Living Together? Your Partner’s DNA Could Shape Your Gut Bacteria

Your roommate’s DNA might be altering your internal biology more than you realize.

Research led by the Centre for Genomic Regulation in Barcelona and the University of California (UC) San Diego shows that a host's gut microbiome is shaped by the genes of their social partners.

The gut microbiome and host genetics

Trillions of microbes live in the digestive tract, forming a community called the gut microbiome. This ecosystem regulates immunity and metabolism, and it has been linked to most physiological functions.

Scientists suspect that our DNA determines which bacteria thrive; however, proving this in humans is difficult. Families and friends share more than DNA, they share meals, homes and habits. These shared environments make it nearly impossible to tell if their bacteria come from their genes or their lifestyle. To date, only two human genes – one for digesting milk and another for blood type – have been linked to these internal microbes with any certainty.

Researchers often look at an individual’s DNA to explain their health, but they rarely consider the genes of the people around them. Could your roommate's DNA change your own internal biology?

The new study used a large animal model to identify these “social” genetic effects.

“We were interested to know if the genetic variability of those animals would influence what was living in their gut,” said co-senior author Dr. Abraham Palmer, a professor at UC San Diego.

Palmer and the team aimed to find robust gene–microbe links and measure how genetic signals spill over from one individual to another.

How social partners change the gut microbiome

The researchers studied over 4,000 genetically distinct rats across 4 independent facilities in the United States. By keeping every animal on the exact same diet, the team removed the noise of food choices.

“This was a nice opportunity because the animals are all eating the same food, so we don't have to worry about genes influencing their gut microbiome via their food choices. It's a much simpler system,” explained Palmer.

The team identified three specific genetic regions that dictate microbial makeup.

The strongest link involved the St6galnac1 gene. This gene adds sugar molecules to the mucus lining the gut, providing a food source for a bacterium called Paraprevotella. Other regions linked mucin genes, which are central to the structural integrity of the gut lining, to Firmicutes and an antimicrobial gene called Pip to Muribaculaceae.

However, the results show that a rat’s microbes are not only shaped by its own DNA.

Using computer models, the team identified “indirect genetic effects”; they found that the genes of a rat’s cage-mate significantly altered its own gut microbiome.

When including these social factors, the genetic influence on some bacteria increased four to eight times.

“We’ve probably only uncovered the tip of the iceberg,” said co-senior author Dr. Amelie Baud, a group leader at the Centre for Genomic Regulation.

“These are the bacteria where the signal is strongest, but many more microbes could be affected once we have better microbiome profiling methods,” she added. 

Future research on the gut microbiome and disease

These findings suggest that genetic influences on health are broader than we thought. If your genes influence your partner's gut microbiome, our understanding of disease risk is currently incomplete.

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“This is not magic, but rather the result of genetic influences spilling over to others through social contact,” said Baud.

“Genes shape the gut microbiome, and we found that it is not only our own genes that matter,” she added.

For example, the human version of the rat gene, ST6GAL1, is linked to Paraprevotella; the team suggests that this could affect how people respond to infections like SARS-CoV-2 or develop kidney disease.

However, “the things that live in their [rats'] gut are similar but not identical,” said Palmer. Rats in cages share a very intimate environment, which differs from human social structures. Using 16S sequencing also limits the data to general groups of bacteria rather than specific species.

Future research could include shotgun sequencing to provide more detail.

“I am obsessed with this bacterium now. Our results are supported by data from four independent facilities. They’re remarkably strong compared with most host–microbiome links. It’s a unique opportunity,” said Baud.

“Although the details will be different in humans from what we find in rats, the study points the way towards understanding the mechanisms of how host and microbial genes work together to produce complex diseases that the microbiome is involved in, which range from cardiovascular disease to obesity to Alzheimer’s,” said co-author Dr. Rob Knight, a professor in the Departments of Pediatrics, Bioengineering and Computer Science and Engineering at UC San Diego and the director of the Center for Microbiome Innovation.

Reference: Tonnelé H, Chen D, Morillo F, et al. Genetic architecture and mechanisms of host-microbiome interactions from a multi-cohort analysis of outbred laboratory rats. Nat Commun. 2025;16(1):10126. doi: 10.1038/s41467-025-66105-z

This article is a rework of a press release issued by the Center for Genomic Regulation. Material has been edited for length and content.