What We Eat May Be Reshaping Our Gut At Astonishing Speed

For thousands of years, humans ate foods pulled from farms, forests, and fields. Our bodies evolved alongside fibers, grains, natural sugars and starches. But today, industrialized diets are full of factory-made starches, added sugars, preservatives and additives. Many of these ingredients entered our food supply only in the last 50–70 years.

Yet the bacteria that help digest our meals appear to already be adapting–and fast, a new study UCLA has revealed. It noted, the trillions of bacteria living in our intestines – our gut microbiome – are evolving rapidly in response to modern diets. And the strongest push seems to be coming from ultra-processed foods.

The study’s findings, published in Nature, scanned the genomes of almost three dozen species of gut bacteria using data from around the world and identified a process called horizontal gene transfer, in which bacteria transfer DNA from one strain to another, as the mechanism for this rapid evolution. Horizontal gene transfer has previously been identified as the mechanism that allows bacteria to evolve antibiotic resistance so quickly, but the prevalence of this process in gut microbes has been relatively unknown until now.

“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,” said UCLA doctoral student and paper first author Richard Wolff. “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.”

Wolff and corresponding author, UCLA professor of ecology and evolutionary biology Nandita Garud, developed a novel statistic that identifies locations in the DNA of 30 gut bacteria species where genes have risen to high frequency, or “swept,” in that species. The statistic looks for tiny regions of homogeneity against a backdrop of immense diversity separating different strains of the same species.

“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,” said Garud.

One key example is maltodextrin, a starch derived from corn and widely used since the 1960s to thicken, stabilize or sweeten processed foods—from chips to energy bars, ready-to-eat meals and baby formula. The study found that a gene that enables bacteria to digest maltodextrin appears only in gut microbes of people living in industrialized populations. That gene is now sweeping through multiple bacterial species.

What shocked many researchers was the speed of this spread. Genes don’t usually dominate entire bacterial species so quickly unless there is strong evolutionary pressure—meaning microbes that can digest these starches have a real advantage inside our guts.

The mechanism appears to be horizontal gene transfer—the same process that makes bacteria develop antibiotic resistance. Bacteria exchange fragments of DNA directly between strains. Instead of waiting for mutations over generations, they simply borrow genetic tricks from other microbes.

The researchers found that different genes are being favored in industrialized and non-industrialized groups, suggesting our gut bacteria are responding to local food habits. In communities where diets remain high in traditional, minimally processed foods—cassava, millet, tubers, fruits—these industrial-food genes were absent or rare.

This raises big questions. If the bacteria living inside us are evolving to digest ultra-processed ingredients, what could that mean for long-term gut health? Could this shift affect metabolism, immunity, or inflammation? Could gut microbes that thrive on refined starches push out beneficial bacteria that evolved with natural diets?

But one lesson is already clear. Our gut microbes respond strongly to what we eat. Processed food ingredients—designed for shelf life, texture and convenience—are not just passing through our bodies. They may be actively reshaping the microbial ecosystem inside us, gene by gene.

The message is simple: every bite matters. Choosing less processed foods may do more than nourish our bodies—it may help preserve the ancient balance between us and the invisible organisms that help keep us healthy.