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Nutrients 2018, 10(5), 576; https://doi.org/10.3390/nu10050576

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

1
Knomics LLC, Skolkovo Innovation Center, Bolshoy Bulvar Str., Building 42, Premise 1, Rooms 1293-1296, Moscow 143026, Russia
2
Computer Technology Department, ITMO University, Kronverkskiy pr., 49, St. Petersburg 197101, Russia
3
Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Institutskiy per. 9, Dolgoprudny, Moscow Region 141700, Russia
4
Department of Natural Science, Novosibirsk State University, Pirogova Str., 1, Novosibirsk 630073, Russia
5
Atlas Biomed Group, 92 Albert Embankment, Lambeth, London SE1 7TT, UK
6
Atlas Medical Center, Kutuzovsky prospekt 34 bld. 14, Moscow 121170, Russia
7
Research Centre of Medical Genetics, Moskvorechye Str., 1, Moscow 115478, Russia
8
School of Systems Biology, George Mason University, Fairfax, VA 22030, USA
9
Department of Genetics, University Medical Center Groningen, University of Groningen, 9712 CP, Groningen, The Netherlands
10
School of Life Sciences, Immanuel Kant Baltic Federal University, Universitetskaya Str. 2, Room 106, Kaliningrad 236040, Russia
11
Winogradsky Institute of Microbiology, Research Centre of Biotechnology RAS, Leninsky prospect 33-2, Moscow 119071, Russia
*
Author to whom correspondence should be addressed.
Received: 11 April 2018 / Revised: 28 April 2018 / Accepted: 4 May 2018 / Published: 8 May 2018
(This article belongs to the Special Issue Gut Microbiome and Human Health)
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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. View Full-Text
Keywords: gut microbiota; personalized diet; microbiome stability; intervention; 16S rRNA metagenomics; citizen science; responders gut microbiota; personalized diet; microbiome stability; intervention; 16S rRNA metagenomics; citizen science; responders
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Klimenko, N.S.; Tyakht, A.V.; Popenko, A.S.; Vasiliev, A.S.; Altukhov, I.A.; Ischenko, D.S.; Shashkova, T.I.; Efimova, D.A.; Nikogosov, D.A.; Osipenko, D.A.; Musienko, S.V.; Selezneva, K.S.; Baranova, A.; Kurilshikov, A.M.; Toshchakov, S.M.; Korzhenkov, A.A.; Samarov, N.I.; Shevchenko, M.A.; Tepliuk, A.V.; Alexeev, D.G. Microbiome Responses to an Uncontrolled Short-Term Diet Intervention in the Frame of the Citizen Science Project. Nutrients 2018, 10, 576.

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