Limited impact of dietary habits on the gut microbiome and resistome of humans. Impact of dietary habits on the gut microbiome and resistome

The human gut microbiome plays a central role in nutrient acquisition, but also in our state of health and disease. Environmental factors, such as lifestyle and diet, are known to shape the gut microbiome as well as the reservoir of resistance genes that these microbes harbour; the resistome. In this study we assessed whether long-term different dietary habits within a single geographical region (the Netherlands) impact the human gut microbiome and resistome in Dutch residents.Faecal samples from Dutch individuals with distinct dietary habits were collected based on their diet lifestyle and categorized into omnivores, pescatarians, vegetarians and vegans. Samples were sequenced using metagenomic shotgun sequencing and ResCap targeted sequencing, to study the microbiome diversity and resistome composition.Most differences were observed when comparing the bacterial diversity of vegans to other diet groups. Among other bacteria, we specifically observed differences in the abundance of lactic acid bacteria. Compared to pescatarians, vegans had lower abundance of Streptococcus thermophilus and Lactococcus lactis. Similarly, S. thermophilus was less abundant in vegans relative to omnivores. Few differences were observed when comparing omnivores, pescatarians and vegetarians, only Eubacterium eligens was found to be present in low abundance in omnivores compared to pescatarians. Despite sequencing a total of 145 different antibiotic resistance genes, limited differences were observed when comparing the resistome composition between diet groups, apart from the significant differences in the low abundant genes lsa(C) and tet(L), detected by ResCap and in tet(X), detected by shotgun metagenome sequencing.Contrary to previous dietary studies, our study shows that long-term dietary habits have limited effects on the microbiome. Additionally, these dietary habits do not seem to associate with a specific signature resistome. Future studies that take place in different populations are, however, necessary in order to confirm our findings in the Dutch population.