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Why Rewilding the Gut Might Not Help Fight the Diseases of Industrialization

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A new article challenges the idea that turning back the clock of our bodies’ bacterial microbiome could fight non-communicable disease.

The community of microorganisms that call our bodies home, the microbiota, have a complicated relationship with human health and disease. Researchers point to studies involving the technique of fecal microbiota transplantation (more colloquially called a “poo transplant”) as evidence that altering the microbiota might benefit our health.

But why would organisms that co-exist with our bodies compromise our health? Over the last five years, the idea that our microbiome is rapidly adapting to our industrialized world has been proposed. This means it may have fallen out of sync with our bodies, which remain steadfastly attuned to hunter-gatherer lifestyles (as anyone with lower back pain can attest). Could winding the clock back on our microbiome lead to health benefits?

This idea, termed ancestral microbiota restoration, has been analyzed in a new perspective piece published in Science by researchers from Harvard University and the University of California San Diego.

The researchers place the microbiome as one corner of a triangle of interactions, between our bodies and the environment. Recent analysis looking at the microbiome of people living in non-industrialized societies, such as the Hadza people of Tanzania, revealed that the composition of their microbiome looks quite different from ours. If we had a Hadza-like microbiome, would diseases associated with industrialized societies, such as autoimmune conditions, fade away?

The authors of this current perspective, Harvard’s Rachel Carmody and Amar Sarkar and UCSD’s Aspen Reese, pour some cold water on this powerful idea. “Implicit in the concept of ancestral microbiota restoration,” the authors write, “are the assumptions that the ancestral microbiota can be accurately characterized, that it promotes health and that microbial manipulations have predictable phenotypic effects.” But our understanding of the ancestral microbiome, in its true sense, is limited to the guts of well-preserved mummies or from fossilized lumps of poo called coprolites. The Hadza, standing in for an “ancestral microbiome”, may have, in reality, a gut flora as different from other non-industrialized societies as from industrialized ones.

The authors also delve into the implicit assumption in this area of research that the changes we see from industrialized microbiota are likely to be damaging to our health. One change pointed out as evidence of this negative impact is that microbiota diversity and function is reduced in the industrialized gut. But some bacterial species that have hung around, such as Bifidobacteria, are widely thought to be beneficial for immunity. In non-industrialized guts, higher levels of bacteria that ferment fibers into short-chain fatty acids (SCFAs) are present. SCFAs have been linked to the progression of Parkinson’s disease.

Even if industrialization made for less health-promoting bacteria, Carmody and her co-authors point out that the human body doesn’t just sit there and succumb to any alterations forced upon by willful bacteria. Instead, it has many ways of funneling the microbiota and controlling it. For example, breast milk contains oligosaccharides that can influence the microbial inputs to babies’ immune systems and pH gradients can prevent the microbiota from entering the small intestine. If the human body has been able to strongly direct the microbiome as the environment changes, a process called canalization, then rewilding the microbiome might harm our industrialized bodies rather than heal them.

Ultimately, the authors suggest that any beneficial changes could vary from society to society and from individual to individual. They suggest that a “scalpel, not sledgehammer” approach will be required to best balance the sides of our microbiome–host–environment triangle. Fossilized poo pills will not be coming to your pharmacy any time soon.

Reference: Carmody RN, Sarkar A, Reese AT. Gut microbiota through an evolutionary lens. Science. 2021;372(6541):462–463. doi: 10.1126/science.abf0590