Your Gut Bacteria Are Evolving to Digest Processed Foods—Here's What That Means

Gut bacteria in industrialized countries are evolving at breakneck speed to digest the novel starches found in ultra-processed foods, according to groundbreaking new research from UCLA. The study found that certain bacterial genes have "swept" through gut microbiomes in industrialized regions within just a few decades—an evolutionary timeline that's remarkably fast for natural selection.

Researchers scanned the genomes of almost three dozen species of gut bacteria using data from around the world and discovered something surprising: bacteria are evolving differently depending on whether people live in industrialized or non-industrialized regions. The key mechanism driving this rapid change is horizontal gene transfer, where bacteria literally swap DNA with each other—the same process that allows bacteria to develop antibiotic resistance so quickly.

What Specific Changes Are Happening in Our Gut Bacteria?

The most striking finding involves a gene that helps bacteria digest maltodextrin, an industrial starch made from cornstarch that's been used in processed foods since the 1960s. This gene has become dominant in gut bacteria populations across industrialized countries, suggesting our microbiomes are adapting to our modern diet in real-time.

"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," said Richard Wolff, the study's first author and a UCLA doctoral student. "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."

How Do These Genetic Changes Spread Between People?

The researchers identified several ways bacteria can share DNA with each other, creating a fascinating web of genetic exchange:

• Direct consumption: Bacteria can literally eat DNA from their environment and incorporate it into their own genetic code
• Viral transmission: Viruses can act as carriers, moving DNA fragments between different bacterial strains
• Physical bridges: Bacteria can clump together and form connections that allow them to directly transfer genetic material

What makes this discovery particularly intriguing is that most people only carry a few strains of each bacterial species, and these strains typically remain stable for years. Yet somehow, these genetic adaptations are spreading rapidly across entire populations.

"Each person might have a couple of different strains of E. coli," explained Nandita Garud, UCLA professor of ecology and evolutionary biology and the study's corresponding author. "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?"

What Does This Mean for Your Health?

The research team developed a novel statistical method to identify locations in bacterial DNA where genes have risen to high frequency across 30 different gut bacteria species. They found that different genes are being selected for in industrialized versus non-industrialized populations, suggesting our gut bacteria are responding to much more than just maltodextrin.

"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 noted.

This rapid bacterial evolution in response to dietary changes suggests that what we eat may play a more complex role in our health than previously understood. The fact that our gut bacteria can adapt so quickly to new food ingredients—within decades rather than centuries—highlights the dynamic relationship between our diet, our microbiome, and potentially our overall health.

The study, published in Nature and funded by the National Institutes of Health and National Science Foundation, opens up new questions about how our modern food system is literally reshaping the microscopic ecosystem living inside us.