For centuries, evolution was thought to be a slow process, visible only over millions of years. However, new research shows that something as close as Our intestinal bacteria can change with astonishing rapidity, adapting to the food we eat day to day.
A team of scientists in the United States has discovered how intestinal microbes respond to modern ultra-processed foods, incorporating genes that allow them to digest industrial starches.
These findings could explain how our diet influences the microscopic evolution that occurs right inside us, EuropaPress reports.
Gut bacteria evolve rapidly in response to different diets, evolutionary biologists at the University of California, Los Angeles (UCLA) report in a new study.
The diet changes, the bacteria too
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As reported in their work published in Nature, the researchers discovered that genetic variants that help microbes digest the starches present in ultra-processed foods have invaded the genomes of some species of intestinal bacteria in industrialized areas of the world.
Since these starches are produced industrially and have only been around for a few decades, scientists believe that natural selection must have acted strongly for these genes to dominate so quickly.
Besides, Researchers have discovered that bacteria evolve differently in industrialized and non-industrialized areas of the world.
Genome analysis
The researchers analyzed the genomes of nearly three dozen species of gut bacteria using data from around the world and identified a process called horizontal gene transferin which bacteria transfer DNA from one strain to another, as the mechanism for this rapid evolution.
Horizontal gene transfer had previously been identified as the mechanism that allows bacteria to develop resistance to antibiotics so quickly, but the prevalence of this process in gut microbes was unknown until now.
“The discovery that the ability to digest new starches is a target of natural selection in intestinal bacteria is interesting, but we found an even stronger and more compelling signal that there are different targets of selection in many genes and species, both in industrialized and non-industrialized populations,” says Richard Wolff, a doctoral student at UCLA and first author of the article.
Wolff and corresponding author Nandita Garud, a professor of ecology and evolutionary biology at UCLA, developed a novel statistic that identifies locations in the DNA of 30 species of gut bacteria where genes have reached a high frequency, or been “swept away,” in that species.
This statistic looks for small regions of homogeneity in a context of immense diversity that separates different strains of the same species.
“Different strains of E. coli, for example, have distanced themselves from each other as much as humans have distanced themselves from chimpanzees, and yet we consider them the same species. Despite this diversity, there are still fragments of DNA shared in many hosts: a hidden common thread that connects our microbiomes,” says Garud.
Apparently, different genes were selected for in industrialized and non-industrialized populations, and one particular gene spread only in industrialized populations.
This gene is associated with the ability to digest maltodextrin, which is made from corn starch and has been used in processed foods since the 1960s.
We observed the adaptive signal very strongly, but we cannot yet determine with certainty whether it specializes on maltodextrin or on a broader class of starch derivatives.
There could be intermediate steps as bacteria adapt to different starch sources, says Wolff. There are many intermediate steps between a diet rich in cassava and breadfruit and a diet rich in hot Cheetos or something similar.
Bacteria can absorb DNA from their environment in many different ways: they can eat it, they can become infected with a virus that carries DNA between them, and they can transmit it when bacteria group together and form a bridge that allows them to move around each other.
What we eat could change our microbial DNA
But humans only possess a few strains of the same species of gut bacteria, and these strains typically stay with each person for many years. Therefore, the pervasiveness of the newly discovered adaptation raises the question of how DNA fragments are shared between human individuals.
“Each person could have a couple of different strains of E. coli,” Garud answers.
“If fragments of DNA are transmitted horizontally between different strains in different hosts, and these strains appear to be faithful to their respective hosts, we don’t know where they recombine, or how they move between individual people to become fixed in an entire population.
Although the answer will emerge with future research, the discovery that gut bacteria evolve rapidly in response to different diets and the possibility that new starches may be exerting strong evolutionary pressure about them suggest that paying careful attention to what we eat could play a more varied role in promoting good health than we think.
Reference:
Richard Wolff & Nandita R. So. Gene-specific selective sweeps are pervasive across human gut microbiomes. Nature. December 17, 2025.
