UCLA researchers have found that gut bacteria are rapidly evolving to digest starches in ultra-processed foods, and that this evolution looks different in industrialized and non-industrialized populations. The work suggests our diets may be reshaping our microbiomes far faster than scientists once thought.
Gut bacteria inside people living in industrialized countries are rapidly evolving to digest ingredients found in ultra-processed foods, according to a new UCLA study — and that evolution appears to be unfolding in just a few decades.
By scanning the genomes of nearly three dozen common gut bacteria species using data from around the world, UCLA evolutionary biologists found that certain gene variants that help microbes break down industrial starches have become dominant in some bacterial species in industrialized populations. These starches, including additives such as maltodextrin made from cornstarch, have only been widely used in processed foods since the mid-20th century.
Because that timeline is so short in evolutionary terms, the team concludes that natural selection must be acting strongly on these microbes in response to modern diets.
The researchers also found that gut bacteria in industrialized and non-industrialized populations are not evolving in the same way. Different genes appear to be favored in different environments, suggesting that lifestyle and diet are leaving distinct evolutionary fingerprints on the microbiome.
The most eye-catching part of the work was not just that bacteria are adapting to new food ingredients, but that their evolutionary targets differ depending on where people live, according to first author Richard Wolff, a UCLA doctoral student.
“The discovery that the ability to digest novel starches is a target of natural selection in gut bacteria is interesting, but we found an even more robust, stronger signal that there are different targets of selection across many genes and many species in industrialized and non-industrialized populations,” Wolff said in a news release. “What are the gut microbiomes in industrialized populations responding to? We’ve picked out one example with these starches, but there’s likely many possibilities we haven’t grappled with yet.”
The study, published in the journal Nature, focused on a process called horizontal gene transfer. Unlike humans, who inherit DNA only from their parents, bacteria can swap genes directly with one another. They can take up free-floating DNA from their environment, receive it via viruses that infect bacteria, or exchange it when they clump together and form tiny bridges.
This genetic handoff is the same mechanism that allows bacteria to develop antibiotic resistance so quickly. But until now, scientists knew far less about how often horizontal gene transfer shapes the gut microbes that live in and on humans.
To track that process, Wolff and senior author Nandita Garud, a UCLA professor of ecology and evolutionary biology, developed a new statistical method to detect places in bacterial DNA where certain gene versions have risen to high frequency, or “swept,” through a species. The method looks for small, unusually similar stretches of DNA against a backdrop of enormous diversity between strains.
Garud explained just how diverse those strains can be.
“Different strains of E. coli, for example, have diverged from each other as much as humans have diverged from chimps, yet we call them the same species. Despite this diversity, there are still shared fragments of DNA present in many hosts — a hidden thread connecting our microbiomes,” she said in the news release.
When the team compared bacteria from industrialized and non-industrialized populations, they saw that different genes had undergone these sweeps in different settings. One gene in particular stood out: It was sweeping only in industrialized populations and is associated with the ability to digest maltodextrin, a common additive in processed foods since the 1960s.
Wolff noted that the signal of adaptation was clear, but the exact target is still being worked out.
“We saw the adaptive signal very strongly, but we can’t say for sure yet if it’s specializing in maltodextrin or a broader class of starch derivatives. There might be intermediate steps as the bacteria adapt to different starch sources,” Wolff added. “There are a lot of steps in between eating a diet full of cassava and breadfruit and a diet full of Hot Cheetos or something like that.”
One puzzle the study raises is how these adaptive genes spread so widely between people.
Each person tends to carry only a few strains of the same bacterial species, and those strains can remain stable in an individual’s gut for years. Yet the UCLA team found that certain advantageous DNA fragments have become common across many hosts.
“Each person might have a couple of different strains of E. coli,” added Garud. “If fragments of DNA are transmitted horizontally across different strains in different hosts, and these strains seemingly are faithful to their respective hosts, where do they recombine? How do they move between individual people to become fixed in a whole population?”
Scientists know that gut microbes can move between people through close contact, shared environments, and even shared food and water. But the details of how specific genes hop from one human host to another, and then become widespread, remain unclear.
The findings add to a growing body of research showing that the human microbiome — the vast community of bacteria, viruses and other microbes that live in and on us — is not just passively along for the ride. It is actively evolving in response to what we eat and how we live.
While the UCLA study does not test health outcomes directly, it suggests that the ingredients in ultra-processed foods may be exerting strong evolutionary pressure on our gut bacteria. That, in turn, could influence how we digest food, how our immune system functions and how we respond to disease.
For now, the work underscores that diet is not only fueling our bodies but also helping to shape the genetic landscape of the microbes that live inside us. Future research will aim to pin down exactly which food components are driving these changes, how they spread between people and what they mean for long-term health.