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 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.
Highlights
The human gut microbiome plays a central role in health and disease
Faecal samples from these four groups were used for metagenomic shotgun sequencing (MSS) in order to study the effect of dietary habits on the gut microbiome
By using the combined power of metagenomic shotgun sequencing (MSS) and resistome capture sequencing approach (ResCap) we were able to detect over 850 different bacterial species and more than 100 unique antibiotic resistance genes (ARGs) in the gut microbiome of participants from the general Dutch population with distinct dietary habits
Summary
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. When studying the effect of longterm dietary habits within a single community on the gut microbiome of vegans, vegetarians and omnivores, Losasso et al only observed differences in bacteria that are present in low abundance, and part of the families Bacteroides, Lachnospiraceae, and Ruminococcaceae[20]. Administered antibiotics are known to select for bacteria that are resistant to these antibiotics, increasing the abundance of these ARGs in the g ut[27,28] This antibiotic-driven enrichment can take place in either the general population or more specific, in clinical settings, where effects on the resistome were observed in a matter of days[29,30,31]. The human gut resistome can be affected by environmental factors such as international travel and living conditions This has been shown in studies comparing urbanized with agricultural populations, in which the use of antibiotics plays an important r ole[32,33]. Zoonotic pathogens such as species of Salmonella and Campylobacter and certain types of Escherichia coli (e.g. Shiga-toxin-producing E. coli (STEC)) are known for causing foodborne infections and are frequent carriers of ARGs39–42
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
