The microbiome of urbanized humans has apparently become less diverse than that of people living rurally due to the looming extinction of three newly discovered species in the microbiota. Consequently, this has foiled the ability to digest cellulose fibre, a vital component boosting overall digestive health, especially in city dwellers, according to reports from a new study published in the journal Science.

The newly discovered cellulose-degrading ruminococcal gut bacteria — Candidatus Ruminococcus primaciens, Ruminococcus hominiciens and Ruminococcus ruminiciens — assemble functional multi-enzymatic cellulosome systems that degrade crystalline cellulose fibre. The production of cellulosomes puts Ruminococcus at the forefront of the fibre-degradation cascade that supports a healthy gut microbiome.

Explaining the complexity involved in degradation of cellulose, Edward Bayer, co-author and cellulosomes expert professor commented, “It’s no easy task to degrade cellulose — few bacteria can do it. 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.”

Evolution of the gut microbiome

The study investigated the bacterial species that are found in the human gut microbiota and capable of degrading complex cellulosic polysaccharides to understand their ability to adapt to varying lifestyle conditions and diets.

The researchers also considered parameters such as the prevalence and abundance of these species across diverse human populations, as well as mammalian species, to obtain insights into their evolution and trajectory. 

The newly identified species were shown to have distinct host preferences. Ruminococcus hominiciens is predominantly found in the microbiome of humans and especially great apes, whereas Candidatus Ruminococcus primaciens was primarily found in the microbiomes of ancient humans and other non-human primates.

Additionally, these bacteria were found to exhibit host-specific diversification and high adaptability, as demonstrated 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 probably 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 continued, “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

The adaptability of microbial species has been honed through their acquisition of genes that degrade specific plant fibers of monocots such as maize, rice and wheat. Despite this adaptability, the microbe’s functionality is diminished by the host’s low consumption of fibre. Industrialised nations heavily rely on processed foods rather than plant-based diets. The researchers assert that this transition away from a fibre-rich diet is responsible for the depletion of important cellulose-degrading microbes in the gut.

The study data revealed that the Ruminococcus strains were most prevalent in the microbiota of ancient human societies and in the contemporary hunter-gatherer communities and rural populations. In industrialised countries, including Denmark, China, Sweden and the United States, the collective prevalence was found to be 4.6 per cent, while it was a whopping 43 per cent among human populations from 1,000 to 2,000 years ago, 21 per cent in hunter-gatherers and 20 per cent in geographically diverse rural societies.

Hadza hunter-gatherers in east Africa are known to consume high-fibre diets, amounting to 80 to 150 grammes per day. Rural populations’ intake was estimated to be around 13 to 14 g per day while industrialised populations consume 8.4 g per day.

“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 Prof. William Martin from Heinrich Heine University Düsseldorf, Germany. 

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

So include lots of fibre in your diet to counteract this evolutionary decline!

(Input from various sources)

(Rehash/Dr. Vineesha V/MSM)