Multi-omics profiles of the intestinal microbiome in irritable bowel syndrome and its bowel habit subtypes Original paper
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Irritable Bowel Syndrome (IBS)
Irritable Bowel Syndrome (IBS)
Irritable Bowel Syndrome (IBS) is a common gastrointestinal disorder characterized by symptoms such as abdominal pain, bloating, and altered bowel habits. Recent research has focused on the gut microbiota's role in IBS, aiming to identify specific microbial signatures associated with the condition.
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Kimberly Eyer
Kimberly Eyer, a Registered Nurse with 30 years of nursing experience across diverse settings, including Home Health, ICU, Operating Room Nursing, and Research. Her roles have encompassed Operating Room Nurse, RN First Assistant, and Acting Director of a Same Day Surgery Center. Her specialty areas include Adult Cardiac Surgery, Congenital Cardiac Surgery, Vascular Surgery, and Neurosurgery.
Microbiome Signatures identifies and validates condition-specific microbiome shifts and interventions to accelerate clinical translation. Our multidisciplinary team supports clinicians, researchers, and innovators in turning microbiome science into actionable medicine.
Karen Pendergrass
Location
United States of America
Sample Site
Feces
Species
Homo sapiens
What Was Studied?
This study investigated the multi-omics profiles of the intestinal microbiome in Irritable Bowel Syndrome (IBS) and its bowel habit subtypes. The researchers aimed to uncover distinct microbial compositions and functional differences in patients with IBS-D (diarrhea-predominant), IBS-C (constipation-predominant), and IBS-M (mixed), compared to healthy controls. This study utilized 16S rRNA sequencing, metatranscriptomics, and untargeted metabolomics to capture both compositional and functional microbial changes. A cohort of 318 IBS patients and 177 healthy controls provided fecal samples, which were analyzed for microbial taxa, gene expression, and metabolic products.
Who Was Studied?
The study included 318 IBS patients, categorized into IBS-D, IBS-C, and IBS-M, alongside 177 healthy controls. These participants were recruited from diverse backgrounds and matched by age, gender, BMI, diet, and anxiety levels to minimize confounding factors. The study used comprehensive multi-omics approaches to investigate microbiome signatures, functional gene expression, and metabolic profiles in these individuals.
What Were the Most Important Findings?
The study identified distinct multi-omics microbial signatures in IBS patients compared to healthy controls. IBS-D patients exhibited increased levels of Bacteroides dorei, alterations in succinate and mannose metabolism, and elevated polyamine synthesis, which are associated with diarrhea severity. Meanwhile, IBS-C patients showed distinct upregulation of butyrate-producing pathways and enrichment in Verrucomicrobiota. The metatranscriptomics analysis revealed heightened expression of genes involved in fructose and polyol metabolism across all IBS subtypes, suggesting a microbiome-driven enhancement of fermentable carbohydrate utilization. Additionally, metabolomic profiling showed increased tyramine, gentisate, and hydrocinnamate in IBS patients, suggesting disruptions in aromatic amino acid metabolism. The multi-omics classifier developed from these findings demonstrated high accuracy (AUC 0.82) in distinguishing IBS patients from healthy controls. Further subclassification models effectively differentiated IBS-D from IBS-C with 86% accuracy, highlighting the role of bile acids, polyamines, and SCFA pathways in bowel habit variability.
| Parameter | Findings in IBS-D | Findings in IBS-C | Findings in IBS-M |
|---|---|---|---|
| Bacterial Diversity | Altered diversity with increased Bacteroides dorei | Elevated Verrucomicrobiota and butyrate-producing pathways | Mixed microbial shifts with no clear dominant phylum |
| Key Genera | Enrichment of Bacteroides dorei, reduction in anti-inflammatory taxa | Increased Verrucomicrobiota and SCFA producers | Variable populations of Firmicutes and Bacteroidetes |
| Metabolic Pathways | Enhanced succinate and mannose metabolism; elevated polyamine synthesis | Upregulation of butyrate-producing pathways | Mixed shifts in carbohydrate fermentation and SCFA production |
| Metatranscriptomics Analysis | Higher expression of genes involved in fructose and polyol metabolism | Butyrate synthesis pathways more prominent | Elevated expression of pathways linked to bile acid metabolism |
| Metabolomic Shifts | Increased levels of tyramine, gentisate, and hydrocinnamate | Elevated levels of butyrate and palmitoleate | Mixed aromatic amino acid metabolism alterations |
| Inflammatory Associations | Linked to diarrhea severity through succinate and bile acid dysregulation | Linked to constipation through lipid metabolism | Mixed inflammation markers reflective of both diarrhea and constipation |
| Diagnostic Potential | Multi-omics classifier with 86% accuracy in distinguishing IBS-D | Effective biomarker profiles for IBS-C | Subtype differentiation through SCFA and bile acid pathways |
What Are the Greatest Implications of This Study?
This study’s findings underscore the role of gut microbiome dysbiosis in IBS pathophysiology, driven by specific metabolic and transcriptional shifts. The identification of subtype-specific microbial signatures highlights the potential for personalized microbiome-based diagnostics and targeted dietary interventions. Notably, the association between fermentable carbohydrate metabolism and symptom severity suggests that dietary modifications—such as low-FODMAP or specific carbohydrate restriction—could be effective therapeutic strategies. Additionally, the development of a multi-omics classifier with high diagnostic accuracy presents a promising non-invasive approach for IBS diagnosis and subtype differentiation.
Irritable Bowel Syndrome (IBS)
Irritable Bowel Syndrome (IBS) is a common gastrointestinal disorder characterized by symptoms such as abdominal pain, bloating, and altered bowel habits. Recent research has focused on the gut microbiota's role in IBS, aiming to identify specific microbial signatures associated with the condition.