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.

Keywords: 16S rRNA metagenomics; citizen science; gut microbiota; intervention; microbiome stability; personalized diet; responders.

Figure 1

Associations of the microbial taxa with long-term dietary habits and other factors from the questionnaire (n = 207 subjects). Analysis was performed for the baseline samples at taxonomic levels from species to phyla. Rows are sorted in alphabetic order. Cell color denotes the value of the linear model coefficient from the MaAsLin analysis. All significant associations (FDR adjusted p < 0.1) are marked with one of the symbols (&, #, @): “&”—associations previously reported by Zhernakova et al., 2016 [41], “#”—reported by Wu et al., 2011 [13], “@”—novel associations.

Figure 2

Major changes in the gut community structure of the volunteers after following the dietary recommendations. Red branches of the cladogram denote the taxa that were increased in abundance, while the blue ones—decreased. Significance criterion: p < 0.05 in metagenomeSeq model and log10 of the effect size >2 in LEfSe method (n = 430 paired samples).

Figure 3

Interindividual variation of gut microbiota response to the diet intervention (n = 215 subjects). Distribution of taxonomic dissimilarity between the metagenomes before and after the intervention for each subject (generalized UniFrac metric) is colored in different ways. In panel (A), the color denotes responders (blue) and non-responders (green). In panels (B) and (C) the color denotes the average Bacteroidetes:Firmicutes ratio for the samples collected before and after the diet, respectively). Abbreviations: B:F ratio—Bacteroidetes:Firmicutes ratio, N—non-responders, R—responders.

Figure 4

Cluster analysis for microbial genera and samples. (A) Cooperatives of microbial genera. Size of the vertices is proportional to the average relative abundance of the genera in all metagenomes. Postfix “_u” denotes all unclassified genera from the respective family. (B) Links between cooperatives and permatypes (principal coordinates analysis [PCoA] using generalized UniFrac metric). (C) Changes in distribution of the participants across permatypes after following the dietary recommendations.

Figure 5

Gut microbiota momentum after the impact of the short-term diet. In the diagram describing the suggested effect, circles denote the location of community structures for typical responders (R) and non-responders (N) before and after the diet in the schematic landscape of possible microbiota configurations. Arrows represent the change of microbiota under the impact of diet.