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. 2018 Nov;3(11):1255-1265.
doi: 10.1038/s41564-018-0257-9. Epub 2018 Oct 22.

Recovery of gut microbiota of healthy adults following antibiotic exposure

Albert Palleja  1   2 , Kristian H Mikkelsen  3 , Sofia K Forslund  4   5   6   7   8 , Alireza Kashani  1   9 , Kristine H Allin  1   10 , Trine Nielsen  1 , Tue H Hansen  1 , Suisha Liang  11   12 , Qiang Feng  11   12 , Chenchen Zhang  11   12 , Paul Theodor Pyl  1 , Luis Pedro Coelho  8 , Huanming Yang  11   12   13 , Jian Wang  11   12   13 , Athanasios Typas  8   14 , Morten F Nielsen  3 , Henrik Bjorn Nielsen  2 , Peer Bork  5   8   15   16 , Jun Wang  17   18   19   20 , Tina Vilsbøll  3 , Torben Hansen  1   21 , Filip K Knop  22   23   24 , Manimozhiyan Arumugam  25 , Oluf Pedersen  26
Affiliations

Recovery of gut microbiota of healthy adults following antibiotic exposure

Albert Palleja et al. Nat Microbiol. 2018 Nov.

Abstract

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 last-resort 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 β-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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