Gut bacteria recover from antibiotics, but they may take six months | Ars Technica

I love studies like this that examine how antibiotics are affecting our normal bacterial flora. This new microbiome paper in Nature Microbiology [1] examines how broad spectrum antibiotics change the gut microbiome immediately following administration and how it recovers over time.

I think Ars missed it with their headline. I mean, it is notable that it takes around 6 months for the gut microbiome to recover after broad spectrum antibiotics. However, this paper also showed that immediately following administration of broad spectrum antibiotics, they saw blooms of pathogenic bacteria like Escherichia coli, Veillonella spp., Klebsiella spp., E. faecalis and F. nucleatum. This raises the question (at least in my mind): does broad spectrum antibiotic use make us susceptible to serious bacterial infections for a period while our normal gut flora is restored? We know this is true for Clostridium difficile infection (and these researchers also showed it survived their broad spectrum regimen in high numbers). This period of vulnerability may be less important for otherwise healthy people, but seems to be critically important for patients undergoing chemotherapy or bone marrow transplant who get blasted with antibiotics for prolonged periods when they are neutropenic and febrile.

A couple notes on their methodology:

  • The broad spectrum antibiotic regimen used included vancomycin, meropenem, and gentamicin; indeed very broad! I’m a little surprised two nephrotoxic agents (vanc and gent) were used. Seems a similar “hit” to the gut microbiome could be achieved without the risk of gentamicin (or perhaps a fluoroquinolone could have been included though that raises its own safety issues).
  • These participants were only given 4 days of antibiotics. It would have been a little more useful if they had only donw 2 days (mimicing a typical 48 hour rule-out). On the flip side, almost all treatment courses of antibiotics are much longer than 4 days so it would be interesting to repeat this methodology with a longer course and examine the same trends.

There’s some great microbiome research going on out there!!


  1. Palleja A, Mikkelsen KH, Forslund SK, Kashani A, Allin KH, Nielsen T, Hansen TH, Liang S, Feng Q, Zhang C, Pyl PT, Coelho LP, Yang H, Wang J, Typas A, Nielsen MF, Nielsen HB, Bork P, Wang J, Vilsbøll T, Hansen T, Knop FK, Arumugam M, Pedersen O. Recovery of gut microbiota of healthy adults following antibiotic exposure. Nat Microbiol. 2018 Nov;3(11):1255–1265. doi: 10.1038/s41564–018–0257–9. Epub 2018 Oct 22. PubMed PMID: 30349083.  ↩

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