Newly discovered fiber-digesting gut bacteria going extinct due to urbanization

19 Mar 2024 --- The microbiome of urbanized humans is becoming less diverse than that of people living rurally due to the looming extinction of three newly discovered species in the microbiota. Consequently, city dwellers are becoming less capable of processing cellulose fiber, which is vital to overall digestive health.

The newly discovered ruminococcal gut bacteria — Candidatus Ruminococcus primaciens, Ruminococcus hominiciens and Ruminococcus ruminiciens — assemble functional multi-enzymatic cellulosome systems that degrade crystalline cellulose fiber. 

“It’s no easy task to degrade cellulose — few bacteria can do it,” comments co-author and cellulosomes expert professor Edward Bayer. “Cellulose is difficult to digest because it is insoluble. Fiber in the gut is like a tree trunk in a swimming pool — it gets wet, but it does not dissolve. Bottom line, cellulosomes turn fiber into sugars that feed an entire community, a formidable engineering feat.”

“Throughout human evolution, fiber has always been a mainstay of the human diet,” adds lead researcher Sarah Moraïs of the Ben-Gurion University (BGU), Israel. “It is also a main component in the diet of our primate ancestors. Fiber keeps our intestinal flora healthy.”

The researchers suggest a fiber-rich diet and specialized probiotics may be the key to reversing the loss of ruminococcal gut bacteria.Evolution of the gut microbiome
The study published in the journal Science investigates the presence of bacterial species capable of degrading complex cellulosic polysaccharides in the human gut microbiota to understand their ability to adapt to varying lifestyles and diets. 

The researchers consider their prevalence and abundance across diverse human populations, as well as mammalian species, to gain insights into their evolution and trajectory. 

The three newly discovered species were shown to have distinct host preferences, with Ruminococcus hominiciens found most commonly in the microbiome of humans and especially great apes, whereas Candidatus Ruminococcus primaciens was most commonly found in the microbiomes of ancient humans and other non-human primates. 

These bacteria were further found to exhibit host-specific diversification and high adaptability, shown by their gene expression (when a gene turns on in a cell to produce RNA and protein), which aligns with the host's diet. 

The analysis suggests that Ruminococcus hominiciens likely originated in the ruminant gut, possibly transferring to humans as part of the domestication process. 

Co-author Itzhak Mizrahi from BGU explains: “These cellulosome-producing bacteria have been around for a long time — their ancestors are important members of the rumen microbiome in cows and sheep.”

“The rumen is the special stomach organ of cows, sheep and deer, where the grass they eat (fiber) is converted into useful food by cellulose-degrading microbes, including Ruminococcus,” he continues. 

“We were surprised to see that the cellulosome-producing bacteria of humans seem to have switched hosts during evolution because the strains from humans are more closely related to the strains from livestock than to the strains from our own primate ancestors.”

Impact of industrialization
According to the findings, the newly discovered species were most prevalent in the microbiota of ancient human societies and, presently, in modern hunter-gatherer communities and rural populations. While the gut bacteria were found to be geographically widespread, they are rarely found in the guts of people living in industrialized settings.

“Our ancestors in Africa 200,000 years ago did not pick up lunch from a drive-through or phone in a home-delivery for dinner,” says professor William Martin of the Heinrich Heine University Düsseldorf, Germany.

The bacteria species’ adaptability has been highlighted through their acquisition of genes that degrade specific plant fibers of monocots such as maize, rice and wheat. Despite this adaptability, the bacteria’s functionality is diminished by the host’s low consumption of fiber. 

According to the paper, the low prevalence of these species among urbanites’ guts is because people living in such environments tend to have the lowest fiber consumption. The modern hunter-gatherer Hadza people living in north Tanzania, who also consume a lower fiber diet, were shown to have a low prevalence of Ruminococcus gut bacteria, though not as low as that of inhabitants of industrialized cities. 

The researchers suggest the potential of intentional reintroduction or enrichment of these species in the human gut through a diet shift and specialized probiotics. For example, a study conducted at Penn State University, US, showed that a diet rich in peanuts, herbs and spices may boost ruminococcal bacteria in the human gut. 

Pomegranate extract has also been observed to increase the prevalence of Ruminococcus bicirculans and Ruminococcus calidus in the gut. 

By Milana Nikolova