Metabolomics: Multi-tissue analysis exploring disruption of the gut-brain axis caused by bacterial infection and treatment

Importance of the Topic

This work addresses how disruption of the gut-brain axis by Clostridioides difficile infection and subsequent treatments alters host metabolic profiles across multiple tissues. Understanding these effects at the metabolite level is crucial for developing targeted interventions in gastrointestinal and neurological disorders linked to microbiome dysbiosis.

Study Objectives and Overview

The study aimed to compare the metabolic impact of two treatment strategies—metronidazole antibiotic therapy versus faecal microbiota transplantation (FMT)—on mice infected with C. difficile. Multi-tissue metabolic profiling was performed on brain, caecum, and faecal samples to capture both central and peripheral biochemical responses.

Methodology and Instrumentation

The experimental design involved infecting antibiotic-pretreated C57BL/6 mice with non-toxigenic strains of C. difficile. Groups included uninfected controls, infected-untreated, infected plus metronidazole, and infected plus FMT. Tissue and faecal samples were extracted using biphasic solvent systems, then analysed by high-resolution LC-MS/MS with data-independent acquisition (DIA).

• Reverse-phase chromatography: Acquity C18 BEH column, 50 °C, water/acetonitrile gradient with 0.1 % formic acid.
• HILIC chromatography: Shim-pack Velox HILIC column, 40 °C, acetonitrile/water gradient with 10 mM ammonium formate and 0.1 % formic acid.
• Mass spectrometry: Shimadzu QTOF LCMS-9030 with ESI±, full scan m/z 65–1010 and DIA-MS/MS m/z 40–1000.

Metabolite identification combined in-house MS/MS libraries for MSI level 1 with online repositories for MSI level 2.

Main Results and Discussion

In the brain, infection and treatments caused significant increases in nucleosides (cytidine, cytosine, inosine, uridine, 5′-methylthioadenosine) and glutamic acid, while aspartic acid, arginine, and histidine decreased. Fatty acids were largely depleted by infection and only restored by metronidazole.

In caecal extracts, metronidazole treatment elevated lysophosphatidylethanolamines (LPE 16:1 and 18:1), malate, proline, and creatine. Infection reduced N-acyl taurines but FMT partially reversed this effect.

In faecal content, taurocholate, creatinine, and cysteate levels rose after infection and returned to control levels following FMT.

Benefits and Practical Applications

This multi-tissue metabolomic approach provides a comprehensive view of gut-brain axis perturbations. The findings demonstrate how antibiotic therapy and microbial restoration differentially modulate key metabolites. Such insights can guide therapeutic strategies for managing C. difficile infections and associated neurological sequelae.

Future Trends and Potential Applications

Advances in DIA-based metabolomics will enable more robust untargeted analyses, increasing coverage of unknown features in complex matrices. Integration with microbiome sequencing and functional assays could refine mechanistic links between microbial shifts and host metabolism. Personalized FMT formulations and antibiotic regimens may emerge from tailored biomarker profiles.

Conclusion

The study highlights distinct metabolic signatures of antibiotic versus FMT treatments in a C. difficile infection model, underlining the value of LC-MS/MS metabolomics for dissecting gut-brain axis dynamics. Metronidazole restores certain lipid and energy metabolites but may perturb other pathways, whereas FMT normalizes bile acid and taurine derivatives without broad metabolic disruption.

Reference

O. Deda, E. G. Armitage, M. Kachrimanidou, N. Loftus, H. Gika. Multi-tissue analysis exploring disruption of the gut-brain axis caused by bacterial infection and treatment. Aristotle University, Shimadzu, 2023.