What is already known on this topic
The gut microbiota can be influenced by many factors, including diet and lifestyle. People migrating to industrialized societies from less industrialized ones tend to show changes in their microbiota composition and diversity. But little is known about how industrialization can shape the genomes of individual bacterial species in the human gut.
What this research adds
By studying thousands of bacterial strains from stool samples of 37 people from 15 communities in seven countries, researchers have found that gut bacterial populations can remake themselves by passing genes among each other. This process — called horizontal gene transfer — occurs more frequently in the microbiota of people living in industrialized societies, likely as a result of their diets and lifestyles.
The findings suggest that gut bacteria can acquire new functions based on their host’s lifestyle and that high rates of horizontal gene transfer may be linked to industrialization.
Unrelated bacterial species often swap genes for a variety of traits, including antibiotic resistance. Now, researchers have found that gut bacteria from people in industrialized countries exchange genes at much higher rates than bacteria from people living in non-industrialized societies.
The findings, published in Cell, suggest that gut bacteria can acquire new functions based on their host’s lifestyle and that high rates of microbial gene swaps may be linked to industrialization.
“One unexpected consequence of humans living in cities may be that we’ve created conditions that are very conducive to the bacteria that inhabit our guts exchanging genes with each other,” says study senior author Eric Alm at the Massachusetts Institute of Technology and the Broad Institute of MIT and Harvard.
Scientists have known that the gut microbiota can be influenced by many factors, including diet and lifestyle. People migrating to industrialized societies from less industrialized ones tend to show changes in their microbiota composition and diversity. But little is known about how industrialization can shape the genomes of individual bacterial species in the human gut.
To address this question, researchers led by Mathieu Groussin and Mathilde Poyet studied more than 4,000 bacterial strains from stool samples of 37 people from 15 communities in seven countries.
The researchers focused on a process called horizontal gene transfer, which occurs when bacterial species pass genes among each other. To estimate with precision when these gene transfers occurred, the team compared genetic differences between different species of gut microbes.
When comparing bacteria from the same person, the researchers found a much higher rate of genetic similarity than that observed in bacteria taken from two different people. This suggests that horizontal gene transfer can happen within the lifetime of a person, the researcher say.
“One of the really exciting things about this paper is we were finally able to answer the question of whether the rate of horizontal transfer has been high in the human microbiome over the last few millennia, or is it true that within each person’s lifetime, the bugs in their gut are constantly trading genes back and forth with each other,” Alm says.
The team found that the microbiota of people from industrialized and urban populations had higher rates of gene swap than gut microbes from individuals in non-industrialized and rural societies. Although it’s unclear what causes bacteria to exchange more genes in specific environments, the study reveals that among pastoralists who treat their livestock with antibiotics, genes for antibiotic resistance are among those exchanged at the highest rates.
The researchers found that the microbiota of people from non-industrialized societies exchanged genes involved in carbohydrate metabolism and fiber degradation. This likely reflects how these populations rely on foods rich in fiber such as fruits and vegetables. On the other hand, microbiota from individuals living in industrialized countries swapped more genes involved in bacterial virulence.
The team now plans to figure out how virulence genes influence inflammatory conditions such as irritable bowel syndrome, which is much more common in industrialized societies than in non-industrialized ones, the authors say.