New research has found that the environment, especially genetic interactions among social peers, are essential factors in shaping the gut microbiome. Although the role and importance of diet has been widely studied, these findings shed light on the lesser-known influence that genetics has on bacterial composition and, indirectly, on each other.

This study suggests that exchanging commensal gut microbes between people may reveal how genes and microbiomes interact in human disease. Certain genes create an intestinal environment that favors certain bacteria, which can then be transmitted to other bacteria through close social interactions.

Researchers at the University of California (UC) San Diego demonstrated this in a controlled experiment involving more than 4,000 rats. The experiments show that gut bacteria are transmitted through interactions between social partners, or animals living in the same cage.

Nutrition Insight speaks with senior corresponding author Dr. Abraham Palmer, professor of psychiatry and associate director of basic research, about the implications of this study for nutrition research and approaches to the microbiome.

“One of the main findings of this paper is that in addition to diet, genetic differences from person to person also influence the microbiome. One of the interesting aspects of this paper is that we showed that it’s not just an individual’s genotype that influences the microbiome, but also the genotypes of our social partners. Our microbiome is shaped by the individuals we interact with.”

Based on their findings, the researchers suggest a new mechanism of action by which one person’s genetic influence can spread throughout a social group and change the biology of others without altering their DNA.

“Although the details in humans will differ from those found in rats, this study points the way toward understanding the mechanisms of how host and microbial genes work together to cause complex diseases that involve the microbiome, from cardiovascular disease to obesity to Alzheimer’s disease,” said co-author Dr. Rob Knight, professor and director of the Center for Microbiome Innovation at the University of California, San Diego.

Rethinking how bacteria form disease

Professor Palmer suggests that assumptions about the relationship between diet and the microbiome may need to be reconsidered, pointing out, for example, how certain strains of E. coli and Salmonella can act as contagious diseases, causing diarrhea that can be transmitted from person to person.

abraham palmer (Image credit: UC San Diego Health Sciences).“Extending that model suggests that the people around us (our ‘social partners’) may have certain genotypes that can influence our microbiome, even if those changes don’t necessarily cause disease.” ”

“There are probably situations in which social partners improve our health, and there are probably situations in which our social partners make us worse,” he says.

What it means for gut health

Palmer also details how socially shared microbes can help explain why people react differently to the same gut health products and diets.

“As a geneticist, I believe there are two important things in the world: an individual’s genotype and everything else, which I often refer to as the environment. Part of the environment is other people and animals with which we interact. Other people and animals are themselves genetically unique. ”

“What we show in this paper is that, at least for rats, not only your own genotype but also the genotype of your social partner influences the microbiome. As a geneticist, what’s interesting about this idea is that some aspects of the environment (your social partner) actually have a genotype, which means we know how to study them using the tools of genetics,” he explains.

Relationship between genes and bacteria

Publications in nature communications We identified three genetic regions associated with bacteria.

socially interacting rats (Image credit: Katie Holl).The strongest association was found between the rat St6galnac1 gene, which is functionally related to the human gene ST6GAL1 and related to the enterobacterial family Paraprevotella. By adding sugar molecules to the intestinal lining, this gene helps determine which bacteria can survive and thrive there.

“I’m obsessed with this bacterium right now,” said Dr. Amélie Bo, lead author of the study and a researcher at Spain’s Center for Genome Regulation.

“Our results are supported by data from four independent facilities, which means we can follow up in any new environment. They are also significantly stronger compared to most host-microbiome connections. This is a unique opportunity.”

In another area, researchers discovered genes involved in the formation of the protective mucus layer of the intestine and associated with Firmicutes bacteria.

The third region contained the Pip gene, which encodes an antimicrobial molecule and is related to Muribaculaceae bacteria. These are common in rodents and humans.

“What we’ve uncovered is probably just the tip of the iceberg,” Bo said. “These are the bacteria with the strongest signals, but more microorganisms may be affected as better microbiome profiling methods are established.”

Researchers note that in humans, only two genes are reliably associated with gut bacteria. One is the lactase gene, which determines whether an adult can digest milk, and the microorganisms that digest milk. The other is the ABO blood group gene, but the mechanism has not yet been elucidated.

The composition of your gut microbiome can be influenced by social interactions, and the genetics of your closest companions determine which bacteria grow together with your diet and environment.The paper explains that it is difficult to know whether genes, environment, and diet specifically shape the microbiome because nature and nurture are difficult to separate in the real world. This is why it was tested on genetically different rats that were fed the same diet while controlling their interactions with other rats.

Personalization includes social groups

Palmer said his research expands on personalized nutrition approaches, rather than complicating them.

“Now we can think not only about an individual’s genotype, but also about the genotype of their social partners. Both are important to the microbiome.”

Additionally, he believes research on indirect genetic effects could help shape the way microbiome and nutritional tests are designed and interpreted.

“A statistician named George Box once said: ‘All models are wrong, but some are useful.’ Our paper shows that better models for explaining an individual’s microbiome can account for both that individual’s genotype and the genotypes of their social partners.”

“It’s not a perfect model yet, because we know there are a lot of environmental factors involved, but we think it’s a better model,” he suggests.