In the oral cavity, the most transmissible species included two microbes that are associated with colorectal cancer and several opportunistic pathogens (bacteria that are usually harmless but can cause serious disease in immunocompromised people). 

“It’s difficult to speculate why this is, but it might be a reflection of their ability to withstand stress,” says Heidrich. “The same traits that help them survive the journey between humans may also allow them to thrive in the inflammatory conditions associated with disease.” 

The findings could help improve microbiome treatments, including probiotic and fecal microbiota transplant therapies, the researchers say. 

“Understanding natural microbiome transmission can inform more targeted artificial transmission solutions,” says Heidrich. “If we can identify the characteristics that makes some microbes more transmissible than others, and the constraints that make beneficial microbes less transmissible, we can apply that to make fecal microbiota transplants much more effective.” 

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This research was supported by funding from the European Research Council, NextGenerationEU, the Italian Ministry of Health, the Associazione Italiana per la Ricerca sul Cancro, and the Italian Ministry of Research. 

Cell Press Blue, Heidrich et al., “Strain transmission links human microbiomes along the oral-gut axis and across cohabiting individuals” https://www.cell.com/cell-press-blue/fulltext/S3051-3839(26)00032-0

Cell Press Blue (@cellpressblue) is a highly selective open-access journal from Cell Press that publishes cutting-edge research from across the sciences. The journal welcomes advances in biology, medicine, chemistry, physics, materials science, energy, environmental science, and sustainability, as well as interdisciplinary work that forges new connections between these fields.