Seasonal Variation in Human Gut Microbiome Composition

Abstract

The composition of the human gut microbiome is influenced by many environmental factors. Diet is thought to be one of the most important determinants, though we have limited understanding of the extent to which dietary fluctuations alter variation in the gut microbiome between individuals. In this study, we examined variation in gut microbiome composition between winter and summer over the course of one year in 60 members of a founder population, the Hutterites. Because of their communal lifestyle, Hutterite diets are similar across individuals and remarkably stable throughout the year, with the exception that fresh produce is primarily served during the summer and autumn months. Our data indicate that despite overall gut microbiome stability within individuals over time, there are consistent and significant population-wide shifts in microbiome composition across seasons. We found seasonal differences in both (i) the abundance of particular taxa (false discovery rate <0.05), including highly abundant phyla Bacteroidetes and Firmicutes, and (ii) overall gut microbiome diversity (by Shannon diversity; P = 0.001). It is likely that the dietary fluctuations between seasons with respect to produce availability explain, at least in part, these differences in microbiome composition. For example, high levels of produce containing complex carbohydrates consumed during the summer months might explain increased abundance of Bacteroidetes, which contain complex carbohydrate digesters, and decreased levels of Actinobacteria, which have been negatively correlated to fiber content in food questionnaires. Our observations demonstrate the plastic nature of the human gut microbiome in response to variation in diet.

Consumption of a Bifidobacterium bifidum Strain for 4 Weeks Modulates Dominant Intestinal Bacterial Taxa and Fecal Butyrate in Healthy Adults

“…16S rRNA gene profiling revealed considerable variation of the fecal microbiota composition of the volunteers enrolled in the PROBIOTA-Bb trial, consistent with previous studies (27,28). These interindividual differences support the choice of the crossover design, in which individual participants serve as their own controls, resulting in the reduction of interindividual variation.…”

Causes of Impaired Oral Vaccine Efficacy in Developing Countries

“…The composition of the bacterial microbiota displays considerable variation by geographic setting [150][151][152], lifestyle [153] and season [154]. As such, the ecological landscape into which an oral vaccine is introduced is likely to vary considerably between infants in high-and low-income countries.…”

New insight into the gut microbiome through metagenomics

“…For example, the shotgun metagenome analysis of two healthy adults revealed a significant metabolic enrichment of glycans, amino acids, and xenobiotics; methanogenesis; and 2-methyl-D-erythritol 4-phosphate pathway-mediated biosynthesis of vitamins and isoprenoids in the human gut microbiome. 28 Moreover, the gut microbiota is not constant, and can be altered by diet, 5,6,29 antibiotic usage, 7,8 aging, 30,31 and many other factors. As well as aiding investigation of the relationship between gut microbiota and human health, metagenomic studies have also necessitated a better understanding of the dynamics of gut microbiome.…”

“…As well as aiding investigation of the relationship between gut microbiota and human health, metagenomic studies have also necessitated a better understanding of the dynamics of gut microbiome. For instance, Davenport et al 29 found that seasonal differences in diet shape the gut microbiome compositions of Hutterite individuals differently between the winter and summer. Rampelli et al 30 observed an age-related reduction of the abundance of genes involved in short-chain fatty acid (SCFA) production, and identified 116 microbial genes that significantly correlated with aging.…”