Your gut harbors genes stolen from sea life | Science

If the seaweeds nori, kombu, or wakame have long been part of your diet, there’s a good chance your gut bacteria harbor genes from sea life. Microbiologists have discovered the human gut microbiome has acquired this exotic DNA multiple times during the history of seaweed consumption in Asia.

Whether these genes can be acquired in a matter of months or thousands of years is still an open question. Regardless, the phenomenon “may help us better understand the origin of [the] many novel genes in the human microbiome,” says Arshan Nasir, a bioinformatician at Moderna interested in microbial evolution.

The human gut hosts thousands of microbial species—mostly bacteria and viruses—of which the bacteria collectively contain about 500,000 genes. Researchers only know what half of those do. Some break complex carbohydrates (such as those found in grains and some vegetables) into energy-rich molecules called fatty acids that the human body can absorb and use. However, these genes can’t break down the complex carbohydrates in seaweed and other marine algae. Could marine organisms have given us a hand in getting nutrients from seaweed?

The first clues that they might came about 10 years ago. Researchers found a cluster of seaweed-digesting genes from a marine bacterium that eats nori in human gut microbes. To find out how common those genes were in people, Eric Martens, a microbiologist at the University of Michigan, Ann Arbor, and his colleagues placed human fecal samples on plates containing seaweed extracts. They then analyzed the genomes of the bacteria that survived on the extracts, reasoning that those microbes were the ones that could digest seaweed.

Some bacteria had the same nori-digesting genes found earlier, whereas others had different genes with the same capability, the team reports today in Cell Host & Microbe. Most of the microbes were Bacteroidetes, a highly diverse group that is among the most common types of bacteria in the gut, soil, and fresh- and saltwater. The genes in the human gut microbes clustered together in mobile packets of DNA, suggesting they likely came from marine Bacteroidetes using a process called horizontal gene transfer. People eating seaweed or other sea life might have ingested these bacteria.

The team also found another set of seaweed-digesting genes in a different group of common gut bacteria, Firmicutes. Because of similarities between those genes and genes in DNA databases, the researchers say those genes may have come from a bacterium found in the guts of fish that people ate. “I’m willing to bet that if we kept on searching, we’d find more [transfer] events,” Martens says.

Next, his postdoc Gabriel Pereira looked for the seaweed-digesting genes in the guts of nearly 2500 people from North and South America, Africa, Europe, and Asia. The researchers found genes for digesting nori in 512 of the 1361 samples from Japanese and Chinese participants, but in very few participants from elsewhere. Those Asian participants were also more likely to have the genes needed to digest other kinds of seaweed.

That makes sense because Asian cultures have long consumed seaweed, says Justin Sonnenburg, a microbiologist at Stanford University who was not involved with the study. The fact that the genes have stuck around in these people suggests they play an important role in helping digest the fiber in the algae, he says.

Martens can’t tell when these genes were acquired by either the Bacteroidetes or the Firmicutes in the gut. He and others suspect it could be hundreds or even thousands of years ago. But it could also take just months of a regular seaweed diet, especially if people live among others who typically eat these foods. (The microbiomes of people who live together tend to become more similar over time.)

This natural experiment could be harnessed for human health, says Nasir, who was not part of the research. Novome Biotechnologies, for example, has endowed a seaweed-digesting bacterium with the ability to degrade dietary oxalate, a compound that can lead to kidney stones. In ongoing clinical trials, people at risk for kidney stones take this modified bacterium as a probiotic and ensure it thrives in the gut by also eating seaweed supplements. If for some reason, they need to get rid of this bacterium, they can simply stop taking the seaweed supplement.

Even if this biomedical application doesn’t pan out, horizontal gene transfer has been good for people, Martens says. Humans “do not have to evolve these functions,” he says. They can simply acquire new ones from bacteria.