Microbiome Responses to an Uncontrolled Short-Term Diet Intervention in the Frame of the Citizen Science Project

Abstract

Personalized nutrition is of increasing interest to individuals actively monitoring their health. The relations between the duration of diet intervention and the effects on gut microbiota have yet to be elucidated. Here we examined the associations of short-term dietary changes, long-term dietary habits and lifestyle with gut microbiota. Stool samples from 248 citizen-science volunteers were collected before and after a self-reported 2-week personalized diet intervention, then analyzed using 16S rRNA sequencing. Considerable correlations between long-term dietary habits and gut community structure were detected. A higher intake of vegetables and fruits was associated with increased levels of butyrate-producing Clostridiales and higher community richness. A paired comparison of the metagenomes before and after the 2-week intervention showed that even a brief, uncontrolled intervention produced profound changes in community structure: resulting in decreased levels of Bacteroidaceae, Porphyromonadaceae and Rikenellaceae families and decreased alpha-diversity coupled with an increase of Methanobrevibacter, Bifidobacterium, Clostridium and butyrate-producing Lachnospiraceae- as well as the prevalence of a permatype (a bootstrapping-based variation of enterotype) associated with a higher diversity of diet. The response of microbiota to the intervention was dependent on the initial microbiota state. These findings pave the way for the development of an individualized diet.

Development of qPCR platform with probes for quantifying prevalent and biomedically relevant human gut microbial taxa

“…Despite this limitation, a general-level profile of the gut microbiome composition provided by the proposed platform can be useful for assessing the general degree of dysbiosis. It can help in more advanced tasks like predicting response to drug therapy (as suggested by the discovered link between cancer immunotherapy response and Bacteroides levels [57]) or diet (for example, high-fiber diet [1]), measuring contribution of gut microbes to microbiome of built environments [58] as well as rapidly assessing the gut microbiome dysbiosis in patients with viral infections like COVID- Table 1 List of the 12 target taxa in the platform.…”

“…The target taxa were selected based on the principles of combining the taxa differentially abundant in subjects with major diseases (obesity, type 2 diabetes, inflammatory bowel diseases [IBD] and atherosclerosis), the taxa enriched in probiotic representatives and the "driver" taxa of the human gut microbiome. We collected a statistical summary of the targets' abundance in the 16S rRNA datasets of stool samples collected from the Russian general population during the OhMyGut crowdfunded project [1] and other studies (see Supplementary Table 2).…”

“…Stool DNA was extracted as described previously [1]. For facilitating PCR amplification, additional purification from PCR inhibitors was performed using AmpliPrime DNK-Sorb-B (Federal State Institution Central Research Institute of Epidemiology of Rospotrebnadzor, Russia) according to the manufacturer's instructions.…”

“…Can change in abundance after high-fiber dietary interventions. [1,29,30] Bifidobacterium Dominates in the gut community of healthy infants. Inversely associated with obesity and Crohn's disease.…”

“…The gut is colonized with 10 13 of microbes belonging to thousands of species. Alterations of microbiome composition are linked to lifestyle changes, short-and long-term diet [1], probiotics intake [1,2], medications including antibiotics [3] and diseases including obesity, type 2 diabetes [4], colorectal cancer [5], Crohn's disease [6] and others. Based on the discovered associations, a number of microbial taxa have been proposed as potential biomarkers.…”