Date Published: March 11, 2014
Publisher: Public Library of Science
Author(s): Emily R. Davenport, Orna Mizrahi-Man, Katelyn Michelini, Luis B. Barreiro, Carole Ober, Yoav Gilad, Lluis Quintana-Murci.
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.
The human gut microbiome varies greatly in content across individuals, both within and between populations , , and is believed to be influenced by many factors such as method of delivery at birth , , antibiotic usage , , and disease status –. Nonetheless, diet is intuitively considered one of the most important determinants of the gut microbiome composition both in infants ,  and in adults –.
In order to characterize temporal variation in the gut microbiome of the Hutterites, we sampled stool from the same 60 individuals in the winter and summer months of one year. The individuals included in the study had not taken antibiotics for 6 months prior to either sampling period. From each sample, we amplified the V4 hypervariable region of the 16S rRNA gene and sequenced the sample using a HiSeq 2000 (see methods). We used two separate DNA extractions from each stool sample as technical replicates.
We characterized the gut microbiome of individuals from a unique population, the Hutterites, whose communal lifestyle minimizes environmental variation across individuals (compared to other sampling schemes in humans). The microbiome of the same individuals was examined during summer and winter months, when the Hutterite diets differ primarily with respect to the proportion of fresh produce they consume. Our goal was to assess the temporal stability of the microbiome and the role that dietary perturbations play in shaping the composition of the microbiota. Similar to other recent studies, we observed a high degree of temporal stability in members of the microbiome within an individual over time . However, there are significant shifts in bacterial abundance and diversity between seasons in this population.
In this study, we demonstrated that there is a large degree of temporal stability in the composition of the gut microbiome of an individual. We also found significant, population-wide shifts in the microbiome between seasons across multiple independent settlements of our population, which are potentially driven by seasonal dietary differences in the Hutterites. Our results also indicate that population-wide samples taken at one time-point for a study might not capture the entire variation that exists in that population over time.