Commensal Bacteria-Dependent Indole Production Enhances Epithelial Barrier Function in the Colon

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Bifidobacteria can protect from enteropathogenic infection through production of acetate

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Short-Chain Fatty Acids Activate GPR41 and GPR43 on Intestinal Epithelial Cells to Promote Inflammatory Responses in Mice

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Listening in on bacteria: acyl-homoserine lactone signalling

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Indole as an intercellular signal in microbial communities

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Bacteria–host communication: the language of hormones

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Dextran Sodium Sulphate Colitis Mouse Model: Traps and Tricks

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Sleep apnoea, gut dysbiosis and cognitive dysfunction

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The Gut Microbiota–Brain Axis Expands Neurologic Function: A Nervous Rapport

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Indole derivatives, microbiome and graft versus host disease

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Indole-3-propionic acid function through PXR and AhR, molecular signaling pathways, and antitoxic role in underlying diseases

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Diet–Microbiota Interplay: An Emerging Player in Macrophage Plasticity and Intestinal Health

O’Mahony, C., Amamou, A., & Ghosh, S. K. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23073901 · Cited by 24

Role of Gut Microbiota in Pulmonary Arterial Hypertension

Wu, P., Zhu, T., Tan, Z. Y. A., Chen, S., & Fang, Z. (2022) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2022.812303 · Cited by 23

Opportunities and challenges for synthetic biology in the therapy of inflammatory bowel disease

Dong, Y., Xu, T., Xiao, G., Hu, Z., & Chen, J. (2022) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2022.909591 · Cited by 23

Preparation and Evaluation of Colon-Targeted Prodrugs of the Microbial Metabolite 3-Indolepropionic Acid as an Anticolitic Agent

Lee, H., Park, S., Ju, S., Kim, S., Yoo, J., Yoon, I., Min, D. S., & Jung, Y. (2021) · Molecular Pharmaceutics · doi:10.1021/acs.molpharmaceut.0c01228 · Cited by 22

Gut Microbiota-Related Cellular and Molecular Mechanisms in the Progression of Nonalcoholic Fatty Liver Disease

Park, E., Jeong, J., Won, S., Sharma, S. P., Gebru, Y. A., Ganesan, R., Gupta, H., Suk, K. T., & Kim, D. J. (2021) · Cells · doi:10.3390/cells10102634 · Cited by 22

The Kynurenine Pathway and Polycystic Ovary Syndrome: Inflammation as a Common Denominator

Jovanović, F., Sudhakar, A., & Knežević, N. N. (2022) · International Journal of Tryptophan Research · doi:10.1177/11786469221099214 · Cited by 23

The Clostridium Metabolite P-Cresol Sulfate Relieves Inflammation of Primary Biliary Cholangitis by Regulating Kupffer Cells

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Double Trouble: How Microbiome Dysbiosis and Mitochondrial Dysfunction Drive Non-Alcoholic Fatty Liver Disease and Non-Alcoholic Steatohepatitis

Bahitham, W., Alghamdi, S., Omer, I., Alsudais, A. S., Hakeem, I., Alghamdi, A., Abualnaja, R., Sanai, F. M., Rosado, A. S., & Sergi, C. M. (2024) · Biomedicines · doi:10.3390/biomedicines12030550 · Cited by 22

The role of the gut microbiome in disorders of gut–brain interaction

Gawey, B. J., Mars, R. A. T., & Kashyap, P. (2024) · FEBS Journal · doi:10.1111/febs.17200 · Cited by 30

Interplay between gut microbiota and tryptophan metabolism in type 2 diabetic mice treated with metformin

Xie, Y.-H., Li, X., Meng, Q., Li, J., Wang, X., Zhu, L., Wang, W., & Li, X. (2024) · Microbiology Spectrum · doi:10.1128/spectrum.00291-24 · Cited by 21

The relationship of the microbiome, associated metabolites and the gut barrier with pancreatic cancer

Daniel, N., Farinella, R., Belluomini, F., Fajkić, A., Rizzato, C., Souček, P., Campa, D., & Hughes, D. J. (2025) · Seminars in Cancer Biology · doi:10.1016/j.semcancer.2025.03.002 · Cited by 23

Understanding the Effects of Metabolites on the Gut Microbiome and Severe Acute Pancreatitis

Ye, S., Si, C., Deng, J., Chen, X., Kong, L., Zhou, X., & Wang, W. (2021) · BioMed Research International · doi:10.1155/2021/1516855 · Cited by 24

Potential roles of gut microbial tryptophan metabolites in the complex pathogenesis of acne vulgaris

Huang, Y., Liu, L., Hao, Z., Chen, L., Yang, Q., Xiong, X., & Deng, Y. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.942027 · Cited by 24

Multi-omics analysis reveals the effects of microbiota on oral homeostasis

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A new suite of tnaA mutants suggests that Escherichia coli tryptophanase is regulated by intracellular sequestration and by occlusion of its active site

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Dietary Strategies to Modulate Gut Microbiota in Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD)

Perazza, F., Leoni, L., Selvatici, B., Girolami, F., Bonalumi, A., Beretta, A., Ferri, S., Petroni, M. L., Piscaglia, F., Ravaioli, F., et al. (2025) · Nutrients · doi:10.3390/nu17111906 · Cited by 25

Gut microbiota – indole-3-acetic acid axis in cancer: dual functions, mechanistic insights, and therapeutic potential

Zhong, L., Boopathi, S., Purushothaman, B., Tu, Q., & Zhang, Y. (2025) · Microbiological Research · doi:10.1016/j.micres.2025.128293 · Cited by 23

Indole reduces the expression of virulence related genes in Vibrio splendidus pathogenic to sea cucumber Apostichopus japonicus

Zhang, S., Zhang, W., Liu, N., Song, T., Liu, H., Zhao, X., Xu, W., & Li, C. (2017) · Microbial Pathogenesis · doi:10.1016/j.micpath.2017.08.032 · Cited by 20

Gut Microbiota-Derived Indole-3-Carboxylate Influences Mucosal Integrity and Immunity Through the Activation of the Aryl Hydrocarbon Receptors and Nutrient Transporters in Broiler Chickens Challenged With Eimeria maxima

Park, I., Nam, H., Goo, D., Wickramasuriya, S. S., Zimmerman, N. P., Smith, A. H., Rehberger, T. G., & Lillehoj, H. S. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.867754 · Cited by 20

The Roles and Mechanisms of Gut Microbiota in Food Allergy

Cheng, Y., Liu, X., Chen, F., Rolnik, B. M., Chleilat, F., Ling, Z., Snyder, M. P., & Zhou, X. (2023) · Advanced Gut & Microbiome Research · doi:10.1155/2023/9575410 · Cited by 22

Mini-review: microbiota have potential to prevent PEDV infection by improved intestinal barrier

Yang, S., Liu, G., Savelkoul, H. F. J., Jansen, C. A., & Li, B. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1230937 · Cited by 20

Modulation of Serotonin-Related Genes by Extracellular Vesicles of the Probiotic Escherichia coli Nissle 1917 in the Interleukin-1β-Induced Inflammation Model of Intestinal Epithelial Cells

Olivo-Martínez, Y., Martínez-Ruiz, S., Cordero-Alday, C., Bosch, M., Badía, J., & Baldomà, L. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25105338 · Cited by 21

Farnesol contributes to intestinal epithelial barrier function by enhancing tight junctions via the JAK/STAT3 signaling pathway in differentiated Caco-2 cells

Fang, Y., Wu, C., Wang, Q., & Tang, J. (2019) · Journal of Bioenergetics and Biomembranes · doi:10.1007/s10863-019-09817-4 · Cited by 20

Bacteria-immune cells dialog and the homeostasis of the systems

Guzman-Bautista, E. R., Suzuki, K., Asami, S., & Fagarasan, S. (2020) · Current Opinion in Immunology · doi:10.1016/j.coi.2020.05.010 · Cited by 21

Intestinal interplay of quorum sensing molecules and human receptors

Krasulová, K., & Illéš, P. (2021) · Biochimie · doi:10.1016/j.biochi.2021.06.010 · Cited by 20

Unveiling gut microbiota's role: Bidirectional regulation of drug transport for improved safety

Wang, J., & Zhou, T. (2024) · Medicinal Research Reviews · doi:10.1002/med.22077 · Cited by 20

Intermittent Fasting and Physical Exercise for Preventing Metabolic Disorders through Interaction with Gut Microbiota: A Review

Zhang, L., Wang, Y., Sun, Y., & Zhang, X. (2023) · Nutrients · doi:10.3390/nu15102277 · Cited by 20

An in vitro evaluation of the effects of a Yucca schidigera extract and chestnut tannins on composition and metabolic profiles of canine and feline faecal microbiota

Pinna, C., Vecchiato, C. G., Cardenia, V., Rodríguez‐Estrada, M. T., Stefanelli, C., Grandi, M., Gatta, P. P., & Biagi, G. (2017) · Archives of Animal Nutrition · doi:10.1080/1745039x.2017.1355039 · Cited by 19

Regulation by gut commensal bacteria of carcinoembryonic antigen‐related cell adhesion molecule expression in the intestinal epithelium

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Metabolic tug-of-war: Microbial metabolism shapes colonization resistance against enteric pathogens

Jones, K., de Brito, C. B., & Byndloss, M. X. (2025) · Cell chemical biology · doi:10.1016/j.chembiol.2024.12.005 · Cited by 20

Time Restricted Eating: A Valuable Alternative to Calorie Restriction for Addressing Obesity?

Parrotta, M. E., Colangeli, L., Scipione, V., Vitale, C., Sbraccia, P., & Guglielmi, V. (2025) · Current Obesity Reports · doi:10.1007/s13679-025-00609-z · Cited by 19

Tryptophan, an important link in regulating the complex network of skin immunology response in atopic dermatitis

Huang, Y., Chen, L., Liu, F., Xiong, X., Ouyang, Y., & Deng, Y. (2024) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1300378 · Cited by 21

The current findings on the gut-liver axis and the molecular basis of NAFLD/NASH associated with gut microbiome dysbiosis

Sharma, S., Tiwari, N., & Tanwar, S. S. (2025) · Naunyn-Schmiedeberg s Archives of Pharmacology · doi:10.1007/s00210-025-04069-z · Cited by 24

Interspecies and Intraspecies Signals Synergistically Regulate Lysobacter enzymogenes Twitching Motility

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The role of the intestinal microbiota in allogeneic HCT: clinical associations and preclinical mechanisms

Nguyen, C. L., Docampo, M. D., van den Brink, M. R. M., & Markey, K. A. (2020) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2020.11.007 · Cited by 17

A mechanism-based understanding of altered drug pharmacokinetics by gut microbiota

Gulnaz, A., Chang, J., Maeng, H., Shin, K., Lee, K., & Chae, Y. (2022) · Journal of Pharmaceutical Investigation · doi:10.1007/s40005-022-00600-z · Cited by 17

The effects of whole grain cereals on tryptophan metabolism and intestinal barrier function: underlying factors of health impact

Liikonen, V., Gómez-Gallego, C., & Kolehmainen, M. (2023) · Proceedings of The Nutrition Society · doi:10.1017/s0029665123003671 · Cited by 15

Nitrate promotes the growth and the production of short-chain fatty acids and tryptophan from commensal anaerobe Veillonella dispar in the lactate-deficient environment by facilitating the catabolism of glutamate and aspartate

Hung, J., Zhang, S., & Huang, S. (2024) · Applied and Environmental Microbiology · doi:10.1128/aem.01148-24 · Cited by 18

Indole alleviates nonalcoholic fatty liver disease in an ACE2 ‐dependent manner

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The Obesity–Epigenetics–Microbiome Axis: Strategies for Therapeutic Intervention

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Multi-Omic Analyses Reveal Bifidogenic Effect and Metabolomic Shifts in Healthy Human Cohort Supplemented With a Prebiotic Dietary Fiber Blend

Kang, J. W., Tang, X., Walton, C. J., Brown, M. J., Brewer, R. A., Maddela, R. L., Zheng, J. J., Agus, J., & Zivkovic, A. M. (2022) · Frontiers in Nutrition · doi:10.3389/fnut.2022.908534 · Cited by 19

Gut microbiota in non-alcoholic fatty liver disease: Pathophysiology, diagnosis, and therapeutics

Pandey, H., Goel, P., Srinivasan, V. M., Tang, D. W. T., Wong, S. H., & Lal, D. (2025) · World Journal of Hepatology · doi:10.4254/wjh.v17.i6.106849 · Cited by 20

Gut microbiota functional profiling in autism spectrum disorders: bacterial VOCs and related metabolic pathways acting as disease biomarkers and predictors

Vernocchi, P., Marangelo, C., Guerrera, S., CHIERICO, F. D., Guarrasi, V., Gardini, S., Conte, F., Paci, P., Ianiro, G., Gasbarrini, A., et al. (2023) · Frontiers in Microbiology · doi:10.3389/fmicb.2023.1287350 · Cited by 17

Exploring the Potential of Probiotics and Prebiotics in Major Depression: From Molecular Function to Clinical Therapy

Yuan, X., Chai, J., Xu, W., & Zhao, Y. (2024) · Probiotics and Antimicrobial Proteins · doi:10.1007/s12602-024-10326-z · Cited by 15

The immune-sleep crosstalk in inflammatory bowel disease

Eissa, N., Mujawar, Q. M., Alabdoulsalam, T., Zohni, S., & El‐Matary, W. (2020) · Sleep Medicine · doi:10.1016/j.sleep.2020.04.020 · Cited by 15

Metabolomics and metagenomics in mice reveal the role of the gut microbiota in tryptophan metabolism

Levé, M., Manghi, P., Bredon, M., Lefèvre, A., Manara, S., Armanini, F., Emond, P., Planchais, J., Rolhion, N., Segata, N., et al. (2025) · iScience · doi:10.1016/j.isci.2025.113751 · Cited by 16

Quorum Sensing: A New Perspective to Reveal the Interaction Between Gut Microbiota and Host

Yang, L., Yuan, T., Wan, Y., Li, W., Liu, C., Jiang, S., & Duan, J. (2022) · Future Microbiology · doi:10.2217/fmb-2021-0217 · Cited by 15

Metabolic Interactions in the Gastrointestinal Tract (GIT): Host, Commensal, Probiotics, and Bacteriophage Influences

Vitetta, L., Hall, S., & Coulson, S. (2015) · Microorganisms · doi:10.3390/microorganisms3040913 · Cited by 15

Potential role of the gut microbiota in neuromyelitis optica spectrum disorder: Implication for intervention

Cui, C., Ruan, Y., & Qiu, W. (2020) · Journal of Clinical Neuroscience · doi:10.1016/j.jocn.2020.11.011 · Cited by 14

Dendrobium huoshanense Polysaccharide Improves High‐Fat Diet Induced Liver Injury by Regulating the Gut‐Liver Axis

Ma, M., Gao, L., Chen, C. W., Gu, F., Wu, S., Li, F., & Han, B. (2023) · Chemistry & Biodiversity · doi:10.1002/cbdv.202300980 · Cited by 13

Microbiota in a long survival discourse with the human host

Ayariga, J. A., Ibrahim, I., Gildea, L., Abugri, J., & Villafañe, R. (2022) · Archives of Microbiology · doi:10.1007/s00203-022-03342-6 · Cited by 12

Biomarkers of geroprotection and cardiovascular health: An overview of omics studies and established clinical biomarkers in the context of diet

Secci, R., Hartmann, A., Walter, M., Grabe, H. J., der Auwera, S. V., Kowald, A., Palmer, D. H., Rimbach, G. H., Fuellen, G., & Barrantes, I. (2021) · Critical Reviews in Food Science and Nutrition · doi:10.1080/10408398.2021.1975638 · Cited by 11

Characterization of the chemical composition of different parts of Dolichos lablab L. and revelation of its anti-ulcerative colitis effects by modulating the gut microbiota and host metabolism

Gao, Y., Huang, R., Qiu, Y., Liu, Y., & Chen, L. (2023) · Journal of Ethnopharmacology · doi:10.1016/j.jep.2023.117629 · Cited by 14

Metabolites mediate the causal associations between gut microbiota and NAFLD: a Mendelian randomization study

Ouyang, C., Liu, P., Liu, Y., Lan, J., & Liu, Q. (2024) · BMC Gastroenterology · doi:10.1186/s12876-024-03277-w · Cited by 13

Intestinal microecology dysbiosis in inflammatory bowel disease: Pathogenesis and therapeutic strategies

Yin, Y., Feng, W., Chen, X., Chen, J., Wang, G., Xia, L., & Wu, K. (2024) · The Innovation Medicine · doi:10.59717/j.xinn-med.2024.100092 · Cited by 11

Gut–Lung Microbiota Interaction in COPD Patients: A Literature Review

Krūmiņa, A., Bogdanova, M., Gintere, S., & Vīksna, L. (2022) · Medicina · doi:10.3390/medicina58121760 · Cited by 12

Potential mechanisms of traditional Chinese medicine in the treatment of liver cirrhosis: a focus on gut microbiota

Sun, S., Zhang, G., Lv, S., & Sun, J. (2024) · Frontiers in Microbiology · doi:10.3389/fmicb.2024.1407991 · Cited by 10

Deletion of ghrelin alters tryptophan metabolism and exacerbates experimental ulcerative colitis in aged mice

Tuchaai, E., Endres, V., Jones, B., Shankar, S., Klemashevich, C. L., Sun, Y., & Wu, C. (2022) · Experimental Biology and Medicine · doi:10.1177/15353702221110647 · Cited by 10

Impact of commensal flora on periodontal immune response to lipopolysaccharide

Fukuhara, D., Irie, K., Uchida, Y., Kataoka, K., Akiyama, K., Ekuni, D., Tomofuji, T., & Morita, M. (2018) · Journal of Periodontology · doi:10.1002/jper.17-0567 · Cited by 10

The role of the gut-liver axis in modulating non-alcoholic fatty liver disease through dietary patterns and microecological agents

Fang, Y., Fang, Z., Li, Z., Yu, R., Zhang, H., Wang, Q., Cheng, X., Le, G., & Wu, G. (2023) · Food Bioscience · doi:10.1016/j.fbio.2023.103335 · Cited by 9

A secondary metabolite of Limosilactobacillus reuteri R2lc drives strain-specific pathology in a spontaneous mouse model of multiple sclerosis

Archer, D., Pérez-Muñoz, M. E., Tollenaar, S. L., Veniamin, S., Hotte, N., Cheng, C. C., Nieves, K., Oh, J., Morceli, L., Muncner, S., et al. (2025) · Cell Reports · doi:10.1016/j.celrep.2025.115321 · Cited by 8

Indole dysbiosis and mucosal inflammation

Kim, J. Y., Cartwright, I. M., & Colgan, S. P. (2025) · Microbiota and Host · doi:10.1530/mah-25-0004 · Cited by 9

Significance of the Gut Microbiome for Viral Diarrheal and Extra-Intestinal Diseases

Desselberger, U. (2021) · Viruses · doi:10.3390/v13081601 · Cited by 10

Diet-mediated metaorganismal relay biotransformation: health effects and pathways

Li, Y., Cao, H., Wang, X., Guo, L., Ding, X., Zhao, W., & Zhang, F. (2021) · Critical Reviews in Food Science and Nutrition · doi:10.1080/10408398.2021.2004993 · Cited by 9

Nicotine Oral Administration Attenuates DSS-Induced Colitis Through Upregulation of Indole in the Distal Colon and Rectum in Mice

Nakajima, A., Shibuya, T., Sasaki, T., Lu, Y., Ishikawa, D., Haga, K., Takahashi, M., Kaga, N., Osada, T., Sato, N., et al. (2021) · Frontiers in Medicine · doi:10.3389/fmed.2021.789037 · Cited by 9

Prebiotics and the Modulation on the Microbiota-GALT-Brain Axis

Franco‐Robles, E., Ramı́rez-Emiliano, J., López-Briones, J. S., & Balcón-Pacheco, C. D. (2019) · IntechOpen eBooks · doi:10.5772/intechopen.89690 · Cited by 10

Microbial tryptophan metabolites modulate blood-brain and gut barriers in vitro

Rosell‐Cardona, C., Knox, E. G., Sánchez-Díaz, P., Leigh, S., Tirelli, E., Goodson, M. S., Kelley‐Loughnane, N., Aburto, M. R., Kittel‐Schneider, S., Cryan, J. F., et al. (2025) · Neuroscience Applied · doi:10.1016/j.nsa.2025.106876 · Cited by 11

Gut microbial metabolism via hippocampal indole-AhR signaling regulates emotional symptoms

Wang, T.-T., Luo, Y.-J., Feng, W., Jiang, L., Yu, Q.-S., He, Y.-T., Guan, L., Zhu, B.-Q., Jiang, H., Li, M., et al. (2026) · Cell Metabolism · doi:10.1016/j.cmet.2026.03.003 · Cited by 8

The role of gut microbiota in acute pancreatitis: new perspectives in pathogenesis and therapeutic approaches

Du, Z.-C., Li, G., Luo, Y., Bai, X., & Sun, B. (2023) · Journal of Pancreatology · doi:10.1097/jp9.0000000000000131 · Cited by 11

Dietary effects of vitamin C on antioxidant capacity, intestinal microbiota and the resistance of pathogenic bacteria in cultured Silver pomfret (Pampus argenteus)

Guo, C., Ding, M., Zhang, S., Wang, Y., Ji, Y., Xu, S., Wang, Y., & Wang, D. (2024) · PLoS ONE · doi:10.1371/journal.pone.0300643 · Cited by 8

Gut microbiota from end-stage renal disease patients disrupt gut barrier function by excessive production of phenol

Wang, X., Hao, Y., Liu, X., Yu, S., Zhang, W., Yang, S., Yu, Z., & Ren, F. (2019) · Journal of genetics and genomics/Journal of Genetics and Genomics · doi:10.1016/j.jgg.2019.03.015 · Cited by 8

Insights into host-microbe interaction: What can we do for the swine industry?

Fan, L., Liu, B., Han, Z., & Ren, W. (2020) · Animal nutrition · doi:10.1016/j.aninu.2020.10.003 · Cited by 9

Effects of probiotics on the improvement and regulation of intestinal barrier dysfunction and immune imbalance in intra‑abdominal infections (Review)

Tang, S., Liu, J., Xu, C., Shang, D., Chen, H., & Zhang, G. (2021) · International Journal of Functional Nutrition · doi:10.3892/ijfn.2021.22 · Cited by 8

Effects of gut bacteria and their metabolites on gut health of animals

Hao, Z., Ding, X., & Wang, J. (2024) · Advances in applied microbiology · doi:10.1016/bs.aambs.2024.02.007 · Cited by 7

Cell Signaling by Tryptophan Catabolism

Torrelli-Diljohn, A., Kulkarni, B., & Vitturi, D. A. (2026) · Biochemistry · doi:10.1021/acs.biochem.6c00179 · Cited by 7

Functional properties of Ganoderma lucidum supplementation in canine nutrition

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Changes in the Serum Metabolome of Patients Treated With Broad-Spectrum Antibiotics

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