Skip to main content
About the Institute
  • English
  • Français
  • Español
  • Russian

Breadcrumb

  1. Home
  2. Microbiota 6 - March 2019
  3. Resilience of healthy adult gut microbiota following antibiotic exposure
  • Our publications
    • News
    • Microbiota Mag
    • Thematic pages
    • Experts' point of view
    • Thematic folders
    • Overviews - Microbiota Magazine
  • About the Institute
    • About us
    • International Microbiota Observatory
    • Press room
    • Partnerships
  • Congresses
    • Congress calendar
    • Congress reviews
  • Continuing Medical Education
    • Accrediting courses
  • Useful documents
    • How to talk about
    • Infographics
    • IBS Diagnosis Check List
    • Patients Stories

    Join the microbiota community

    • Facebook
    • Twitter
    • LinkedIn
    • YouTube
    • Instagram
    • Bluesky

Lay public section

Find here your dedicated section
Gastroenterology
Gynecology
Pediatrics
General Medicine

Breadcrumb

  1. Home
  2. Microbiota 6 - March 2019
  3. Resilience of healthy adult gut microbiota following antibiotic exposure
Gastroenterology

Resilience of healthy adult gut microbiota following antibiotic exposure

Antibiotics
Gastroenterology

Commented articles - Adults' section

By Pr. Harry Sokol
Gastroenterology and Nutrition, Saint-Antoine Hospital, Paris, France

Gastroenterology
Gynecology
Pediatrics
General Medicine
  • Our publications
    • News
    • Microbiota Mag
    • Thematic pages
    • Experts' point of view
    • Thematic folders
    • Overviews - Microbiota Magazine
  • About the Institute
    • About us
    • International Microbiota Observatory
    • Press room
    • Partnerships
  • Congresses
    • Congress calendar
    • Congress reviews
  • Continuing Medical Education
    • Accrediting courses
  • Useful documents
    • How to talk about
    • Infographics
    • IBS Diagnosis Check List
    • Patients Stories

    Join the microbiota community

    • Facebook
    • Twitter
    • LinkedIn
    • YouTube
    • Instagram
    • Bluesky

Lay public section

Find here your dedicated section

Sources

This article is based on scientific information

Sharing is caring

Your colleagues might be interested in this topic. Why not share it?

  • Facebook
  • Twitter
  • LinkedIn
  • Mail

Sections

About this article

Author

Image_DT FMT H Sokol Prof Harry Sokol
Created 26 August 2021
Updated 12 August 2024

Comments of the original article of Palleja et al. (Nature Microbiology 2018)

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.[1]

What is already known about this topic? 

The human gut microbiota forms a complex and balanced ecosystem. Perturbations of this ecosystem can play a role in the development of infections, obesity, diabetes as well as neurological and inflammatory disorders. It is estimated that antibiotics have added 2 to 10 years to our life expectancy, but early exposure to these drugs has also been associated with noxious metabolic, inflammatory and neurological effects, both in animal models and in humans. When microbial communities are exposed to antibiotics, not only do they react by shifting their composition, but also by evolving, optimizing and disseminating antibiotic resistant genes (ABR genes) which collectively form the resistome.[2] The human gut microbiota is a reservoir of ABR genes which are exchanged between the resident strains, thereby propagating resistance.[3] The development and spread of antibiotic-resistant bacteria constitute a serious threat to public health. Only a few studies have investigated the effects of specific antibiotics on intestinal ecosystems and their associated resistomes. In previous work it was shown that antibiotic administration induces a decrease in microbiota diversity and an in- crease in the carriage of ABR genes.[4, 5] However, the effects of a combination of antibiotics on the microbiota and the role of ABR genes in microbial persistence have not yet been studied. In this study, 12 healthy men aged 18 to 40 years received a cocktail of three last-resort antibiotics (vancomycin, gentamicin and meropenem). The authors analysed the impact of this treatment on the gut microbiota by shotgun sequencing of faecal samples taken before and at four time points over a 6-month period following antibiotic administration.

Image

Cornerstone of the modern therapeutic arsenal, antibiotics saved millions of lives. On the other hand, their excessive and sometimes inappropriate use can lead to the emergence of multiple forms of resistance in microorganisms. Each year, the World Health Organization (WHO) organizes the World AMR Awareness Week (WAAW) to increase awareness of this public health issue. Read the dedicated page:

Microbiota at the forefront of antibiotic resistance

The largescale and sometimes inappropriate use of antibiotics is making them in…

What is the World AMR Awareness Week?

Each year, since 2015, the WHO organizes the World AMR Awareness Week (WAAW), which aims to increase awareness of global antimicrobial resistance. Held on 18-24 November, this campaign encourages the general public, healthcare professionals and decision-makers to use antimicrobials carefully, to prevent the further emergence of antimicrobial resistance.

What are the main results of this study? 

At D4, immediately after the intervention, microbiota diversity and richness were notably reduced compared to baseline. However, despite the use of very broad spectrum antibiotics, many species were still detectable at D4 (Figure 1a). By D8, microbiota diversity (measured by the Shan- non index) had considerably increased, suggesting that surviving microorganisms had begun to regrow (Figure 1b). At 6 months, microbiota diversity was almost completely restored to baseline levels but this was not the case for richness, suggesting that some strains had been permanently (or at least extendedly) eradicated.

Some of the early observable changes included blooms of normally subdominant commensals like Escherichia coli, Veillo- nella spp., Klebsiella spp., Enterococcus faecalis and Fusobacterium nucleatum and a sharp depletion of butyrate-producers like Faecalibacterium prausnitzii, Roseburia hominis, Anaerostipes hadrus, Coprococcus spp. and Eubacterium spp. These shifts in microbiota composition were no longer significant at D42.

The authors then investigated the role of ABR genes in microbiota recovery. In particular, they found that β-lactamase-harbouring metagenomic species had significantly higher odds of survival (OR = 1.64 [1.24-2.17]) at D8. In addition, metagenomic species not detected at baseline had better odds of subsequent de novo colonization if they harboured ABR genes against one of the three antibiotic classes used.

Key points

  • The intestinal microbiota of healthy young adults is resilient to 4 days of broad-spectrum antibiotic treatment with an approximate 6-month recovery of most bacterial communities.

  • The recovery of individual species is modulated by ABR gene carriage.

  • The impact of prolonged or repetitive antibiotic treatment requires further study, especially in paediatric populations.

What are the practical consequences? 

These findings indicate that the gut micro- biota of healthy young adults is resilient to a 4-day intervention with broad spectrum antibiotics with recovery of the majority of bacterial communities after about 6 months. The recovery of individual species is modulated by carriage of ABR genes. Further studies are needed to assess the impact of repetitive perturbations and/or over longer periods and to determine whether these findings also hold true in children whose immune system and microbiota are immature. It is possible that repetitive use of antibiotics over long periods selects for bacteria carrying ABR genes at the expense of other commensals, with prolonged or permanent effects on the microbiota. In such cases, corrective intervention with exogenous supply of microorganisms could be considered. The effects of antibiotics on the intestinal microbiota are therefore important and their use must be rationalized.

Conclusion

Broad spectrum antibiotics negatively impact the gut microbiota in an immediate, significant and durable manner for some species. In healthy young adults, the gut microbiota is resilient but near-complete recovery takes about six months. Modulated by ABR gene carriage, the capacity of species to regenerate is more favourable to diversity than to richness.

Sources

1 Palleja A, Mikkelsen KH, Forslund SK, et al. Recovery of gut microbiota of healthy adults following antibiotic exposure. Nature Microbiol 2018 ; 3 : 1255-65.

2 Wright GD. The antibiotic resistome: the nexus of chemical and genetic diversity. Nat Rev Microbiol 2007 ; 5 : 175-86.

3 van Schaik W. The human gut resistome. Phil Trans R Soc 2015 ; B 370 : 20140087.

4 Rashid MU, Zaura E, Buijs MJ,et al. Determining the long-term effect of antibiotic administration on the human normal intestinal microbiota using culture and pyrosequencing methods. Clin Infect Dis 2015 ; 60 : S77–S84.

5 Zaura E, Brandt BW, Teixeira de Mattos MJ, et al. Same exposure but two radically different responses to antibiotics: resilience of the salivary microbiome versus long-term microbial shifts in feces. mBio 2015 ; 6 : e01693-15.

Tags
Gastroenterology Antibiotics World Antimicrobial Awareness Week WAAW Dysbiosis Gut microbiota Public health Microbiome Flora

    See also

    Antibiotics: Dr Jekyll and Mr Hyde
    Photo: Antibiotic resistance is a web of several problems (HCPs) Antibiotic resistance is a web of several problems
    Focus
    Microbiota 6 - March 2019
    • Overview
      • Microbiota and celiac disease
    • Commented articles
      • Resilience of healthy adult gut microbiota following antibiotic exposure
      • Feeding practices from birth to 12 months: impact on the gut microbiota and the risk of being overweight
    • Congress review
      • Fecal transplantation - ready for prime time?
      • The gut microbiota: issues and challenges in the management of metabolic disorders
    • Press review
      • Proton pump inhibitors modify gut microbiome
      • Gut microbiota involved in the pathogenesis of non-alcoholic fatty liver disease
    Created 26 August 2021
    Updated 12 August 2024

    About this article

    To know more about this topic.

    Main topic

    Antibiotics

    Medical practice

    Gastroenterology

    Content type

    Commented article

    Author

    Image_DT FMT H Sokol Prof Harry Sokol
    Microbiota and celiac disease
    Feeding practices from birth to 12 months: impact on the gut microbiota and the risk of being overweight
    Focus

    Microbiota 6 - March 2019

    Overview

    Microbiota and celiac disease

    Commented articles

    Resilience of healthy adult gut microbiota following antibiotic exposure Feeding practices from birth to 12 months: impact on the gut microbiota and the risk of being overweight

    Congress review

    Fecal transplantation - ready for prime time? The gut microbiota: issues and challenges in the management of metabolic disorders

    Press review

    Proton pump inhibitors modify gut microbiome Gut microbiota involved in the pathogenesis of non-alcoholic fatty liver disease
    Gastroenterology
    07.05.2025

    The microbial-metabolic nexus in colon cancer

    Read the article
    07.02.2025

    Your functional dyspepsia diagnosis check list

    Read the article
    17.04.2025

    Sensitivity to the additive E466: the role of the microbiota

    Read the article
    Photo HCPs: Clinical context over quick fix: the fresh consensus on microbiome testing
    11.04.2025

    Clinical context over quick fix: the fresh consensus on microbiome testing

    Read the article
    22.11.2023

    Is vaginal microbiota transfer the new miracle for C-section babies?

    Read the article
    Actu PRO : Alcoolisme : expliquer les troubles sociaux grâce au microbiote
    27.01.2021

    Alcoholism: explaining social disorders thanks to the microbiota

    Read the article

    Association between fungal dysbiosis and environment

    The fungal portion of the gut microbiota (or mycobiota) has been much less studied than the bacterial...

    Find out more
    20.03.2025

    Entacapone and the gut: a hidden impact on parkinson’s care

    Read the article
    • Our publications
      • News
      • Microbiota Mag
      • Thematic pages
      • Experts' point of view
      • Thematic folders
      • Overviews - Microbiota Magazine
    • About the Institute
      • About us
      • International Microbiota Observatory
      • Press room
      • Partnerships
    • Congresses
      • Congress calendar
      • Congress reviews
    • Continuing Medical Education
      • Accrediting courses
    • Useful documents
      • How to talk about
      • Infographics
      • IBS Diagnosis Check List
      • Patients Stories

      Join the microbiota community

      • Facebook
      • Twitter
      • LinkedIn
      • YouTube
      • Instagram
      • Bluesky

    Lay public section

    Find here your dedicated section
    Gastroenterology
    Gynecology
    Pediatrics
    General Medicine
    • English
    • Français
    • Español
    • Russian

    Browse the site

    • Our publications
      • News
      • Microbiota Mag
      • Thematic pages
      • Experts' point of view
      • Thematic folders
      • Overviews - Microbiota Magazine
    • About the Institute
      • About us
      • International Microbiota Observatory
      • Press room
      • Partnerships
    • Congresses
      • Congress calendar
      • Congress reviews
    • Continuing Medical Education
      • Accrediting courses
    • Useful documents
      • How to talk about
      • Infographics
      • IBS Diagnosis Check List
      • Patients Stories

      Join the microbiota community

      • Facebook
      • Twitter
      • LinkedIn
      • YouTube
      • Instagram
      • Bluesky

    Lay public section

    Find here your dedicated section

    Discover

    Gastroenterology
    Gynecology
    Pediatrics
    General Medicine

    Join the microbiota community

    • Facebook
    • Twitter
    • LinkedIn
    • YouTube
    • Instagram
    • Bluesky

    Lay public section

    Find here your dedicated section

    Redirection

    You are about to be redirected and leave our website

    • Be redirected
    • Stay on the Biocodex Microbiota Institute's website

    Stay with us !

    Join the Microbiota Community of HCPs and researchers and receive “Microbiota Digest” and "Microbiota Mag" to stay up to date on the latest news about microbiota.

    * Mandatory Fields

    BMI 20-35

    Explore

    07.05.2025

    The microbial-metabolic nexus in colon cancer

    Read the article
    02.05.2025

    A new lens on chlamydia: beyond behavior, into the microbiome

    Read the article
    17.04.2025

    Sensitivity to the additive E466: the role of the microbiota

    Read the article

    Stay updated

    Join the Microbiota Community of HCPs and researchers and receive “Microbiota Digest” and "Microbiota Mag" to stay up to date on the latest news about microbiota.

    * Mandatory Fields

    BMI 20-35

    • Our publications
      • News
      • Microbiota Mag
      • Thematic pages
      • Experts' point of view
      • Thematic folders
      • Overviews - Microbiota Magazine
    • About the Institute
      • About us
      • International Microbiota Observatory
      • Press room
      • Partnerships
    • Congresses
      • Congress calendar
      • Congress reviews
    • Continuing Medical Education
      • Accrediting courses
    • Useful documents
      • How to talk about
      • Infographics
      • IBS Diagnosis Check List
      • Patients Stories

      Join the microbiota community

      • Facebook
      • Twitter
      • LinkedIn
      • YouTube
      • Instagram
      • Bluesky

    Lay public section

    Find here your dedicated section

    Discover

    Gastroenterology
    Gynecology
    Pediatrics
    General Medicine

    Lay public section

    Find here your dedicated section

    Join the microbiota community

    • Facebook
    • Twitter
    • LinkedIn
    • YouTube
    • Instagram
    • Bluesky

    © 2025 Biocodex. All rights reserved.

    • Legal notice
    • GTU
    • Data protection policy
    • Sitemap
    • Cookies settings
    • Digital accessibility : partially compliant
    Biocodex logo