Impact of long-term dietary habits on the human gut resistome in the Dutch population
Stege, Paul B.; Hordijk, Joost; Shetty, Sudarshan A.; Visser, Michael; Viveen, Marco C.; Rogers, Malbert R.C.; Gijsbers, Esther; Dierikx, Cindy M.; van der Plaats, Rozemarijn Q.J.; van Duijkeren, Engeline; Franz, Eelco; Willems, Rob J.L.; Fuentes, Susana; Paganelli, Fernanda L.
(2022) Scientific Reports, volume 12, issue 1, pp. 1 - 13
(Article)
Abstract
The human gut microbiome plays a central role in 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 dietary habits within
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a single geographical region (the Netherlands) impact the human gut resistome. Faecal samples from Dutch omnivores, pescatarians, vegetarians and vegans were analysed by metagenomic shotgun sequencing (MSS) (n = 149) and resistome capture sequencing approach (ResCap) (n = 64). Among all diet groups, 119 and 145 unique antibiotic resistance genes (ARGs) were detected by MSS or ResCap, respectively. Five or fifteen ARGs were shared between all diet groups, based on MSS and ResCap, respectively. The total number of detected ARGs by MSS or ResCap was not significantly different between the groups. MSS also revealed that vegans have a distinct microbiome composition, compared to other diet groups. Vegans had a lower abundance of Streptococcus thermophilus and Lactococcus lactis compared to pescatarians and a lower abundance of S. thermophilus when compared to omnivores. In summary, our study showed that long-term dietary habits are not associated with a specific resistome signature.
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Keywords: Adult, Bacteria/drug effects, Diet, Diet, Vegan, Diet, Vegetarian, Drug Resistance, Bacterial/genetics, Feces/microbiology, Feeding Behavior, Female, Gastrointestinal Microbiome, Gastrointestinal Tract/microbiology, Humans, Male, Meat, Metagenome, Metagenomics, Middle Aged, Netherlands, Nutritive Value, Seafood, Time Factors, Vegetables, General, Journal Article, Research Support, Non-U.S. Gov't, Comparative Study
ISSN: 2045-2322
Publisher: Nature Publishing Group
Note: Funding Information: The authors thank Angela van Hoek for her insights on the analysis and for corrections of the manuscript. We would like to thank Dr. Philip Clausen (Technical University of Denmark) for the technical assistance on KMA (k-mer alignment). Funding Information: This work was supported by the Netherlands Centre of One Health (NCOH metagenome call), the Dutch Ministry of Health, Welfare and Sport (Grant number V/050305/AA and the Strategic Program RIVM (SPR)) and Utrecht Exposome Hub of Utrecht Life Sciences ( www.uu.nl/exposome ), funded by the Executive Board of Utrecht University. Publisher Copyright: © 2022, The Author(s).
(Peer reviewed)