People close to you influence your gut bacteria

By Dr. Tim Sandle
SCIENCE EDITOR

DIGITAL JOURNAL 
December 25, 2025

People crowd the beach in Valencia on July 5, 2024 - Copyright AFP ERNESTO BENAVIDES

Microbiologists studying thousands of rats discovered that gut bacteria are shaped by both personal genetics and the genetics of social partners. The research shows how genes promote certain microbes that can spread between individuals living together.

When researchers accounted for this ‘social sharing’, genetic influence on the microbiome turned out to be much stronger than previously thought. The study suggests genes can affect others indirectly, without DNA ever being exchanged.

Genes shape the gut microbiome and researchers found that it is not just our own genes that matter.

In essence, the findings point to a new way genetics and social interactions are connected. Certain commensal gut microbes can move between individuals through close contact.

While genes themselves stay put, microbes do not. The study showed that some genes promote the growth of specific gut bacteria, and those bacteria can spread socially.
Why the gut microbiome matters

The gut microbiome consists of trillions of microorganisms living in the digestive tract. These organisms play important roles in digestion and overall health. Diet and medications are known to strongly influence these microbial communities, but understanding how genetics contributes has been far more challenging.
Social interaction

Genes can shape diet and lifestyle choices, which then influence the gut microbiome. At the same time, families and friends often share food, living spaces, and microbes, making it hard to separate nature from nurture.
Animal models

The researchers used rats for their research since rats share many key aspects of mammalian biology and can be raised under tightly controlled conditions, including identical diets.

Each rat in the study was genetically unique and belonged to one of four separate cohorts. These cohorts were housed at different facilities across the United States and followed different care routines, allowing researchers to test whether genetic effects remained 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 association involved the gene St6galnac1, which adds sugar molecules to the mucus lining of the gut. This gene was linked to higher levels of Paraprevotella, a bacterium believed to feed on these sugars. This connection appeared in every cohort.


Paraprevotella is a Gram-negative, non-spore-forming, pleomorphic and anaerobic genus of bacteria.

There is a possible link to IgA nephropathy, an autoimmune kidney disease. The bacterium Paraprevotella may alter the immunoglobulin IgA, an antibody that normally protects the gut. When altered, IgA can leak into the bloodstream and form clumps that damage the kidneys, which is a defining feature of IgA nephropathy.

A second genetic region included several 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 from the Muribaculaceae family. These bacteria are common in rodents and are also found in humans

.Bacteriologist taking a bacterial culture from a Petri dish. Image: Tim Sandle
Key findings

The researchers developed a computational model to separate the influence of a rat’s own genes on its gut microbes from the influence of its social partners.

The scientists found that the abundance of some Muribaculaceae bacteria was shaped by both direct and indirect genetic influences. This indicates that certain genetic effects can spread socially through the exchange of microbes.


Muribaculaceae are major utilisers of mucus-derived monosaccharides in the gut.
Research significance

The large size of the study allowed researchers to estimate how much of a rat’s microbiome was shaped by its own genes versus the genes of the rats it lived with.

A familiar example of this concept, known as indirect genetic effects, occurs when a mother’s genes influence her offspring’s growth or immune system through the environment she provides.

What the research points to is that genetic effects from one individual can spread through social groups by way of gut microbes, changing the biology of others without altering their DNA. This means we need to consider how genes shape not only an individual’s disease risk, but also the disease risk of people around them.

The research appears in the journal Nature Communications, titled “Genetic architecture and mechanisms of host-microbiome interactions from a multi-cohort analysis of outbred laboratory rats”.