Case Report: The effect of intravenous and oral antibiotics on the gut microbiome and breath volatile organic compounds over one year

Farah Shahi*, Sarah Forrester, Kelly Redeker, James P J Chong, Gavin Barlow

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


BACKGROUND: Antimicrobial resistance (AMR) is a global concern and better understanding of the gut microbiome, a known 'amplifier' of AMR, may allow future clinicians to tailor therapy to minimise this risk and offer a personalised medicine approach. To examine the gut microbiome, patients are required to provide faecal samples; more convenient and cheaper solutions need to be found.

METHODS: As part of a pilot study looking at how routes of administration affect the gut microbiome in NHS patients undergoing routine clinical management for infections, we hypothesised that effects on the gut microbiome varied with the route and metabolism of antibiotic used, and these changes may be reflected in breath metabolites. We present a case report of a patient with an unusual clinical history, alongside breath metabolite and gut microbiome data taken before, during and after antibiotic therapy over a period of one year.

RESULTS: We noted a shift in the dominant Bacteroides strain in the patient's gut microbiome between pre- and post-therapy samples, along with an alteration in the composition of breath metabolites.

CONCLUSIONS: This study provides a framework for similar future work and highlights the need for further research on the relationships between changes in microbial gut communities and antimicrobial exposure, patient clinical status, and the metabolites of human breath.

Original languageEnglish
Article number50
Number of pages22
JournalWellcome Open Research
Early online date11 Feb 2022
Publication statusPublished - 5 Dec 2022

Bibliographical note

Copyright: © 2022 Shahi F et al.


  • microbiome
  • Volatile organic compounds
  • antibiotics
  • breath
  • metabolites
  • resistance
  • antimicrobials

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