# Integrated Metabolomics and Microbial Profiling in Patients with Irritable Bowel Syndrome

**Authors:** Yeongseo Kim, Mee-Hyun Lee, Seung-Ho Seo, Juhan Pak, Soobin Bae, Gayoun Lee, Gi Dae Kim, Hyun Sik Kim, Young-Ho Moon, Hong-Seok Son

PMC · DOI: 10.4014/jmb.2511.11041 · Journal of Microbiology and Biotechnology · 2026-01-22

## TL;DR

This study explores how gut microbes and metabolic changes are linked in people with irritable bowel syndrome.

## Contribution

The study integrates metabolomics and microbial profiling to reveal functional interactions in IBS pathophysiology.

## Key findings

- IBS patients showed higher abundance of specific gut microbes like Christensenellaceae R-7 group and Clostridium sensu stricto 1.
- Metabolite analysis identified 34 significant plasma metabolites linked to carbohydrate, amino acid, and fatty acid metabolism.
- Fatty acid metabolism was connected to gut microbes such as Clostridium sensu stricto 1 and Negativibacillus.

## Abstract

This study was conducted to identify metabolic and gut microbial changes associated with the pathophysiology of irritable bowel syndrome (IBS) by comparing the plasma/urinary metabolite profiles and gut microbiota composition between healthy controls (HC) and IBS patients. There was no significant difference in overall microbial diversity; however, IBS patients showed relatively higher abundance of Christensenellaceae R-7 group, Clostridium sensu stricto 1, and Negativibacillus. Metabolite analysis identified statistically significant differences in 34 plasma metabolites (VIP > 1.2, q < 0.05). Metabolite set abundance analysis indicated that commonly disturbed metabolic pathways in both plasma and urinary metabolites were mainly related to carbohydrate, amino acid, and fatty acid metabolism. Among these metabolic pathways, fatty acid metabolism was associated with three metabolites that showed significant correlations with the discriminating gut microbial features, namely Clostridium sensu stricto 1, Negativibacillus, and Klebsiella. This study demonstrated that integrating the three datasets—plasma metabolites, urinary metabolites, and gut microbial communities—provides a comprehensive overview of IBS pathophysiology. Together, these findings indicate that functional interactions between discriminative gut microbial features and systemic metabolic alterations, particularly within fatty acid metabolism, may represent a mechanistic link between gut dysbiosis and the metabolic manifestations of IBS.

## Linked entities

- **Diseases:** irritable bowel syndrome (MONDO:0005052)
- **Species:** Negativibacillus (taxon 1980693), Klebsiella (taxon 570)

## Full-text entities

- **Genes:** VIP (vasoactive intestinal peptide) [NCBI Gene 7432] {aka PHM27}, TRPV1 (transient receptor potential cation channel subfamily V member 1) [NCBI Gene 7442] {aka VR1}, PRRT2 (proline rich transmembrane protein 2) [NCBI Gene 112476] {aka BFIC2, BFIS2, DSPB3, DYT10, EKD1, FICCA}, AOC1 (amine oxidase copper containing 1) [NCBI Gene 26] {aka ABP, ABP1, DAO, DAO1, KAO, KDAO}, DAO (D-amino acid oxidase) [NCBI Gene 1610] {aka DAAO, DAMOX, OXDA}
- **Diseases:** organic bowel diseases (MESH:D015212), Celiac disease (MESH:D002446), cramping (MESH:D009120), Crohn's disease (MESH:D003424), metabolic (MESH:D008659), diarrhea (MESH:D003967), HC (MESH:D000067329), IBS (MESH:D043183), organic disorders (MESH:D019965), visceral hypersensitivity (MESH:D004342), gut dysbiosis (MESH:D064806), abdominal pain (MESH:D015746)
- **Chemicals:** pyridine (MESH:C023666), SCFAs (MESH:D005232), galactose (MESH:D005690), ketones (MESH:D007659), MSTFA (MESH:C086665), glycine (MESH:D005998), psicose (MESH:C003243), C7-C40 alkane (-), dodecanoic acid (MESH:C030358), fructose (MESH:D005632), acetonitrile (MESH:C032159), glucose (MESH:D005947), methanol (MESH:D000432), levoglucosan (MESH:C014989), formic acid (MESH:C030544), leucine (MESH:D007930), betaine (MESH:D001622), amino acid (MESH:D000596), hexose (MESH:D006601), butyrate (MESH:D002087), lipid (MESH:D008055), fatty acid (MESH:D005227), amino sugar (MESH:D000606), valine (MESH:D014633), 1,5-Anhydroglucitol (MESH:C006584), alcohols (MESH:D000438), H (MESH:D006859), proline (MESH:D011392), alanine (MESH:D000409), water (MESH:D014867), creatine (MESH:D003401), lactose (MESH:D007785), mannose (MESH:D008358), Glycerophospholipid (MESH:D020404), ribitol (MESH:D012255), acid (MESH:D000143), serine (MESH:D012694), carbohydrate (MESH:D002241), threonine (MESH:D013912), pyroglutamic acid (MESH:D011761), starch (MESH:D013213), sucrose (MESH:D013395), 1,4-benzenedicarboxylic acid (MESH:C011363), Benzoic acid (MESH:D019817), helium (MESH:D006371), phosphate (MESH:D010710), isoleucine (MESH:D007532), EDTA (MESH:D004492)
- **Species:** Faecalibacterium (genus) [taxon 216851], Megamonas (genus) [taxon 158846], Klebsiella (genus) [taxon 570], gut metagenome (species) [taxon 749906], Bacteroides (genus) [taxon 816], Homo sapiens (human, species) [taxon 9606], Negativibacillus (genus) [taxon 1980693], Clostridium (genus) [taxon 1485]

## Full text

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## Figures

7 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12861726/full.md

## References

47 references — full list in the complete paper: https://tomesphere.com/paper/PMC12861726/full.md

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Source: https://tomesphere.com/paper/PMC12861726