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Volume 7, Issue 6

Effect of antibiotic administration on persistence and gut microbiome–metabolome dynamics in an irritable bowel syndrome longitudinal case study Open Access

Abstract

, the most prevalent microbial eukaryote in humans, has a global distribution. Studies have linked its presence with distinct gut microbiome and metabolome profiles compared to those where the organism is absent. However, the interplay of antibiotic administration, and the surrounding gut microbiome remains understudied. This case study aimed to explore antibiotic consumption and the presence of with subsequent changes in the gut microbiome and metabolome of an individual diagnosed with irritable bowel syndrome (IBS).

Stool samples from an IBS patient, collected at 12 time points, were tested for the presence of using real-time PCR targeting the rRNA gene, followed by sequencing of positive samples. Illumina sequencing determined the gut microbiome composition, while one-dimensional proton NMR spectroscopy was used to analyse the metabolome composition. Statistical analyses were conducted to identify relationships between antibiotic consumption, bacterial diversity, metabolome composition and presence.

Antibiotics significantly impacted the gut microbiome, with diversity declining early in the antibiotic course, then recovering later and post-course. was detected early, late and post-course but was not detectable mid-course, coinciding with the decline in bacterial diversity. Significant differences were observed between -positive and -negative samples, with bacterial composition significantly changing between samples collected before, early and after the antibiotic course compared to those collected mid-course. Metabolite groups, including short-chain fatty acids, amino acids and succinate, exhibited changes throughout the antibiotic course, indicating that gut metabolite composition is affected by antibiotic consumption.

While antibiotics did not significantly impact colonization, they did cause a mid-course decline in microbial diversity and presence. The study also revealed significant alterations in important metabolites such as short-chain fatty acids and amino acids throughout the antibiotic course, with an altered metabolome observed post-course. This case study underscores the complex interactions between antibiotics, gut microbiota and metabolites, highlighting the resilience of in the gut ecosystem.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): antibiotics , Blastocystis , gut metabolome , gut microbiome and irritable bowel syndrome (IBS)
Funding
This study was supported by the:
  • Biotechnology and Biological Sciences Research Council (Award South Coast Biosciences Doctoral Training Partnership (SoCoBio DTP))
    • Principle Award Recipient: WilliamJS Edwards
  • European Cooperation in Science and Technology (Award CA21105)
    • Principle Award Recipient: AnastasiosD. Tsaousis
  • University of Kent (Award Kent Health studentship)
    • Principle Award Recipient: AnastasiosD. Tsaousis
© 2025 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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2025-06-26
2025-07-10
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Effect of antibiotic administration on Blastocystis persistence and gut microbiome–metabolome dynamics in an irritable bowel syndrome longitudinal case study
Access Microbiology 7, 000926.v4 (2025); https://doi.org/10.1099/acmi.0.000926.v4
/content/journal/acmi/10.1099/acmi.0.000926.v4
/content/journal/acmi/10.1099/acmi.0.000926.v4
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