Untargeted faecal metabolomics for the discovery of biomarkers and treatment targets for inflammatory bowel diseases

The gut microbiome has been recognised as a key component in the pathogenesis of inflammatory bowel diseases (IBD), and the wide range of metabolites produced by gut bacteria are an important mechanism by which the human microbiome interacts with host immunity or host metabolism. High-throughput metabolomic profiling and novel computational approaches now allow for comprehensive assessment of thousands of metabolites in diverse biomaterials, including faecal samples. Several groups of metabolites, including short-chain fatty acids, tryptophan metabolites and bile acids, have been associated with IBD. In this Recent Advances article, we describe the contribution of metabolomics research to the field of IBD, with a focus on faecal metabolomics. We discuss the latest findings on the significance of these metabolites for IBD prognosis and therapeutic interventions and offer insights into the future directions of metabolomics research.

• Publication year

  2024

• Venue

  Gut

• Publication date

  2024-07-01

• Fields of study

  Biology, Medicine, Chemistry

• Identifiers
  DOI 10.1136/gutjnl-2023-329969PMID 39002973PMCID 11503092
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Host genetic regulation of human gut microbial structural variation

  2024cited by this paper
• Limited predictive value of the gut microbiome and metabolome for response to biological therapy in inflammatory bowel disease

  2024cited by this paper
• Defining predictors of responsiveness to advanced therapies in Crohn’s disease and ulcerative colitis: protocol for the IBD-RESPONSE and nested CD-metaRESPONSE prospective, multicentre, observational cohort study in precision medicine

  2024cited by this paper
• Linking microbial genes to plasma and stool metabolites uncovers host-microbial interactions underlying ulcerative colitis disease course.

  2024cited by this paper
• Heavy arch: from inflammatory bowel diseases to metabolic disorders

  2024cited by this paper
• Nutritional regulation of microbiota-derived metabolites: Implications for immunity and inflammation.

  2024cited by this paper
• Pathobionts in IBD: Origins, Underlying Mechanisms, and Implications for Clinical Care.

  2023cited by this paper
• Key metabolomic alterations are associated with ulcerative colitis disease state and activity: a validation analysis

  2023cited by this paper
• The Involvement of Intestinal Tryptophan Metabolism in Inflammatory Bowel Disease Identified by a Meta-Analysis of the Transcriptome and a Systematic Review of the Metabolome

  2023cited by this paper
• Multi-omic integration of microbiome data for identifying disease-associated modules

  2023cited by this paper
• Gut Microbiome Composition is associated with future onset of Crohn's Disease in Healthy First-Degree Relatives.

  2023cited by this paper
• Knowledge-based Integration of Multi-Omic Datasets with Anansi: Annotation-based Analysis of Specific Interactions

  2023cited by this paper
• Human metabolome variation along the upper intestinal tract

  2023cited by this paper
• Phage-display immunoprecipitation sequencing of the antibody epitope repertoire in inflammatory bowel disease reveals distinct antibody signatures.

  2023cited by this paper
• Inflammation and malnutrition in inflammatory bowel disease.

  2023cited by this paper
• Human microbiome variance is underestimated.

  2023cited by this paper
• Translating metabolomics into clinical practice

  2023cited by this paper
• Amino acids-targeted metabolomics reveals novel diagnostic biomarkers for ulcerative colitis and Crohn’s disease

  2023cited by this paper
• FinnGen provides genetic insights from a well-phenotyped isolated population

  2023cited by this paper
• Faecal metabolome and its determinants in inflammatory bowel disease

  2023influential reference
• Dysbiosis and associated stool features improve prediction of response to biological therapy in inflammatory bowel disease.

  2023cited by this paper
• Reverse metabolomics for the discovery of chemical structures from humans

  2023cited by this paper
• Microbiome and metabolome features in inflammatory bowel disease via multi-omics integration analyses across cohorts

  2023cited by this paper
• Enterobacteriaceae Growth Promotion by Intestinal Acylcarnitines, a Biomarker of Dysbiosis in Inflammatory Bowel Disease

  2023cited by this paper
• Bile acids and the gut microbiota: metabolic interactions and impacts on disease

  2022cited by this paper
• MIMOSA2: a metabolic network-based tool for inferring mechanism-supported relationships in microbiome-metabolome data

  2022cited by this paper
• Rewiring the altered tryptophan metabolism as a novel therapeutic strategy in inflammatory bowel diseases

  2022cited by this paper
• Influence of the microbiome, diet and genetics on inter-individual variation in the human plasma metabolome

  2022cited by this paper
• Mucosal and Plasma Metabolomes in New-onset Paediatric Inflammatory Bowel Disease: Correlations with Disease Characteristics and Plasma Inflammation Protein Markers

  2022cited by this paper
• Diet fuelling inflammatory bowel diseases: preclinical and clinical concepts

  2022cited by this paper
• Location-specific signatures of Crohn’s disease at a multi-omics scale

  2022cited by this paper
• The metabolic nature of inflammatory bowel diseases

  2022cited by this paper
• Using MetaboAnalyst 5.0 for LC–HRMS spectra processing, multi-omics integration and covariate adjustment of global metabolomics data

  2022cited by this paper
• Studying Metabolism by NMR-Based Metabolomics

  2022cited by this paper
• Sphingosine 1-phosphate modulation and immune cell trafficking in inflammatory bowel disease

  2022cited by this paper
• Genome–microbiome interplay provides insight into the determinants of the human blood metabolome

  2022influential reference
• Diets for inflammatory bowel disease: What do we know so far?

  2022cited by this paper
• PUFA-induced metabolic enteritis as a fuel for Crohn's disease.

  2022cited by this paper
• OUP accepted manuscript

  2022cited by this paper
• Multi-omics reveal microbial determinants impacting responses to biologic therapies in inflammatory bowel disease.

  2021cited by this paper
• Mass spectrometry-based metabolomics: a guide for annotation, quantification and best reporting practices

  2021cited by this paper
• Review: microbial transformations of human bile acids

  2021cited by this paper
• Metabolomics facilitate the personalized management in inflammatory bowel disease

  2021cited by this paper
• OUP accepted manuscript

  2021cited by this paper
• Impact of short-chain fatty acid supplementation on gut inflammation and microbiota composition in a murine colitis model.

  2021cited by this paper
• Western and Carnivorous Dietary Patterns are Associated with Greater Likelihood of IBD Development in a Large Prospective Population-based Cohort

  2021cited by this paper
• Integrative analysis of the Inflammatory Bowel Disease serum metabolome improves our understanding of genetic etiology and points to novel putative therapeutic targets.

  2021cited by this paper
• Healthy cotwins share gut microbiome signatures with their inflammatory bowel disease twins and unrelated patients.

  2021cited by this paper
• Mass spectrometry-based metabolomics in microbiome investigations

  2021cited by this paper
• The Effect of Phenotype and Genotype on the Plasma Proteome in Patients with Inflammatory Bowel Disease

  2021cited by this paper
• IBD metabonomics predicts phenotype, disease course, and treatment response

  2021cited by this paper
• Multi-omics analyses of the Ulcerative Colitis gut microbiome link Bacteroides vulgatus proteases with disease severity

  2021cited by this paper
• Decoding the language of microbiomes using word-embedding techniques, and applications in inflammatory bowel disease

  2020cited by this paper
• Gut microbiota-derived metabolites as key actors in inflammatory bowel disease

  2020cited by this paper
• Global chemical effects of the microbiome include new bile-acid conjugations

  2020cited by this paper
• Dysbiosis-Induced Secondary Bile Acid Deficiency Promotes Intestinal Inflammation.

  2020cited by this paper
• Metabonomics and the gut microbiome associated with primary response to anti-TNF therapy in Crohn's disease.

  2020cited by this paper
• Multi-"-Omics" Profiling in Patients With Quiescent Inflammatory Bowel Disease Identifies Biomarkers Predicting Relapse.

  2020cited by this paper
• Integrating multi-OMICS data through sparse canonical correlation analysis for the prediction of complex traits: a comparison study

  2020cited by this paper
• Multi-omic Analysis of the Interaction between Clostridioides difficile Infection and Pediatric Inflammatory Bowel Disease.

  2020cited by this paper
• Gut microbiota in human metabolic health and disease

  2020cited by this paper
• The Gut Microbiota at the Service of Immunometabolism.

  2020cited by this paper
• Author Correction: Nutriome–metabolome relationships provide insights into dietary intake and metabolism

  2020cited by this paper
• Gastrointestinal Surgery for Inflammatory Bowel Disease Persistently Lowers Microbiome and Metabolome Diversity

  2020cited by this paper
• Correction: Decoding the language of microbiomes using word-embedding techniques, and applications in inflammatory bowel disease

  2020cited by this paper
• Mitochondrial dysfunction in inflammatory bowel disease alters intestinal epithelial metabolism of hepatic acylcarnitines.

  2020cited by this paper
• A reference map of potential determinants for the human serum metabolome

  2020cited by this paper
• Learning accurate representations of microbe-metabolite interactions

  2019cited by this paper
• The global, regional, and national burden of inflammatory bowel disease in 195 countries and territories, 1990–2017: a systematic analysis for the Global Burden of Disease Study 2017

  2019cited by this paper
• Therapeutic Opportunities in Inflammatory Bowel Disease: Mechanistic Dissection of Host-Microbiome Relationships.

  2019cited by this paper
• The intestinal microbiota fuelling metabolic inflammation

  2019cited by this paper
• Corrigendum: Short Chain Fatty Acids (SCFAs)-Mediated Gut Epithelial and Immune Regulation and Its Relevance for Inflammatory Bowel Diseases

  2019cited by this paper
• Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases

  2019cited by this paper
• Bacteroides-Derived Sphingolipids Are Critical for Maintaining Intestinal Homeostasis and Symbiosis.

  2019cited by this paper
• Short Chain Fatty Acids (SCFAs)-Mediated Gut Epithelial and Immune Regulation and Its Relevance for Inflammatory Bowel Diseases

  2019cited by this paper
• The Role of Dietary Nutrients in Inflammatory Bowel Disease

  2019cited by this paper
• The 1000IBD project: multi-omics data of 1000 inflammatory bowel disease patients; data release 1

  2019cited by this paper
• Microbial tryptophan catabolites in health and disease

  2018cited by this paper
• Gut Microbiota Regulation of Tryptophan Metabolism in Health and Disease.

  2018cited by this paper
• The fecal metabolome as a functional readout of the gut microbiome

  2018cited by this paper
• Gut microbiota composition and functional changes in inflammatory bowel disease and irritable bowel syndrome

  2018cited by this paper
• Gut microbiome structure and metabolic activity in inflammatory bowel disease

  2018cited by this paper
• Review of recent developments in GC–MS approaches to metabolomics-based research

  2018cited by this paper
• Microbiota-Derived Indole Metabolites Promote Human and Murine Intestinal Homeostasis through Regulation of Interleukin-10 Receptor.

  2018cited by this paper
• Fecal Microbiota Signatures Are Associated with Response to Ustekinumab Therapy among Crohn’s Disease Patients

  2018cited by this paper
• Microbiota-derived short-chain fatty acids promote Th1 cell IL-10 production to maintain intestinal homeostasis

  2018cited by this paper
• Plasma Nuclear Magnetic Resonance Metabolomics Discriminates Between High and Low Endoscopic Activity and Predicts Progression in a Prospective Cohort of Patients With Ulcerative Colitis

  2018cited by this paper
• Dietary and metabolomic determinants of relapse in ulcerative colitis patients: A pilot prospective cohort study

  2017influential reference
• Prediction of complicated disease course for children newly diagnosed with Crohn's disease: a multicentre inception cohort study.

  2017cited by this paper
• Gut Microbiome Function Predicts Response to Anti-integrin Biologic Therapy in Inflammatory Bowel Diseases.

  2017cited by this paper
• Alterations in lipid, amino acid, and energy metabolism distinguish Crohn’s disease from ulcerative colitis and control subjects by serum metabolomic profiling

  2017cited by this paper
• Dysbiosis and the immune system

  2017cited by this paper
• Cross sectional evaluation of the gut-microbiome metabolome axis in an Italian cohort of IBD patients

  2017cited by this paper
• The gut microbiota of siblings offers insights into microbial pathogenesis of inflammatory bowel disease

  2017cited by this paper
• Comparing metabolite profiles of habitual diet in serum and urine.

  2016cited by this paper
• The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

  2015cited by this paper
• Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations

  2015cited by this paper
• The strengths and weaknesses of NMR spectroscopy and mass spectrometry with particular focus on metabolomics research.

  2015cited by this paper
• Fecal Microbiota in Pediatric Inflammatory Bowel Disease and Its Relation to Inflammation

  2015cited by this paper
• UK Biobank: An Open Access Resource for Identifying the Causes of a Wide Range of Complex Diseases of Middle and Old Age

  2015cited by this paper

• Current status and future perspectives of fecal immunological markers in the differential diagnosis of Clostridioides difficile infection in children.

  2026cites this paper
• Multi-omics Analyses of Facial Skin in Acne Identify Distinct Microbial and Metabolic Features at Lesional and Non-lesional Sites

  2026cites this paper
• Unlocking therapeutic impacts of the gut microbiota with computational tools

  2026cites this paper
• A 4-guanidinobutanoic acid-SLC36A1 axis drives a microbiota‒host feedback loop to regulate intestinal homeostasis.

  2026cites this paper
• Metabolic profiles of amino acids in patients with crohn’s disease-associated perianal fistulas and cryptoglandular anal fistulas

  2026cites this paper
• Effect of traditional Chinese medicine on disturbances of untargeted metabolomics in ulcerative colitis.

  2026cites this paper
• The interplay mechanisms between gut microbiota and ferroptosis in inflammatory bowel disease

  2026cites this paper
• Two-Dimensional PCR for Simultaneous Detection of Fecal Bacterial Markers in the Diagnosis and Management of Inflammatory Bowel Disease

  2026cites this paper
• A synbiotic combination of arabinogalactan and Bacteroides thetaiotaomicron ameliorates ulcerative colitis in mice.

  2026cites this paper
• Lactobacillus rhamnosus GG Alleviates Post-Weaning Stress-Induced Intestinal Barrier Damage and Inflammation by Promoting Intestinal Health and Modulating the Gut Microbiota in Piglets.

  2026cites this paper
• Nutritional Deficiencies and Reduced Bone Mineralization in Ulcerative Colitis

  2025cites this paper
• Elevated butyric acid and histamine in feces and serum as an indicator of onset of necrotic enteritis in broiler chickens

  2025cites this paper
• Assessing the safety of microbiome perturbations.

  2025cites this paper
• The Effects of Fecal Microbial Transplantation on the Symptoms in Autism Spectrum Disorder, Gut Microbiota and Metabolites: A Scoping Review

  2025cites this paper
• Application of machine learning in the discovery of antimicrobial peptides: exploring their potential for ulcerative colitis therapy

  2025cites this paper
• Faecalibacterium prausnitzii Ameliorates DSS-Induced Colitis via Modulating Bile Acid Metabolism and Regulating FXR Signaling

  2025cites this paper
• Kynurenic acid derived from mesentery regulates mesenteritis and colitis via inducing white adipose browning in Crohn’s disease

  2025cites this paper
• Integrated Metabolomics and Gut Microbiome Analysis Reveal the Role of Demethylzeylasteral in Alleviating Ulcerative Colitis in Mice.

  2025cites this paper
• The dysbiosis of gut microbiota and dysregulation of metabolites in IgA nephropathy and membranous nephropathy

  2025cites this paper
• Metabolomics-Based Investigation Elucidates the Anti-Ulcerative Colitis Effect of Kaempferol.

  2025cites this paper
• Antioxidative nanozyme-fucoidan embedded nanoclay gel mediated mitochondrial energy recovery and bile acid balance against ulcerative colitis

  2025cites this paper
• Chronic Exposure to Sunset Yellow Promotes Susceptibility to Experimental Colitis in Mice through Gut Microbiota.

  2025cites this paper
• Synergistic protective effects of β-glucan and Lactobacillus johnsonii NSP009 in ulcerative colitis.

  2025cites this paper
• Microbiome and Metabolome Alterations in Nrf2 Knockout Mice With Induced Gut Inflammation and Fed With Phenethyl Isothiocyanate and Cranberry Enriched Diets

  2025cites this paper
• Identification of Biomarkers for Treatment Escalation of Ulcerative Colitis Based on Untargeted Metabolomics and Machine Learning Algorithms: A Prospective Cohort Study

  2025cites this paper
• Metabolomics reveals the hindgut metabolic changes and physiological impacts in weaned piglets subjected to ETEC infection and berberine intervention

  2025cites this paper
• Characterization of Intestinal Mycobiome in Surgical Resections from Inflammatory Bowel Disease Patients: A Deeper Analysis in Complicated Crohn’s Disease Phenotypes

  2025cites this paper
• A missense mutation in Muc2 promotes gut microbiome and metabolome-dependent colitis-associated tumorigenesis

  2025cites this paper
• (R)-Bambuterol Attenuates DSS-Induced Chronic Colitis by Suppressing Inflammation, Repairing Intestinal Barrier, and Modulating Gut Microbiota and Serum Metabolomic Profile.

  2025cites this paper
• Gut microbiota modulation by polysaccharide from Aloe gel: Potential prebiotic and targeted regulatory effects.

  2025cites this paper
• From pathogenic mechanisms to therapeutic perspectives: a review of gut microbiota and intestinal mucosal immunity in inflammatory bowel disease

  2025cites this paper
• Targeting Fcgr1 to repress FAPy-adenine-induced osteoporosis in osteosarcoma receiving chemotherapy

  2025cites this paper
• Nutrigenomics meets multi-omics: integrating genetic, metabolic, and microbiome data for personalized nutrition strategies

  2025cites this paper
• Engineering probiotics for inflammatory bowel disease: Strategies and perspectives

  2025cites this paper
• Integrating gut microbiota and metabolomics in pediatric inflammatory bowel disease: insights into pathogenesis and potential role of precision medicine

  2025cites this paper
• Machine learning approach and internet of things technologies to unravel the complex interaction between microbiome-metabolome in inflammatory bowel disease: a new frontier in precision medicine

  2025cites this paper
• Gut microbiota metabolites in the immunoregulation of enteritis: research progress

  2025cites this paper
• Sulforaphane Ameliorates DSS-Induced Colitis and Secondary Liver Injury in Mice: Proposed Mechanism in the SCFAs-FFAR2/3-Macrophage Polarization Axis.

  2025cites this paper
• Metabolic Dysregulation Reshapes the Immune Landscape: The Gut Microbiota-mTOR Axis in Respiratory Viral Infection Immunity.

  2025cites this paper
• Altered Metabolites at Birth in Individuals With Later Inflammatory Bowel Disease: A Danish Cohort Study.

  2025cites this paper
• A missense mutation in Muc2 promotes gut microbiome- and metabolome-dependent colitis-associated tumorigenesis

  2025cites this paper
• Larch Arabinogalactan Alleviates Colitis by Modulating Gut Microbiota and Promoting Bacteroides thetaiotaomicron.

  2025cites this paper
• Exploring diet-microbiota interactions and therapeutic nutrition management in inflammatory bowel disease

  2025cites this paper
• Precision microbial regulation: Strategies for modulating GIT microbiota for host health

  2025cites this paper
• Quzhou Aurantii Fructus Flavonoids Ameliorate Inflammatory Responses, Intestinal Barrier Dysfunction in DSS-Induced Colitis by Modulating PI3K/AKT Signaling Pathway and Gut Microbiome

  2025cites this paper
• Uncovering de novo polyamine biosynthesis in the gut microbiome and its alteration in inflammatory bowel disease

  2025cites this paper
• Tryptophan metabolites profile predict remission with dietary therapy in pediatric Crohn’s disease

  2025cites this paper
• Untargeted Metabolomic Profiling of Colonic Mucosa in Individuals with Irritable Bowel Syndrome

  2025cites this paper
• Integrating multi-omics data to reveal the host-microbiota interactome in inflammatory bowel disease

  2025cites this paper
• Fecal microbiota transplantation: application scenarios, efficacy prediction, and factors impacting donor-recipient interplay

  2025cites this paper
• Molecular Mechanisms and Emerging Precision Therapeutics in the Gut Microbiota-Cardiovascular Axis

  2025cites this paper
• Rewiring Tryptophan Metabolism via Programmable Probiotic Integrated by Dual-Layered Microcapsule Protects against Inflammatory Bowel Disease in Mice.

  2024cites this paper
• Bile Acids in Inflammatory Bowel Disease: From Pathophysiology to Treatment

  2024cites this paper
• The prebiotic and targeted regulatory effects of konjac glucomannan on gut microbiota via multi-omics analysis

  year unknowncites this paper