Diet influences the functions of the human intestinal microbiome

Abstract

Gut microbes programme their metabolism to suit intestinal conditions and convert dietary components into a panel of small molecules that ultimately affect host physiology. To unveil what is behind the effects of key dietary components on microbial functions and the way they modulate host-microbe interaction, we used for the first time a multi-omic approach that goes behind the mere gut phylogenetic composition and provides an overall picture of the functional repertoire in 27 fecal samples from omnivorous, vegan and vegetarian volunteers. Based on our data, vegan and vegetarian diets were associated to the highest abundance of microbial genes/proteins responsible for cell motility, carbohydrate-and protein-hydrolyzing enzymes, transport systems and the synthesis of essential amino acids and vitamins. A positive correlation was observed when intake of fiber and the relative fecal abundance of flagellin were compared. Microbial cells and flagellin extracted from fecal samples of 61 healthy donors modulated the viability of the human (HT29) colon carcinoma cells and the host response through the stimulation of the expression of Toll-like receptor 5, lectin RegIIIα and three interleukins (IL-8, IL-22 and IL-23). Our findings concretize a further and relevant milestone on how the diet may prevent/mitigate disease risk. Comprising 10 12-14 cells from 100-1000 species, the human intestinal microbiome is a complex entity living in our body. It affects human health, sustenance and well-being 1. Functioning as an extra organ 2 , the intestinal microbiome uses nutrients from ingested foods, releases harmful or beneficial metabolites and regulates the immune system 3,4. Dysbiosis of the intestinal microbiome has been associated to various gastrointestinal (GI) and non-GI diseases, such as obesity, heart-, kidney-and liver-related diseases, cancer and autism 5-7 , but the dilemma whether it acts as cause or consequence remains too far from the solution. Because the simple phylogenetic characterization does not provide deep information on functional repertoires 8,9 , a number of projects and studies have employed the whole-community shotgun sequencing to combine the composition and gene content of the human intestinal microbiome 2,10. Current meta-genomic data show limited differences among individuals, which hypothesize the existence of a stable core microbiome and similar metabolic traits 10. Notwithstanding the relevance of these findings, they do not necessarily imply similar in vivo microbial activities. Indeed, a panel of factors (e.g., diet, host genetics and pharmacological treatments) markedly affect such activities 11. Dietary components have the capability to modulate the composition and mainly the function of the intestinal microbiome 3,12,13. Correlations between entero-gradients/types and vegetable-rich (Prevotella and Lachnospira) or animal protein-rich diets (Bacteroides and Clostridia/Ruminococcus) have been already highlighted 12,14 , but the impact of dietary components still remains unclear. Previously, we...

The Controversial Role of Human Gut Lachnospiraceae

“…Furthermore, it was observed that Roseburia and Lachnospira were strongly associated with vegetable diets (vegetarian and vegan diets), and also displayed a negative association (p < 0.01) with the omnivore diet. On the same line, a recent study positively correlated Lachnospira to the intake of beta-carotene, vitamin E and vegetable fat whereas a negative correlation was found with meat, total proteins, and cholesterol (FDR <0.05) [185]. Oppositely, L-Ruminococcus, Blautia, and Lachnobacterium were included in the cluster of bacterial taxa that positively correlated with animal-derived nutrients and negatively correlated with vegetable-based diet patterns [195].…”

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Diet, Plasma, Erythrocytes, and Spermatozoa Fatty Acid Composition Changes in Young Vegan Men

“…Recent studies have further shed light on the potential benefits of this dietary pattern. One study showed enhanced gut cell metabolism in vegan adults, with changes positively influencing host's health (De Angelis et al, 2020). Although anti‐inflammatory properties of the vegan diet have been purposed, recent studies showed no overall differences in inflammatory biomarkers between vegans and omnivore young adults (Lederer et al, 2020; Menzel et al, 2020).…”

Strengthening national nutrition research: rationale and options for a new coordinated federal research effort and authority

“…Similar opportunities exist for greater scientific investments to allow regular DRI updates ( 200 ). Additional areas for accelerated research include major food groups for which health effects are currently poorly understood, and the interrelationships between nutrition and the gut microbiome, immunity, epigenetics, vascular health, food allergies, and other physiological systems—all with tremendous implications for human health ( 229–232 ). The complex effects of nutrition on health, the often provocative messages from the media and other influencers, and the many real unanswered and emerging questions in nutrition science have created significant public confusion ( 233 ).…”