From the Journals

Diet’s impact on the microbiome: It’s real, and broad


AT GMFH 2022

Dietary fiber impacts not only the composition of the gut microbiome, but the production of a broad spectrum of microbiota-produced metabolites – including amino acid metabolites – that may modify health, said Gary D. Wu, MD, of the University of Pennsylvania, Philadelphia.

During the 2022 Gut Microbiota for Health World Summit, organized by the American Gastroenterological Association and the European Society of Neurogastroenterology and Motility, Dr. Wu led a plenary session in which the impact of diet on the microbiome was characterized as important, rapid, personalized, likely modest relative to other contributing ecological factors, influenced by the process of cooking, and exceedingly difficult to tease apart and characterize in human studies.

In a human study published in 2021, Dr. Wu and coinvestigators performed a controlled feeding experiment with 30 healthy volunteers, randomizing them to several weeks of a vegan diet, an omnivore diet (a typical American diet), and an exclusive enteral nutrition diet (EEN) devoid of dietary fiber.

They compared the composition and metabolic function of the gut microbiome during three phases: an initial dietary phase (days 1-5), a purge phase in which antibiotics and polyethylene glycol were administered to transiently reduce bacterial load in the gut (days 6-8), and a recovery phase (days 9-15).

Diversity of the gut microbiota recovered from the purge phase in both vegans and omnivores, but not in those receiving EEN. “The EEN diet was having a profound effect on the [short-term] recovery of microbiota,” said Dr. Wu, the Ferdinand G. Weisbrod Professor in Gastroenterology, in describing the Food And Resulting Microbial Metabolites study.

Using genetic sequencing, microbial culturing, and bioinformatics processing, the researchers also determined that EEN subsequently led to metabolites that were distinct from omnivores and vegans. Unexpectedly, bacterial metabolites of amino acid origin – not only carbohydrate origin – were altered in the EEN group, suggesting a broad impact of dietary fiber on the bacterial metabolome. EEN-induced alterations in the microbiome and metabolome resolved after the study period, he noted.

In other words, “depriving or supplying the gut microbiome with one dietary component (i.e., fiber) can directly impact metabolites of an unrelated portion of the diet (i.e., amino acids) via the induction of specific gut bacterial taxa,” Dr. Wu and colleagues wrote.

Clinically, the results as a whole suggest that the combination of antibiotics with EEN may be less effective in patients with Crohn’s disease than EEN alone, and can be potentially harmful, they said.

At the meeting, sponsored by the American Gastroenterological Association and the European Society for Neurogastroenterology and Motility, Dr. Wu said that, for patients in the ICU on EEN treatment and antibiotics, “we do need to think carefully about microbiota reconstitution because it could have a very significant effect not only on short-chain fatty acid metabolites but on amino acid metabolites that may be good or bad in the setting of disease.”

The scientific rationale for the effectiveness of EEN for IBD is still not well understood, he noted. “All I can say is that EEN works in IBD, but there are aspects about the microbiota and diet and IBD that we don’t understand.”


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