Get to know B. fragilis, a bacterium that enters your intestines and evolves to get home

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MIT researchers analyzed population genomics and metagenomics to study the evolution of the microbiome of Bacteroides fragilis, one of the most common bacteria in the large intestine of humans. In an article published on April 23 in the newspaper Cell Host & Microbe, the authors describe how the common intestinal microbe adapts and evolves within individuals as well as Western and Eastern cultures.

"The strains of B. fragilis Humans who grow up in humans live in this environment similar to that of the intestines for millions of years. The idea of ​​meeting the intestine of a new host would induce a set of new adaptive mutations, and that these commensals would evolve rapidly, surprised us, "says Eric Alm, professor of biological engineering and co-director of Center for Informatics and Therapeutics of Microbiome at MIT.

Analyzes from Alm and his colleagues revealed that at least sixteen genes underwent an intra-individual evolution and that the majority of mutations targeted pathways involved in fiber uptake by the cell and the cell. biosynthesis of the cell envelope. While the observed mutations occurred repeatedly in the same gene types and in similar locations, the particular gene that acquired the mutations in each person was often different, suggesting continuing customization of the bacterium. "Bacteroides The species help to digest the complex fibers of the large intestine, which come from the food you consume, so their adaptation may be tied to the personalized diet, "says Shijie Zhao, co-author and lab member of the lab. Alm.

However, the explanation of why these genes are targeted is not limited to dietary choices. For example, it is possible that rapid evolution is a necessary tactic to avoid phages and immune cells. "These mutations could be responsible for changing the path B. fragilis Tami Lieberman, co-first author and now adjunct professor in the Department of Civil and Environmental Engineering at MIT. "This could also be a technique to boost their ability to repel attacks from other members of the microbiome."

In addition, the authors found differences in mutations between Western and Eastern metagenomes, an allele being highly selected among Western participants – with an independent mutation in each person – but rare in Chinese subjects. This striking difference lies in a gene whose biological role is unknown, but the authors believe that determining the source of different pressures across continents could allow new discoveries.

Usually, when researchers are considering modifying the microbiome, they want to know if the specific composition of the microbiome remains constant and not what might change within a given species. But in light of these findings, it may be more important to keep an eye on the coping abilities of individual commensals, particularly with respect to probiotic choices and microbial treatments.

"It's not a scary thing – I think we just need to be aware of the fact that you can do extensive testing in a lab, but when a commensal arrives on the ground and becomes a real person in the real world, it can evolve – its phenotype can change – and it's something that can be hard to anticipate, "says Alm.

In the future, the authors plan to undertake more mechanistic studies and perform metagenomic and genomic analyzes in different species of commensals, under conditions of disease and health, in order to better understand the Extent of evolution within the microbiome.

"If this pattern of intestinal bacteria evolving very quickly after introduction into a new host holds up, we will probably see totally different pathways depending on the types of bacteria, and this is going to be very exciting," Alm said.