How Your Roommate’s Genes Can Shape Your Gut Microbiome Through Shared Microbes

Scientists have long known that our genes influence our health, but a new large-scale study suggests those genetic effects may not stop at our own bodies. Research published in Nature Communications shows that genes can influence the health of others indirectly, by shaping the gut microbes we share through social contact. In simple terms, the genes of the individuals you live with may affect the bacteria living in your gut, even though their DNA never enters your body.

This discovery comes from an extensive study of rats and reveals a previously underappreciated way in which genetics and social life intersect—through the exchange of gut microbes.

Genes and Gut Bacteria Are More Social Than We Thought

The gut microbiome is made up of trillions of microorganisms that live in the digestive tract. These microbes play essential roles in digestion, metabolism, immunity, and overall health. Diet, medication, and environment are well-known factors that shape the microbiome, but understanding the role of genetics has been far more challenging.

One major problem is that in humans, genes and environment are deeply intertwined. Families and friends tend to share meals, homes, habits, and microbes. This makes it difficult to separate whether a particular gut bacterium is influenced by genetics, lifestyle, or simple proximity to other people.

To get around this problem, researchers turned to rats.

Why Rats Were the Perfect Model

The study was led by scientists at the Center for Genomic Regulation (CRG) in Barcelona, in collaboration with the University of California San Diego. Rats are ideal for this type of research because they share many biological features with humans, yet they can be raised under highly controlled conditions.

In this case, the researchers analyzed more than 4,000 genetically unique rats. All animals were fed controlled diets, but they came from four different cohorts, each housed in a different facility in the United States with slightly different care routines. This design allowed the scientists to test whether genetic effects on gut microbes were consistent across environments.

The result was one of the largest and most detailed datasets ever assembled to study host genetics and the gut microbiome.

Three New Gene–Microbe Links Discovered

By combining genetic data with microbiome sequencing from all 4,000 rats, the researchers identified three genetic regions that consistently influenced gut bacteria across all four cohorts.

The strongest and most consistent link involved the gene St6galnac1. This gene helps add sugar molecules to the mucus lining of the gut. The study found that rats with certain variants of this gene had higher levels of Paraprevotella, a type of bacterium that likely feeds on these sugar molecules. This association was observed in all four facilities, making it particularly robust.

A second genetic region contained several mucin genes, which are responsible for producing the mucus layer that protects the gut lining. Variations in these genes were linked to changes in bacteria from the Firmicutes group, a large bacterial family that includes many species involved in digestion and energy metabolism.

The third region included the Pip gene, which encodes an antibacterial molecule. Variants in this gene were associated with differences in bacteria belonging to the Muribaculaceae family. These bacteria are common in rodents and are also found in humans, making the finding especially interesting for future research.

Genes Can Have Social Effects Without Moving Between Bodies

One of the most striking findings of the study is that genes can affect the microbiome indirectly, through social interactions. This concept is known as indirect genetic effects.

Genes themselves do not jump from one individual to another. Microbes, however, can. When animals live together, they exchange microbes through close contact, shared environments, and grooming. If certain genes favor the growth of specific microbes, those microbes can then spread to other individuals.

Using the large dataset, the researchers built a computational model that separated the effects of a rat’s own genes from the effects of the genes of its cage mates. This allowed them to quantify how much of the gut microbiome was shaped directly by an individual’s genetics and how much was shaped indirectly through social microbial transmission.

They found that some bacteria, particularly members of the Muribaculaceae family, were influenced by both direct and indirect genetic effects. When these social genetic effects were included in the analysis, the total estimated genetic influence increased by four to eight times for the newly discovered gene–microbe links.

This suggests that many genetic influences on the microbiome may have been dramatically underestimated in past studies.

What This Could Mean for Human Health

Although the study was conducted in rats, the findings raise important questions about humans. There is growing evidence that the human gut microbiome plays a role in conditions ranging from immune disorders and metabolic disease to mental health and behavior.

If similar indirect genetic effects exist in humans, it could mean that one person’s genes influence not only their own disease risk, but also the disease risk of people they live with. In large population studies, this social layer of genetic influence is rarely considered.

The study also provides clues about potential shared mechanisms across species. The rat gene St6galnac1 is functionally related to the human gene ST6GAL1, which has been linked in other research to Paraprevotella levels in the human gut. This suggests that the way the gut is coated with sugars may be a conserved biological mechanism shaping microbial communities.

Possible Links to Infection and Autoimmune Disease

The researchers also discuss intriguing hypotheses about how these gene–microbe interactions could affect disease.

ST6GAL1 has previously been linked to breakthrough SARS-CoV-2 infections, where individuals become infected with COVID-19 despite vaccination. Separately, Paraprevotella has been shown to induce the degradation of digestive enzymes that viruses use to enter host cells. This raises the possibility that genetic variation in ST6GAL1 could influence Paraprevotella abundance and, indirectly, susceptibility to viral infection.

Another hypothesis relates to IgA nephropathy, an autoimmune kidney disease. Paraprevotella may alter IgA antibodies in the gut. When IgA is modified in certain ways, it can leak into the bloodstream, form clumps, and damage the kidneys. While these ideas remain speculative, the study provides a genetic and microbial framework for testing them.

Why This Study Matters

This research highlights a powerful and often overlooked idea: genes have social lives. By shaping the microbes we carry, our genes can influence the biology of others without ever changing their DNA.

The authors emphasize that their findings likely represent only the tip of the iceberg. As microbiome profiling becomes more precise, many more gene–microbe links may emerge, along with their social effects.

For now, the study offers a new lens through which to view genetics, health, and social interaction—not as isolated factors, but as deeply connected systems.

Research paper:
Genetic architecture and mechanisms of host-microbiome interactions from a multicohort analysis of outbred laboratory rats, Nature Communications (2025).
https://doi.org/10.1038/s41467-025-66105-z