A new rat study published in Nature Communications on December 18 suggests that the genes of a “roommate” can influence the bacteria living in your gut—and that this effect may work both ways.

After studying more than 4,000 rats, researchers found that a rat’s gut microbiome is shaped not only by its own DNA but also by the genetics of the animals it lives with.

Figure 1. Genes shaping your gut—and your roommate’s—via shared bacteria

The findings reveal a new link between genetics and social interactions, showing that while genes themselves are not shared, the gut microbes they help sustain can pass between individuals. Certain genes favor specific bacteria, which can then spread through close social contact.

Researchers Uncover Three Gene–Microbe Connections in Rats

The gut microbiome consists of trillions of microorganisms inhabiting the digestive tract that aid digestion and support overall health. While diet and medications are known to strongly shape these microbial communities, understanding the specific influence of genetics has proven far more challenging.

In humans, only two genes have so far been convincingly linked to gut bacteria. The lactase gene, which determines whether adults can digest milk, is associated with microbes involved in milk digestion. The ABO blood group gene has also been shown to influence gut bacterial communities, although how it does so remains unclear.

Researchers believe many more gene–microbe connections exist, but proving them is challenging because real life blends genetics and environment. Genes can influence diet and lifestyle, which in turn shape the gut microbiome. Meanwhile, family members and friends often share food, living spaces, and microbes, making it difficult to disentangle genetic effects from those of a shared environment.

To overcome these challenges, scientists at the Centre for Genomic Regulation and the University of California San Diego turned to rats. Rats share many key aspects of mammalian biology, and they can be raised under tightly controlled conditions, such as being fed identical diets.

Each animal in the study was genetically distinct and assigned to one of four separate cohorts, each housed at a different U.S. facility with its own care practices. This design allowed researchers to test whether genetic effects were consistent across environments.

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

The strongest link was between the gene St6galnac1, which attaches sugar molecules to gut mucus, and the bacterium Paraprevotella, thought to feed on those sugars; this relationship was observed in all four cohorts.

A second genetic region included multiple mucin genes that help form the gut’s protective mucus layer and was associated with bacteria from the Firmicutes group. A third region contained the Pip gene, which produces an antibacterial molecule, and was linked to bacteria in the Muribaculaceae family, common in both rodents and humans.

Genes with a social side

Thanks to the large dataset, researchers were able, for the first time, to estimate how much of a rat’s microbiome was shaped by its own genes versus the genes of other rats it lived with.

This concept, known as indirect genetic effects, is familiar from cases like a mother’s genes influencing her offspring’s growth or immunity through the environment she provides.

In this study, the controlled conditions allowed scientists to explore indirect genetic effects in a new context. They developed a computational model to distinguish between genetic influences on a rat’s own microbes and those arising from its social partners.

The researchers found that the abundance of certain Muribaculaceae bacteria was influenced by both direct and indirect genetic effects, indicating that some gene-driven impacts can spread socially through microbe exchange between individuals.

When these social (indirect) effects were incorporated into a statistical model, the overall genetic influence on the three identified gene–microbe links increased by four- to eight-fold. The team notes, however, that this boost likely represents only a portion of the full effect.

Dr. Baud notes that the study likely reveals only the strongest signals, with many more microbes potentially affected as profiling improves. By linking genetic effects with microbe transmission, the research shows how one individual’s genes can influence others’ biology. If similar processes occur in humans, genetic impact on health may be underestimated, affecting both personal and social disease risk.

Implications for Human Health

Dr. Baud emphasizes that while the microbiome is linked to immunity, metabolism, and behavior, causal relationships remain unclear [1]. Controlled animal studies like hers help move from correlation to testable mechanisms.

The rat gene St6galnac1 is functionally similar to human ST6GAL1, which is also linked to Paraprevotella, suggesting a conserved mechanism where gut mucus sugars shape microbial communities. The team hypothesizes this interaction could influence infectious diseases like COVID-19, by affecting viral entry, and autoimmune conditions such as IgA nephropathy, via changes in gut antibodies.

Next, they plan to investigate how St6galnac1 modulates Paraprevotella and its downstream effects on the gut and overall health. Dr. Baud highlights the strength and reproducibility of these findings across four facilities, noting the bacterium offers a unique opportunity for follow-up studies.

References:

1. https://scitechdaily.com/your-genes-could-be-affecting-someone-elses-gut/

Cite this article:

Janani R (2025), Your Genes May Shape Someone Else’s Gut, AnaTechMaz, pp. 638