Diet is a primary factor involved in shaping both the composition and function of the gut microbiota. Although previous research showed an association of the Prevotella genus with a plant-based diet and Bacteroides with a diet rich in animal protein and fat, more information is needed about whether these associations remain true for different species in each of the genera.

A new study, led by Dr. Danilo Ercolini from the Department of Agricultural Sciences at the University of Naples Federico II in Portici (Italy), has found that sub-genera of commensal bacteria are related to specific dietary patterns and metabolome.

The researchers analysed the diversity within Prevotella and Bacteroides genera in faecal samples of omnivore (n = 44) and non-omnivore (self-declared ovo-lacto vegetarians and vegans, n = 93) Italian subjects from a previously studied cohort by oligotyping of 16S ribosomal ribonucleic acid (rRNA) gene sequencing data. Oligotyping decomposes a given taxon into high-resolution units (called “oligotypes”) by considering the nucleotide positions identified as the most information-rich, which allows resolution at the species level and below. The traditional approach, based on exploring the gut microbiome through 16S rRNA gene reads, clusters sequencing reads into operational taxonomic units and generally limits the level of taxonomic assignments to the genus level.

Different Prevotella and Bacteroides oligotypes showed different abundances depending on the dietary pattern. Specifically, some Bacteroides oligotypes were more abundant in omnivores, whereas others were more prevalent in non-omnivores. Within the genera Prevotella the researchers found a similar tendency.

Oligotypes associated with an omnivore diet were positively correlated with urinary levels of trimethylamine oxide (TMAO), a metabolite previously related to the development of cardiovascular diseases. By contrast, oligotypes related to a vegetable-based diet positively correlated with levels of short-chain fatty acids (SCFAs), which are the end products of fermentation of non-digestible carbohydrates in the large intestine by the anaerobic gut microbiota and have been linked to anti-inflammatory and anti-carcinogenic effects on the host. These data suggest that focusing only on associations between bacterial genera and dietary patters may not be enough when studying the effect of diet on the gut microbiota. According to the authors of the study, “sub-genus differences must be taken into account when planning gut microbiota modulation for health benefits”.

In conclusion, studying the gut microbiome at the species level and below allows the identification of different relationships between Prevotella and Bacteroides genera and dietary patterns. In further studies that explore the role of diet in shaping the gut microbiota, a focus on the diversity existing within the same genus or even within the same species, and how they differently respond to diet, will depict a clearer picture of diet-host-gut microbiome interactions.



De Filippis F, Pellegrini N, Laghi L, Gobbetti M, Ercolini D. Unusual sub-genus associations of faecal Prevotella and Bacteroides with specific dietary patterns. Microbiome. 2016; 4(1):57. doi: 10.1186/s40168-016-0202-1.