Bacteroidetes is one of the most abundant phyla in the gut, and studies have suggested that Prevotella spp. are associated with a high-fibre diet, whereas Bacteroides spp. are associated with the consumption of animal fat and a protein-rich diet. De Filippis et al. used oligotyping of 16S rRNA sequencing data to analyse differences in populations of Prevotella spp. and Bacteroides spp. in faecal samples from omnivores and non-omnivores. The authors identified 24 and 51 oligotypes for Prevotella spp. and Bacteroides spp., respectively. However, different oligotypes in these genera had a differential relative abundance in both groups. The heterogeneity in these genera and the correlation to dietary components and the metabolome suggest that the association of genera in the Bacteroidetes with a specific diet may oversimplify diet-dependent microbiota–host associations, and that diversity at the sub-genus level may need to be taken into account in diet-based intervention studies.