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

Natalia Klimenko,Sergey Musienko,Alexander Kurilshikov,Dmitry Alexeev,Margarita Shevchenko,Ilya Altukhov,Daria Efimova,Ancha Baranova,Anna Popenko,Dimitry D Ischenko ,Anatoly S Vasiliev ,Kseniya S Selezneva ,Nazar I Samarov ,Stepan V Toshchakov ,Dmitrii A Osipenko ,Tatiana I Shashkova ,A.v Tepliuk ,Alexander V Tyakht ,Dimitri A Nikogosov ,Aleksei A Korzhenkov

doi:10.3390/nu10050576

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.

Highlights

The importance of gut microbiota to human health is hard to overestimate
260 subjects initially enrolled to the study, both samples before and after the diet intervention were provided by 248 subjects, demonstrating a relatively high compliance
A growing body of evidence accumulated by studies of gut microbiota in world populations emphasizes that lifestyle and especially diet strongly impact microbiota composition and, human health

Summary

Introduction

The importance of gut microbiota to human health is hard to overestimate. Due to the immense variability in microbial composition at the species level, the jury is still out on what may constitute the elusive “golden standard” of a healthy gut [7]. Microbiota modulations rapidly develop as an avenue of personalized medicine. The international randomized study Food4Me recently concluded that individualized nutritional recommendations lead to better health outcomes than a “one-size-fits-all” dietary approach [8]. Another large-scale study showed that microbiota-tailored diets strongly influence a postprandial glycaemic response, allowing for the personalized control of metabolic status [9]. The durability of the microbiota-driven response to drastic dietary changes is far from being confirmed [10]

Methods

Results

Conclusion