Stool microRNA profiles reflect different dietary and gut microbiome patterns in healthy individuals

Abstract

ObjectivesMicroRNA (miRNA) profiles have been evaluated in several biospecimens in relation to common diseases for which diet may have a considerable impact. We aimed at characterising how specific diets are associated with the miRNome in stool of vegans, vegetarians and omnivores and how this is reflected in the gut microbial composition, as this is still poorly explored.DesignWe performed small RNA and shotgun metagenomic sequencing in faecal samples and dietary recording from 120 healthy volunteers, equally distributed for the different diets and matched for sex and age.ResultsWe found 49 miRNAs differentially expressed among vegans, vegetarians and omnivores (adj. p <0.05) and confirmed trends of expression levels of such miRNAs in vegans and vegetarians compared with an independent cohort of 45 omnivores. Two miRNAs related to lipid metabolism, miR-636 and miR-4739, were inversely correlated to the non-omnivorous diet duration, independently of subject age. Seventeen miRNAs correlated (|rho|>0.22, adj. p <0.05) with the estimated intake of nutrients, particularly animal proteins, phosphorus and, interestingly, lipids. In omnivores, higher Prevotella and Roseburia and lower Bacteroides abundances than in vegans and vegetarians were observed. Lipid metabolism-related miR-425-3p and miR-638 expression levels were associated with increased abundances of microbial species, such as Roseburia sp. CAG 182 and Akkermansia muciniphila, specific of different diets. An integrated analysis identified 25 miRNAs, 25 taxa and 7 dietary nutrients that clearly discriminated (area under the receiver operating characteristic curve=0.89) the three diets.ConclusionStool miRNA profiles are associated with specific diets and support the role of lipids as a driver of epigenetic changes and host-microbial molecular interactions in the gut.

Multiomics Analysis Reveals the Impact of Microbiota on Host Metabolism in Hepatic Steatosis

“…[ 13 ] Roseburia sp CAG 182 shows higher abundance in healthy vegetarians/vegans compared to omnivores and it is related to lipid metabolism. [ 14 ] Firmicutes bacterium CAG 95 is associated with dietary patterns and its abundance shows a strongly positive correlation with healthy plant‐ or animal‐based foods while less correlation with less healthy plant‐ or animal‐based foods. [ 15 ] In addition, both Firmicutes bacterium CAG 95 and Firmicutes bacterium CAG 110 are associated with the dysregulation of fatty acid metabolism and an inflammatory surrogate GlycA in host.…”

Mechanistic Insights Into Gut Microbiome Dysbiosis-Mediated Neuroimmune Dysregulation and Protein Misfolding and Clearance in the Pathogenesis of Chronic Neurodegenerative Disorders

“…MicroRNAs (miRNA) are single-stranded, short RNAs that post-transcriptionally regulate gene expression by binding to the 3 untranslated region (UTR) and silencing the target genes (Chopra et al, 2020;Li et al, 2020). They can be detected in the brain, biofluids [urine, cerebrospinal fluid (CSF), and blood], and, more recently, in stool samples (Tarallo et al, 2021). With a growing number of studies elucidating the role of miRNAs in various disease processes, the gut-residing microbes can further modulate miRNA expression and regulate host pathophysiology.…”

“…Astonishingly, the number of bacteria present in our body shows a nearly equal ratio to human cells (1.3:1). It boasts immense metabolic capabilities as the gut-microbiota may contain up to 23 million genes -a number that dwarfs the human genome (Claesson et al, 2009;Sender et al, 2016;Tierney et al, 2019). Since gut-residing bacteria are vital for host survival, understanding their influence can broaden the horizon for diagnosis and therapy for complex multifactorial diseases, including neurodegenerative diseases.…”

MicroRNA and Gut Microbiota: Tiny but Mighty—Novel Insights into Their Cross-talk in Inflammatory Bowel Disease Pathogenesis and Therapeutics

“…Indeed, recent studies have demonstrated direct links between faecal miRNA profiles, diet, and gut microbial composition. 62 , 63 Teng and colleagues showed that miRNAs found in edible plants, enclosed in derived exosome-like nanoparticles, can be taken up preferentially by bacteria issuing changes in the microbiome composition, growth, and localisation. 62 Exogenous miRNAs from plants may also be taken up by the host and accumulate in serum and tissue.…”