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

Abstract

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.

Hypoxic volatile metabolic markers in the MDA-MB-231 breast cancer cell line

“…MeCl, acetone, n-hexane and styrene are clinically interesting compounds requiring further investigation. The compounds reported here have been reported as present in human breath (44) and we have shown that these compounds vary in response to cellular stress, from previously published doxorubicin (4) and here, hypoxic stress. Together this suggests they are able to differentiate cellular response due to pathophysiological differences.…”

MAGqual: A standalone pipeline to assess the quality of metagenome-assembled genomes

“…A small metagenomics dataset from a gut microbiome was procured from ENA project PRJEB44880 (Shahi et al, 2022) corresponding to a Nanopore metagenome assembly polished with Illumina shortreads and seven samples of short-read Illumina raw sequencing data. Three popular metagenomic binning tools were chosen for comparison, CONCOCT (v1.1.0), Metabat2 (v2.12.1) and Binsanity (v0.5.4) (Alneberg et al, 2014;Graham, Heidelberg and Tully, 2017;Kang et al, 2019) all three tools use abundance information for binning which was generated using BWA (v0.7.17) (Li, 2013) to map the Illumina short reads back to the assembly generating a BAM file for each short-read sample.…”

“…To demonstrate the use of MAGqual as a bin comparison tool a simple gut microbiome metagenome (Shahi et al, 2022) was re-binned using three different metagenomic binning tools, CONCOCT, MetaBAT2 and Binsanity (Alneberg et al, 2014;Graham, Heidelberg and Tully, 2017;Kang et al, 2019) and then refined using the pipeline from MetaWRAP and DAStool (Sieber et al, 2018;Uritskiy, DiRuggiero and Taylor, 2018). MAGqual was used to analyse the bins generated using these five different tools.…”