期刊
NATURE MICROBIOLOGY
卷 3, 期 11, 页码 1255-1265出版社
NATURE PUBLISHING GROUP
DOI: 10.1038/s41564-018-0257-9
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资金
- Novo Nordisk Foundation Center for Basic Metabolic Research [NNF10CC1016515]
- TARGET research initiative (Danish Strategic Research Council) [0603-00484B]
- Danish Diabetes Academy - Novo Nordisk Foundation
- Danish Council for Independent Research (Medical Sciences)
- FP7 METACARDIS [HEALTH-F4-2012-305312]
- Danish Diabetes Association
- Lundbeck Foundation [R140-2013-13528] Funding Source: researchfish
- NNF Center for Basic Metabolic Research [Arumugam Group] Funding Source: researchfish
To minimize the impact of antibiotics, gut microorganisms harbour and exchange antibiotics resistance genes, collectively called their resistome. Using shotgun sequencing-based metagenomics, we analysed the partial eradication and subsequent regrowth of the gut microbiota in 12 healthy men over a 6-month period following a 4-day intervention with a cocktail of 3 lastresort antibiotics: meropenem, gentamicin and vancomycin. Initial changes included blooms of enterobacteria and other pathobionts, such as Enterococcus faecalis and Fusobacterium nucleatum, and the depletion of Bifidobacterium species and butyrate producers. The gut microbiota of the subjects recovered to near-baseline composition within 1.5 months, although 9 common species, which were present in all subjects before the treatment, remained undetectable in most of the subjects after 180 days. Species that harbour beta-lactam resistance genes were positively selected for during and after the intervention. Harbouring glycopeptide or aminoglycoside resistance genes increased the odds of de novo colonization, however, the former also decreased the odds of survival. Compositional changes under antibiotic intervention in vivo matched results from in vitro susceptibility tests. Despite a mild yet long-lasting imprint following antibiotics exposure, the gut microbiota of healthy young adults are resilient to a short-term broad-spectrum antibiotics intervention and their antibiotics resistance gene carriage modulates their recovery processes.
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