Beyond the plate: A pilot study exploring the microbial landscape of omnivores and vegans through amplicon sequencing and metagenomics

Previous studies have described benefits and risks on human health associated with a vegan diet. Although it is recognized that diet affects the gut microbiota, there is no consensus on the effects of a vegan diet compared to omnivorous diet on the gut microbiota. We have conducted a pilot study to assess the differences between the gut microbiome of vegans and omnivores in 2017 and 2021. Fecal samples of 23 vegans and 23 omnivores (n = 46) were collected in 2017 and 2021 together with more than 300 dietary, lifestyle, and health related characteristics. The fecal microbiome was assessed comparing both amplicon sequencing and metagenome sequencing, to determine robust signals agnostic of sequencing approaches. Dietary grouping itself explained a small (∼4%) but significant proportion of the individual variation between microbiota. Natural clustering of microbiomes explained an even larger proportion. We found Ruminococcus torques to be relatively enriched in omnivores compared to vegans across methods and years. Interestingly, this species has been previously associated with unfavorable health outcomes. Despite a low sample size, we found some consistent differences between microbiota of individuals consuming either a vegan or omnivorous diet. These results were consistent with recently published gut microbiome signatures of vegans and omnivores across three different countries. Therefore, this small dataset allows a first insight into the gut microbiota of another county's omnivores and vegans whereby detailed and relevant dietary, lifestyle and health related characteristics collected in this study aid in understanding of the connection between respective diets and the microbiome.