Longitudinal Multi-omics Reveals Subset-Specific Mechanisms Underlying Irritable Bowel Syndrome
Open accessAbstract
The gut microbiome has been implicated in multiple human chronic gastrointestinal (GI) disorders. Determining its mechanistic role in disease has been difficult due to apparent disconnects between animal and human studies and lack of an integrated multi-omics view of disease-specific physiological changes. We integrated longitudinal multi-omics data from the gut microbiome, metabolome, host epigenome, and transcriptome in the context of irritable bowel syndrome (IBS) host physiology. We identified IBS subtype-specific and symptom-related variation in microbial composition and function. A subset of identified changes in microbial metabolites correspond to host physiological mechanisms that are relevant to IBS. By integrating multiple data layers, we identified purine metabolism as a novel host-microbial metabolic pathway in IBS with translational potential. Our study highlights the importance of longitudinal sampling and integrating complementary multi-omics data to identify functional mechanisms that can serve as therapeutic targets in a comprehensive treatment strategy for chronic GI diseases. VIDEO ABSTRACT.
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An integrated longitudinal multi-omics analysis of the gut microbiome, metabolome, host epigenome and transcriptome, in the context of host symptoms and physiology in patients with IBS-D and IBS-C, identified subtype-specific and symptom-related variations in microbial composition and function.
“However, an integrated longitudinal multi-omics analysis of the gut microbiome, metabolome, host epigenome and transcriptome, in the context of host symptoms and physiology in patients with IBS-D and IBS-C, identified subtype-specific and symptom-related variations in microbial composition and function.76”
From British Society of Gastroenterology guidelines on the management of irritable bowel syndrome (2021) · cites this paper as [76]
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Yu, Y., Mai, Y., Zheng, Y., & Shi, L. M. (2024) · Genome biology · doi:10.1186/s13059-024-03401-9 · Cited by 231 · see citing works
“Batch effects can be commonly seen in omics data, such as genomics [5–8], transcriptomics [4, 9, 10], proteomics, metabolomics [11], and multiomics integration [12, 13].”
BackgroundSasso, J. M., Ammar, R. M., Tenchov, R., Lemmel, S. A., Kelber, O., Grieswelle, M., & Zhou, Q. A. (2023) · ACS Chemical Neuroscience · doi:10.1021/acschemneuro.3c00127 · Cited by 217 · see citing works
Mechanisms and implications of the gut microbial modulation of intestinal metabolic processes
Jyoti, & Dey, P. (2025) · npj Metabolic Health and Disease · doi:10.1038/s44324-025-00066-1 · Cited by 216 · see citing works
“Longitudinal multi-omics investigations of stool samples from individuals with IBD have shown reduced amounts of SCFA levels and purine deprivation, necessary for glutathione formation and maintenance of a redox microenvironment 112 .”
Host genetic regulation of human gut microbial structural variation
Zhernakova, D. V., Wang, D., Liu, L., Andreu-Sánchez, S., Zhang, Y., Ruiz-Moreno, A. J., Peng, H., Plomp, N., Del Castillo-Izquierdo, Á., Gacesa, R., et al. (2024) · Nature · doi:10.1038/s41586-023-06893-w · Cited by 174 · see citing works
Multi-omic approaches for host-microbiome data integration
Chetty, A., & Blekhman, R. (2024) · Gut Microbes · doi:10.1080/19490976.2023.2297860 · Cited by 183 · see citing works
Self-citationThe Gut Microbial Bile Acid Modulation and Its Relevance to Digestive Health and Diseases
Fogelson, K. A., Dorrestein, P. C., Zarrinpar, A., & Knight, R. (2023) · Gastroenterology · doi:10.1053/j.gastro.2023.02.022 · Cited by 177 · see citing works
Guo, C., Che, X., Briese, T., Ranjan, A. K., Allicock, O. M., Yates, R. A., Cheng, A., March, D., Hornig, M., Komaroff, A. L., et al. (2023) · Cell Host & Microbe · doi:10.1016/j.chom.2023.01.004 · Cited by 175 · see citing works
“65,66”
Priya, S., Burns, M. B., Ward, T., Mars, R. A. T., Adamowicz, E. M., Lock, E. F., Kashyap, P., Knights, D., & Blekhman, R. (2022) · Nature Microbiology · doi:10.1038/s41564-022-01121-z · Cited by 171 · see citing works
Self-citationGut enterochromaffin cells drive visceral pain and anxiety
Bayrer, J. R., Castro, J., Venkataraman, A., Touhara, K. K., Rossen, N. D., Morrie, R. D., Maddern, J., Hendry, A., Braverman, K. N., Garcia‐Caraballo, S., et al. (2023) · Nature · doi:10.1038/s41586-023-05829-8 · Cited by 163 · see citing works
The enteric nervous system in gastrointestinal disease etiology
Holland, A. M., Bon‐Frauches, A. C., Keszthelyi, D., Melotte, V., & Boesmans, W. (2021) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-021-03812-y · Cited by 164 · see citing works
Gut Microbiota-Derived Metabolites in Irritable Bowel Syndrome
Xiao, L., Liu, Q., Luo, M., & Xiong, L. (2021) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2021.729346 · Cited by 161 · see citing works
“There are significant differences in the concentration of BAs in feces and serum between IBS-C and IBS-D patients (Wong et al., 2012).”
BackgroundInfluentialPalma, G. D., Shimbori, C., Reed, D. E., Yu, Y., Rabbia, V., Lu, J., Jiménez-Vargas, N. N., Sessenwein, J. L., López-López, C., Pigrau, M., et al. (2022) · Science Translational Medicine · doi:10.1126/scitranslmed.abj1895 · Cited by 159 · see citing works
“(H) Shown is the relative abundance of the hdc gene in the fecal microbiota of healthy controls (HC) and patients with IBS in a published study (16).”
BackgroundMethodInfluentialSavarino, E., Zingone, F., Barberio, B., Marasco, G., Akyuz, F., Akpınar, H., Bărboi, O., Bodini, G., Bor, S., Chiarioni, G., et al. (2022) · United European Gastroenterology journal · doi:10.1002/ueg2.12259 · Cited by 136 · see citing works
“Overall there is substantial heterogeneity among available studies regarding a link between specific microbiota alterations and IBS subtypes and symptom patterns,(108) even though more recent studies suggest an association with IBS symptom severity(109) and specific subtypes when using a longitudinal multi‐ omics appr…”
Vanuytsel, T., Berčík, P., & Boeckxstaens, G. E. (2023) · Gut · doi:10.1136/gutjnl-2020-320633 · Cited by 157 · see citing works
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Teng, H., Wang, Y., Sui, X., Fan, J., Li, S., Lei, X., Shi, C., Sun, W., Song, M., Wang, H., et al. (2022) · Cancer Cell · doi:10.1016/j.ccell.2022.11.013 · Cited by 151 · see citing works
Pan, R., Wang, L., Xu, X., Chen, Y., Wang, H., Wang, G., Zhao, J., & Chen, W. (2022) · Nutrients · doi:10.3390/nu14183704 · Cited by 149 · see citing works
“In addition, chronic intestinal disease is accompanied by disease exacerbation and remission; a single cross-sectional sampling cannot fully characterize the bacterial composition of the disease which is characterized by temporal heterogeneity [22].”
BackgroundInfluentialNoninvasive, microbiome-based diagnosis of inflammatory bowel disease
Zheng, J., Sun, Q., Zhang, M., Liu, C., Su, Q., Zhang, L., Xu, Z., Lu, W., Ching, J. Y. L., Tang, W., et al. (2024) · Nature Medicine · doi:10.1038/s41591-024-03280-4 · Cited by 144 · see citing works
Mucosal Biofilms Are an Endoscopic Feature of Irritable Bowel Syndrome and Ulcerative Colitis
Baumgartner, M., Lang, M., Holley, H., Crepaz, D., Hausmann, B., Pjevac, P., Moser, D., Haller, F., Hof, F., Beer, A., et al. (2021) · Gastroenterology · doi:10.1053/j.gastro.2021.06.024 · Cited by 142 · see citing works
Lippa, K. A., Aristizabal‐Henao, J. J., Beger, R. D., Bowden, J. A., Broeckling, C. D., Beecher, C., Davis, W. C., Dunn, W. B., Flores, R., Goodacre, R., et al. (2022) · Metabolomics · doi:10.1007/s11306-021-01848-6 · Cited by 140 · see citing works
Probiotics synergized with conventional regimen in managing Parkinson’s disease
Sun, H., Zhao, F., Liu, Y., Ma, T., Jin, H., Quan, K., Leng, B., Zhao, J., Yuan, X., Li, Z., et al. (2022) · npj Parkinson's Disease · doi:10.1038/s41531-022-00327-6 · Cited by 136 · see citing works
Self-citationBushyhead, D. W., & Quigley, E. M. M. (2022) · Gastroenterology · doi:10.1053/j.gastro.2022.04.002 · Cited by 135 · see citing works
Faecal microbiome-based machine learning for multi-class disease diagnosis
Su, Q., Liu, Q., Lau, R. I., Zhang, J., Xu, Z., Yeoh, Y. K., Leung, T. W. H., Tang, W., Zhang, L., Liang, Q., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-34405-3 · Cited by 135 · see citing works
‘Multi-omics’ data integration: applications in probiotics studies
Kwoji, I. D., Aiyegoro, O. A., Okpeku, M., & Adeleke, M. A. (2023) · npj Science of Food · doi:10.1038/s41538-023-00199-x · Cited by 135 · see citing works
Gut microbiota-motility interregulation: insights from in vivo, ex vivo and in silico studies
Waclawiková, B., Codutti, A., Alim, K., & Aidy, S. E. (2022) · Gut Microbes · doi:10.1080/19490976.2021.1997296 · Cited by 129 · see citing works
“Moreover, both tryptophan and tryptamine were significantly increased in fecal samples from diarrhea-predominant irritable bowel syndrome (IBS-D) patients, suggesting that these metabolites might be responsible for the higher water content of feces in IBS-D.(118) Another gut bacterial metabolite of tryptophan is indol…”
BackgroundArıkan, M., & Muth, T. (2023) · Molecular Omics · doi:10.1039/d3mo00089c · Cited by 128 · see citing works
Nishijima, S., Stankevič, E., Aasmets, O., Schmidt, T., Nagata, N., Keller, M. I., Ferretti, P., Juel, H. B., Fullam, A., Robbani, S. M., et al. (2024) · Cell · doi:10.1016/j.cell.2024.10.022 · Cited by 126 · see citing works
Zhai, L., Xiao, H., Lin, C., Wong, H. L. X., Lam, Y. Y., Gong, M., Wu, G. G., Ning, Z., Huang, C., Zhang, Y., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-40552-y · Cited by 127 · see citing works
Multi ‘omic data integration: A review of concepts, considerations, and approaches
Santiago-Rodríguez, T. M., & Hollister, E. B. (2021) · Seminars in Perinatology · doi:10.1016/j.semperi.2021.151456 · Cited by 124 · see citing works
Jacobs, J. P., Lagishetty, V., Hauer, M. C., Labus, J. S., Dong, T. S., Toma, R., Vuyisich, M., Naliboff, B. D., Lackner, J. M., Gupta, A., et al. (2023) · Microbiome · doi:10.1186/s40168-022-01450-5 · Cited by 123 · see citing works
“IBS-D was characterized by increased cholate and isoursodeoxycholate, which is consistent with prior studies reporting increased levels of cholate in IBS-D compared to IBS-C and bile acid malabsorption in IBS-D [14, 16].”
ResultMulti-omic integration of microbiome data for identifying disease-associated modules
Muller, E., Shiryan, I., & Borenstein, E. (2024) · Nature Communications · doi:10.1038/s41467-024-46888-3 · Cited by 132 · see citing works
Irritable bowel syndrome: treatment based on pathophysiology and biomarkers
Camilleri, M., & Boeckxstaens, G. E. (2022) · Gut · doi:10.1136/gutjnl-2022-328515 · Cited by 122 · see citing works
Self-citationWei, L., Singh, R., Ro, S., & Ghoshal, U. C. (2021) · JGH Open · doi:10.1002/jgh3.12528 · Cited by 127 · see citing works
Immune activation in irritable bowel syndrome: what is the evidence?
Aguilera‐Lizarraga, J., Hussein, H., & Boeckxstaens, G. E. (2022) · Nature reviews. Immunology · doi:10.1038/s41577-022-00700-9 · Cited by 109 · see citing works
Singh, R., Zogg, H., Ghoshal, U. C., & Ro, S. (2022) · Frontiers in Pharmacology · doi:10.3389/fphar.2022.808195 · Cited by 106 · see citing works
“Gut dysmotility and visceral pain are associated with elevated BA levels in IBS-D patients (Mars et al., 2020).”
BackgroundYang, S.-Y., Han, S. M., Lee, J., Kim, K. S., Lee, J. E., & Lee, D. (2025) · Journal of Microbiology and Biotechnology · doi:10.4014/jmb.2412.12001 · Cited by 112 · see citing works
“Notably, multi-omics research on irritable bowel syndrome (IBS) has identified symptom-associated microbial compositions and functional phenotypes, underscoring the potential of this approach to uncover disease-specific microbial markers in heterogeneous conditions [168, 169].”
Self-citationGut microbial DL-endopeptidase alleviates Crohn’s disease via the NOD2 pathway
Gao, J., Zhao, X., Hu, S., Huang, Z., Hu, M., Jin, S., Lu, B., Sun, K., Wang, Z., Fu, J., et al. (2022) · Cell Host & Microbe · doi:10.1016/j.chom.2022.08.002 · Cited by 103 · see citing works
Gut virome in inflammatory bowel disease and beyond
Tun, H. M., Peng, Y., Massimino, L., Sin, Z. Y., Parigi, T. L., Facoetti, A., Rahman, S., Danese, S., & Ungaro, F. (2023) · Gut · doi:10.1136/gutjnl-2023-330001 · Cited by 93 · see citing works
“The concept of the human ‘virotype’ 29 or that the virome regulates transcription in asymptomatic hosts depending on host genetics is particularly intriguing in the setting of IBS.”
BackgroundWang, D., Doestzada, M., Chen, L., Andreu‐Sánchez, S., van den Munckhof, I., Augustijn, H. E., Koehorst, M., Ruiz-Moreno, A. J., Bloks, V. W., Riksen, N. P., et al. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2021.11.003 · Cited by 94 · see citing works
The role of microbiota-mitochondria crosstalk in pathogenesis and therapy of intestinal diseases
Zhang, Y., Zhang, J., & Duan, L. (2022) · Pharmacological Research · doi:10.1016/j.phrs.2022.106530 · Cited by 92 · see citing works
A key genetic factor governing arabinan utilization in the gut microbiome alleviates constipation
Zhang, C., Yu, L., Ma, C., Jiang, S., Zhang, Y., Wang, S., Tian, F., Xue, Y., Zhao, J., Zhang, H., et al. (2023) · Cell Host & Microbe · doi:10.1016/j.chom.2023.10.011 · Cited by 90 · see citing works
Role of gut microbiota-derived signals in the regulation of gastrointestinal motility
Zheng, Z., Tang, J., Hu, Y., & Zhang, W. (2022) · Frontiers in Medicine · doi:10.3389/fmed.2022.961703 · Cited by 91 · see citing works
“Accordingly, a longitudinal multi-omics study in humans demonstrates that tryptamine is elevated in the stools of a subset of IBS patients with diarrhea (107).”
BackgroundDiet and gut microbiome in gastrointestinal disease
Trakman, G., Fehily, S. R., Basnayake, C., Hamilton, A. L., Russell, E., Wilson-O'Brien, A. L., & Kamm, M. A. (2021) · Journal of Gastroenterology and Hepatology · doi:10.1111/jgh.15728 · Cited by 88 · see citing works
Napolitano, M., Fasulo, E., Ungaro, F., Massimino, L., Sinagra, E., Danese, S., & Mandarino, F. V. (2023) · Microorganisms · doi:10.3390/microorganisms11102369 · Cited by 91 · see citing works
“By modifying epigenetic processes controlling host gene expression, microbial metabolites may contribute to intestinal and neural changes underlying IBS [73,74].”
BackgroundResultThe Influence of Nutrition on Intestinal Permeability and the Microbiome in Health and Disease
Inczefi, O., Bacsúr, P., Resál, T., Keresztes, C., & Molnár, T. (2022) · Frontiers in Nutrition · doi:10.3389/fnut.2022.718710 · Cited by 85 · see citing works
“Novel results in microbiome studies suggest that microbial metabolic products are common factors that determine health or disease conditions (77).”
BackgroundApplications of human organoids in the personalized treatment for digestive diseases
Wang, Q., Guo, F., Jin, Y., & Ma, Y. (2022) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-022-01194-6 · Cited by 81 · see citing works
The gut microbiome-metabolome dataset collection: a curated resource for integrative meta-analysis
Muller, E., Algavi, Y. M., & Borenstein, E. (2022) · npj Biofilms and Microbiomes · doi:10.1038/s41522-022-00345-5 · Cited by 79 · see citing works
Enteric Microbiota-Mediated Serotonergic Signaling in Pathogenesis of Irritable Bowel Syndrome
Mishima, Y., & Ishihara, S. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms221910235 · Cited by 77 · see citing works
Wu, J., Singleton, S. S., Bhuiyan, U., Krammer, L., & Mazumder, R. (2024) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2023.1337373 · Cited by 83 · see citing works
The gut microbiome in disorders of gut–brain interaction
Kraïmi, N., Ross, T., Pujo, J., & Palma, G. D. (2024) · Gut Microbes · doi:10.1080/19490976.2024.2360233 · Cited by 86 · see citing works
Mujagic, Z., Kasapi, M., Jonkers, D. M. A. E., García‐Pérez, I., Vork, L., Weerts, Z. Z. R. M., Serrano-Contreras, J. I., Zhernakova, A., Kurilshikov, A., Scotcher, J., et al. (2022) · Gut Microbes · doi:10.1080/19490976.2022.2063016 · Cited by 77 · see citing works
Integrative multi-omics approaches to explore immune cell functions: Challenges and opportunities
Wang, X., Dian, F., Yang, Y., Gimple, R. C., & Zhou, S. (2023) · iScience · doi:10.1016/j.isci.2023.106359 · Cited by 79 · see citing works
“83 In addition, microbial taxonomic shifts and prognosis related microbial taxa were also confirmed by metagenomics in patients with hepatobiliary cancers before and during anti-PD-1 therapy.”
Self-citationLu, L., Dong, J., Liu, Y., Qian, Y., Zhang, G., Zhou, W., Zhao, A., Ji, G., & Xu, H. (2022) · Frontiers in Pharmacology · doi:10.3389/fphar.2022.964793 · Cited by 73 · see citing works
Gut Microbiota and its Metabolites: Bridge of Dietary Nutrients and Alzheimer’s Disease
Zhu, G., Zhao, J., Zhang, H., Wang, G., & Chen, W. (2023) · Advances in Nutrition · doi:10.1016/j.advnut.2023.04.005 · Cited by 75 · see citing works
A meta-analysis study of the robustness and universality of gut microbiome-metabolome associations
Muller, E., Algavi, Y. M., & Borenstein, E. (2021) · Microbiome · doi:10.1186/s40168-021-01149-z · Cited by 73 · see citing works
“A smaller subset of such studies further apply machine learning techniques for this purpose, and new machine learning-based tools have been recently introduced [20, 33, 34, 41, 90, 91].”
BackgroundGut Microbiome in Anesthesiology and Pain Medicine
Minerbi, A., & Shen, S. (2022) · Anesthesiology · doi:10.1097/aln.0000000000004204 · Cited by 73 · see citing works
“tate), alterations in luminal bile acids, and dysregulation of the purine salvage pathway.(90) Finally, the utility of gut microbiome manipulation by means of dietary measures,(93) probiotics, and fecal microbiome transplantation(43,94) have”
BackgroundGut microbiota supports male reproduction via nutrition, immunity, and signaling
Cai, H., Cao, X.-H., Qin, D., Liu, Y.-D., Liu, Y., Hua, J., & Peng, S. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.977574 · Cited by 65 · see citing works
“With the establishment of gene expression profiles and metabolomics, researchers can now locate the transverse spatial organization and longitudinal phase states of GM (Tropini et al., 2017; Mars et al., 2020).”
BackgroundHost-microbial interactions in the metabolism of different dietary fats
Chadaideh, K. S., & Carmody, R. N. (2021) · Cell Metabolism · doi:10.1016/j.cmet.2021.04.011 · Cited by 63 · see citing works
Multi-Omics Analyses Show Disease, Diet, and Transcriptome Interactions With the Virome
Mihindukulasuriya, K. A., Mars, R. A. T., Johnson, A. J., Ward, T., Priya, S., Lekatz, H. R., Kalari, K. R., Droit, L., Zheng, T., Blekhman, R., et al. (2021) · Gastroenterology · doi:10.1053/j.gastro.2021.06.077 · Cited by 64 · see citing works
Self-citationXiao, K., Liang, X., Lu, H., Li, X., Zhang, Z., Lu, X., Wang, H., Meng, Y., Roy, A., Luo, W., et al. (2022) · The ISME Journal · doi:10.1038/s41396-022-01247-2 · Cited by 59 · see citing works
Xu, Y., Wang, J., Wu, X., Jing, H., Zhang, S., Hu, Z., Rao, L., Chang, Q., Wang, L., & Zhang, Z. (2023) · Gut Microbes · doi:10.1080/19490976.2023.2168101 · Cited by 61 · see citing works
“Gut microbiota are being recognized as vital masters in maintaining host health, especially normal gastrointestinal functions, and fecal microbiome alterations are being accepted as essential etiological causes for numerous gastroenteric disorders, such as inflammatory bowel disease (IBD) and irritable bowel syndrome…”
BackgroundRengarajan, S., Knoop, K. A., Rengarajan, A., Chai, J. N., Grajales‐Reyes, J. G., Samineni, V. K., Russler-Germain, E. V., Ranganathan, P., Fasano, A., Sayuk, G. S., et al. (2020) · Cell Reports Medicine · doi:10.1016/j.xcrm.2020.100124 · Cited by 61 · see citing works
“44 Notably, IBS-D patients displayed significantly higher IgA-bound fecal bacteria than healthy individuals (Figure 5A), as well as patients with intestinal (celiac sprue) and non-intestinal (rheumatoid arthritis) immune disorders (Figure S5A).”
Self-citationWei, L., Singh, R., & Ghoshal, U. C. (2022) · Journal of Neurogastroenterology and Motility · doi:10.5056/jnm22008 · Cited by 65 · see citing works
“Gut microbiota dysbiosis induces alternations in the bile acid (BA) pool.67,68 On the contrary, reduction in BA levels influences gut microbial diversity leading to gut microbiota dysbiosis.69 A higher amount of BAs results in increased intestinal fluid secretion.10 Excess fecal BAs in diarrhea-predominant IBS (IBSD)…”
BackgroundInfluentialOmics and Multi-Omics in IBD: No Integration, No Breakthroughs
Fiocchi, C. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms241914912 · Cited by 62 · see citing works
Microbiota dysbiosis in primary Sjögren’s syndrome and the ameliorative effect of hydroxychloroquine
Wang, X., Pang, K., Wang, J., Zhang, B., Liu, Z., Lu, S., Xu, X., Zhu, L., Zhou, Z., Niu, M., et al. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.111352 · Cited by 55 · see citing works
Huang, Z., Liu, K., Ma, W., Li, D., Mo, T., & Liu, Q. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.1018594 · Cited by 59 · see citing works
“The biomarkers detected by these -omics technologies could help to elucidate potential mechanisms of these commensals in health and disease (LloydPrice et al., 2019; Zhou et al., 2019; Mars et al., 2020).”
BackgroundLow FODMAP diet for treatment of irritable bowel syndrome
Young, E., Vasquez, L. S. R., Lim, A. H. W., & Philpott, H. (2022) · Cochrane Database of Systematic Reviews · doi:10.1002/14651858.cd014029 · Cited by 55 · see citing works
Microbiome and Allergy: New Insights and Perspectives
Zubeldia‐Varela, E., Barker‐Tejeda, T. C., Obeso, D., Villaseñor, A., Barber, D., & Pérez‐Gordo, M. (2022) · Journal of Investigational Allergology and Clinical Immunology · doi:10.18176/jiaci.0852 · Cited by 56 · see citing works
Shang, Z., Pai, L., & Patil, S. (2024) · Frontiers in Nutrition · doi:10.3389/fnut.2024.1395664 · Cited by 54 · see citing works
“The fermentation of fiber by these bacteria produces short-chain fatty acids (SCFAs)—which are organic acids produced by gut bacteria during the fermentation of dietary fiber (Table 1), which possess anti-inflammatory properties and contribute to gut health (15, 16).”
BackgroundMars, R. A. T., Frith, M., & Kashyap, P. (2020) · Gastroenterology · doi:10.1053/j.gastro.2020.10.058 · Cited by 54 · see citing works
Self-citationXie, C., Teng, J., Wang, X., Xu, B., Niu, Y., Ma, L., & Yan, X. (2021) · Animal nutrition · doi:10.1016/j.aninu.2021.10.010 · Cited by 53 · see citing works
IgA in human health and diseases: Potential regulator of commensal microbiota
Takeuchi, T., & Ohno, H. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.1024330 · Cited by 53 · see citing works
“In addition to IBD, it has been recognized that irritable bowel syndrome (IBS) is also associated with altered gut microbiota and their metabolites (101, 102), which is characterized by an increase in pathobionts such as the family Enterobacteriaceae (101).”
BackgroundWhat Has Longitudinal ‘Omics’ Studies Taught Us about Irritable Bowel Syndrome? A Systematic Review
Ng, Q. X., Yau, C. E., Yaow, C. Y. L., Chong, R. I. H., Chong, N. Z.-Y., Teoh, S. E., Lim, Y. L., Soh, A. Y. S., Ng, W. K., & Thumboo, J. (2023) · Metabolites · doi:10.3390/metabo13040484 · Cited by 53 · see citing works
Chang, D., Gupta, V. K., Hur, B., Cobo-López, S., Cunningham, K. Y., Han, N. S., Lee, I., Kronzer, V. L., Teigen, L. M., Karnatovskaia, L. V., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-51651-9 · Cited by 50 · see citing works
Iribarren, C., Magnusson, M. K., Vigsnæs, L. K., Aziz, I., Amundsen, I. D., Šuligoj, T., Juge, N., Patel, P., Sapnara, M., Johnsen, L. G., et al. (2021) · Nutrients · doi:10.3390/nu13113836 · Cited by 49 · see citing works
“Patients with IBS may present alterations in the gut microbiota composition [4,5] and function [6,7], or activation of the mucosal immune system [8,9], in some cases correlated to severity [4] or psychological symptoms [10].”
Microbiota of the gastrointestinal tract: Friend or foe?
Senchukova, M. A. (2023) · World Journal of Gastroenterology · doi:10.3748/wjg.v29.i1.19 · Cited by 55 · see citing works
Tryptophan metabolites get the gut moving
Benech, N., Rolhion, N., & Sokol, H. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2021.01.009 · Cited by 49 · see citing works
Gut microbiome-metabolome interactions predict host condition
Shtossel, O., Koren, O., Shai, I., Rinott, E., & Louzoun, Y. (2024) · Microbiome · doi:10.1186/s40168-023-01737-1 · Cited by 48 · see citing works
“Longitudinal samples fecal microbiome and metabolites (over 6 months) from patients with irritable bowel syndrome (IBS) and controls [90].”
BackgroundGut microbial structural variation associates with immune checkpoint inhibitor response
Liu, R., Zou, Y., Wang, W.-Q., Chen, J.-H., Zhang, L., Feng, J., Yin, J.-Y., Mao, X.-Y., Li, Q., Luo, Z.-Y., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-42997-7 · Cited by 45 · see citing works
“Speci fi cally, associations have been reported between bile acids and microbial SVs, and bacterial genes linked to host bile acid metabolism or indirectly involved in the alteration of primary bile acids have been identi fi ed 26,27 .”
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“…focused on the association of certain microbes with speci fi c diseases by analyzing the abundance and distribution of microbial strains 18,19,73 – 76 , we describe here an approach which leverages disease-related sequencing data to connect the bio-synthesis of functional metabolites directly to…”
- Authors
- Mars, R. A. T., Yang, Y., Ward, T., Houtti, M., Priya, S., Lekatz, H. R., Tang, X., Sun, Z., Kalari, K. R., Korem, T., Bhattarai, Y., Zheng, T., Bar, N., Frost, G., Johnson, A. J., van Treuren, W., Han, S., Ordog, T., Grover, M., Sonnenburg, J., D’Amato, M., Camilleri, M., Elinav, E., Segal, E., Blekhman, R., Farrugia, G., Swann, J. R., Knights, D., & Kashyap, P. C.
- Affiliations
- Mayo Clinic (US)
- Imperial College London (GB)
- University of Minnesota (US)
- Canadian Institute for Advanced Research (CA)
- Monash University (AU)
- Weizmann Institute of Science (IL)
- Stanford University (US)
- German Cancer Research Center (DE)
- University of Southampton (GB)
- Corresponding author
- Knights, Dan
- Kashyap, Purna C.
- ORCID
- Mars, Ruben A.T.
- Houtti, Mo
- Priya, Sambhawa
- Tang, Xiaojia
- Sun, Zhifu
- Kalari, Krishna R.
- Korem, Tal
- Bhattarai, Yogesh
- Zheng, Tenghao
- Frost, Gary
- Johnson, Abigail J.
- Han, Shuo
- Ordog, Tamas
- Grover, Madhusudan
- Sonnenburg, Justin
- D’Amato, Mauro
- Camilleri, Michael
- Elinav, Eran
- Segal, Eran
- Blekhman, Ran
- Farrugia, Gianrico
- Swann, Jonathan R.
- Knights, Dan
- Kashyap, Purna C.
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2020-09
- Volume
- 182
- Issue
- 6
- Pages
- 1460-1473.e17
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC8109273
- OpenAlex
- W3084404023
- Cited by
- 456
- References
- 49
- Citations by year
- 2026: 59 · 2025: 69 · 2024: 99 · 2023: 78 · 2022: 92 · 2021: 53 · 2020: 5
- FWCI
- 18.48
- Type
- journal article
- Language
- en
- Update notices
- erratum (2020-11-12)
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- ePrints Soton (University of Southampton) (acceptedVersion)
- ePrints Soton (University of Southampton) (submittedVersion)
- Funders
- Foundation for the National Institutes of Health
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Health Sciences › Medicine › Gastroenterology › Gastrointestinal motility and disorders
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Inflammatory Bowel Disease
- Keywords
- irritable bowel syndrome, gut microbiota, microbial metabolites, purine metabolism, host-microbe interactions, IBS subtypes, host transcriptome, host metabolome, chronic gastrointestinal diseases, therapeutic target
- MeSH terms
- Gastrointestinal Microbiome, Host Microbial Interactions, Animals, Bile Acids and Salts, Biopsy, Butyrates, Chromatography, Liquid, Cross-Sectional Studies, Feces, Female, Gene Expression Regulation, Humans, Longitudinal Studies, Male, Prospective Studies, Purines, Software, Hypoxanthine, Irritable Bowel Syndrome, Mice, Tandem Mass Spectrometry, Metabolome, Epigenomics, Transcriptome, Observational Studies as Topic
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