Gut bacteria have evolved rapidly to digest starches in ultra-processed foods

(Press-News.org) Gut bacteria evolve rapidly in response to different diets, UCLA evolutionary biologists report in a new study. The researchers found that gene variants that help microbes digest starches found in ultra-processed foods have “swept” the genomes of some species of gut bacteria in industrialized parts of the world. Because these starches are industrially produced and have only been around for a few decades, scientists believe natural selection must have been acting strongly to make these genes dominant so quickly. What’s more, the researchers have discovered that bacteria are evolving differently in industrialized and non-industrialized parts of the world.

 

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.

 

Different genes appeared to be selected for in industrialized and non-industrialized populations, and one gene in particular was sweeping only in industrialized populations. That gene is associated with the ability to digest maltodextrin, which is made from cornstarch and has been used in processed foods since the 1960s.

 

“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,” said Wolff. “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.”

 

Bacteria can take up DNA from their environment in many different ways: They can eat it; they can be infected by a virus that carries DNA between them; and it can be transmitted when bacteria clump together and form a bridge that allows them to move between each other. 

 

But humans have only a few strains of the same species of gut bacteria, and these strains typically stay with each person for many years. So the pervasiveness of the newly discovered adaptation raises the question: How do DNA fragments become shared between individual humans?

 

“Each person might have a couple of different strains of E. coli,” said 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?”

 

While the answer will emerge with future research, the discovery that gut bacteria evolve rapidly in response to different diets, and the possibility that novel starches may be exerting strong evolutionary pressure on them, suggest that careful attention to what we eat could play a more varied role in promoting good health than we think.

 

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