Unusual sub-genus associations of faecal Prevotella and Bacteroides with specific dietary patterns

Abstract

Background: Diet has a recognized effect in shaping gut microbiota. Many studies link an increase in Prevotella to high-fibre diet, while Bacteroides abundance is usually associated with the consumption of animal fat and protein-rich diets. Nevertheless, closely related species and strains may harbour different genetic pools; therefore, further studies should aim to understand whether species of the same genus are consistently linked to dietary patterns or equally responsive to diet variations. Here, we used oligotyping of 16S rRNA gene sequencing data to exploit the diversity within Prevotella and Bacteroides genera in faecal samples of omnivore and non-omnivore subjects from a previously studied cohort.

Results: A great heterogeneity was found in oligotype composition. Nevertheless, different oligotypes within the same genus showed distinctive correlation patterns with dietary components and metabolome. We found that some Prevotella oligotypes are significantly associated with the plant-based diet but some are associated with animal-based nutrients, and the same applies to Bacteroides. Therefore, an indiscriminate association of Bacteroidetes genera with specific dietary patterns may lead to an oversimplified vision that does not take into account sub-genus diversity and the different possible responses to dietary components.

Conclusions: We demonstrated that Prevotella and Bacteroides oligotypes show distinctive correlation patterns with dietary components and metabolome. These results substantiate a current oversimplification of diet-dependent microbe-host associations and highlighted that sub-genus differences must be taken into account when planning gut microbiota modulation for health benefits.

Keywords: Gut microbiota; Oligotyping; Omnivore diet; Plant-based diet.

Fig. 1

Differences in oligotype composition between omnivores and non-omnivores. Dendrogram of Prevotella (a) and Bacteroides (b) oligotype representative sequences and their average relative abundance in omnivores (inner circle) and non-omnivores (outer circle). Asterisks denote oligotypes significantly different in abundance between the two groups (*P < 0.05; **P < 0.01). Yellow circles denote oligotypes showing 100 % match with sequences in the NCBI nr database

Fig. 2

Correlation patterns between oligotypes and diet. Correlation between Prevotella (a) and Bacteroides (b) oligotypes and dietary data. Heatplot showing Spearman’s correlations between oligotypes and dietary data. Rows and columns are clustered by Euclidean distance and Ward linkage hierarchical clustering. The intensity of the colours represents the degree of association between oligotypes and foods/nutrients as measured by Spearman’s correlations. Asterisks denote significant correlations after P value corrections (P < 0.05)