{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,7]],"date-time":"2026-05-07T12:33:42Z","timestamp":1778157222461,"version":"3.51.4"},"reference-count":86,"publisher":"MDPI AG","issue":"15","license":[{"start":{"date-parts":[[2024,8,2]],"date-time":"2024-08-02T00:00:00Z","timestamp":1722556800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Recent research indicates that the microbiome has a significant impact on the progression of inflammatory bowel disease (IBD) and that creating therapies that change its composition could positively impact the outcomes of IBD treatment. This review summarizes the results of extensive studies that examined IBD patients undergoing several therapies, including anti-TNF medication, vedolizumab, ustekinumab, probiotics, and fecal microbiota transplantation (FMT), and the alterations in their gut microbiota\u2019s composition and function. The objective was to investigate the variety and effectiveness of microbial species in order to discover new biomarkers or therapeutic targets that could improve the outcome of treatment for these patients. This research aimed to offer useful insights into personalized medicine techniques for managing IBD. Beneficial bacteria such as Faecalibacterium prausnitzii and Roseburia have been consistently linked to favorable clinical outcomes, whereas pathogenic bacteria such as Escherichia coli and Clostridioides difficile are associated with worsening disease conditions. Although many studies have examined the role of gut microbiota in IBD, there is still a need for more targeted research on the connection between specific microbial communities and treatment outcomes. This study sought to address this gap by exploring the intricate relationship between the gut microbiota composition and the effectiveness of IBD medications.<\/jats:p>","DOI":"10.3390\/ijms25158451","type":"journal-article","created":{"date-parts":[[2024,8,2]],"date-time":"2024-08-02T13:14:42Z","timestamp":1722604482000},"page":"8451","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":18,"title":["Healing from Within: How Gut Microbiota Predicts IBD Treatment Success\u2014A Systematic Review"],"prefix":"10.3390","volume":"25","author":[{"given":"Luana","family":"Alexandrescu","sequence":"first","affiliation":[{"name":"Gastroenterology Department, \u201cSf. Apostol Andrei\u201d Emergency County Hospital, 145 Tomis Blvd., 900591 Constanta, Romania"},{"name":"Medicine Faculty, \u201cOvidius\u201d University of Constanta, 1 Universitatii Street, 900470 Constanta, Romania"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6702-7086","authenticated-orcid":false,"given":"Alina Doina","family":"Nicoara","sequence":"additional","affiliation":[{"name":"Medicine Faculty, \u201cOvidius\u201d University of Constanta, 1 Universitatii Street, 900470 Constanta, Romania"},{"name":"Internal Medicine Department, \u201cSf. Apostol Andrei\u201d Emergency County Hospital, 145 Tomis Blvd., 900591 Constanta, Romania"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4057-348X","authenticated-orcid":false,"given":"Doina Ecaterina","family":"Tofolean","sequence":"additional","affiliation":[{"name":"Medicine Faculty, \u201cOvidius\u201d University of Constanta, 1 Universitatii Street, 900470 Constanta, Romania"},{"name":"Pneumology Department, \u201cSf. Apostol Andrei\u201d Emergency County Hospital, 145 Tomis Blvd., 900591 Constanta, Romania"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alexandra","family":"Herlo","sequence":"additional","affiliation":[{"name":"Department XIII, Discipline of Infectious Diseases, \u201cVictor Babes\u201d University of Medicine and Pharmacy Timisoara, 2 Eftimie Murgu Square, 300041 Timisoara, Romania"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5872-4381","authenticated-orcid":false,"given":"Andreea","family":"Nelson Twakor","sequence":"additional","affiliation":[{"name":"Internal Medicine Department, \u201cSf. Apostol Andrei\u201d Emergency County Hospital, 145 Tomis Blvd., 900591 Constanta, Romania"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cristina","family":"Tocia","sequence":"additional","affiliation":[{"name":"Gastroenterology Department, \u201cSf. Apostol Andrei\u201d Emergency County Hospital, 145 Tomis Blvd., 900591 Constanta, Romania"},{"name":"Medicine Faculty, \u201cOvidius\u201d University of Constanta, 1 Universitatii Street, 900470 Constanta, Romania"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anamaria","family":"Trandafir","sequence":"additional","affiliation":[{"name":"Medicine Faculty, \u201cOvidius\u201d University of Constanta, 1 Universitatii Street, 900470 Constanta, Romania"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9550-3537","authenticated-orcid":false,"given":"Andrei","family":"Dumitru","sequence":"additional","affiliation":[{"name":"Gastroenterology Department, \u201cSf. Apostol Andrei\u201d Emergency County Hospital, 145 Tomis Blvd., 900591 Constanta, Romania"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7268-3723","authenticated-orcid":false,"given":"Eugen","family":"Dumitru","sequence":"additional","affiliation":[{"name":"Gastroenterology Department, \u201cSf. Apostol Andrei\u201d Emergency County Hospital, 145 Tomis Blvd., 900591 Constanta, Romania"},{"name":"Medicine Faculty, \u201cOvidius\u201d University of Constanta, 1 Universitatii Street, 900470 Constanta, Romania"},{"name":"Academy of Romanian Scientist, 3 Ilfov Street, 050044 Bucharest, Romania"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cristian Florentin","family":"Aftenie","sequence":"additional","affiliation":[{"name":"Medicine Faculty, \u201cOvidius\u201d University of Constanta, 1 Universitatii Street, 900470 Constanta, Romania"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ionela","family":"Preotesoiu","sequence":"additional","affiliation":[{"name":"Medicine Faculty, \u201cOvidius\u201d University of Constanta, 1 Universitatii Street, 900470 Constanta, Romania"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Elena","family":"Dina","sequence":"additional","affiliation":[{"name":"Gastroenterology Department, \u201cSf. Apostol Andrei\u201d Emergency County Hospital, 145 Tomis Blvd., 900591 Constanta, Romania"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ioan Tiberiu","family":"Tofolean","sequence":"additional","affiliation":[{"name":"Gastroenterology Department, \u201cSf. Apostol Andrei\u201d Emergency County Hospital, 145 Tomis Blvd., 900591 Constanta, Romania"},{"name":"Medicine Faculty, \u201cOvidius\u201d University of Constanta, 1 Universitatii Street, 900470 Constanta, Romania"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2024,8,2]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1823","DOI":"10.1042\/BCJ20160510","article-title":"Introduction to the human gut microbiota","volume":"474","author":"Thursby","year":"2017","journal-title":"Biochem. J."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1106","DOI":"10.14336\/AD.2022.0104","article-title":"Functions of Gut Microbiota Metabolites, Current Status and Future Perspectives","volume":"13","author":"Liu","year":"2022","journal-title":"Aging Dis."},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Yoo, J.Y., Groer, M., Dutra, S.V.O., Sarkar, A., and McSkimming, D.I. (2020). Gut Microbiota and Immune System Interactions. Microorganisms, 8, Erratum in Microorganisms 2020, 8, 2046.","DOI":"10.3390\/microorganisms8122046"},{"key":"ref_4","unstructured":"McDowell, C., Farooq, U., and Haseeb, M. (2024, July 11). Inflammatory Bowel Disease, StatPearls [Internet], Available online: https:\/\/www.ncbi.nlm.nih.gov\/books\/NBK470312\/."},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Herlo, L.-F., Salcudean, A., Sirli, R., Iurciuc, S., Herlo, A., Nelson-Twakor, A., Alexandrescu, L., and Dumache, R. (2024). Gut Microbiota Signatures in Colorectal Cancer as a Potential Diagnostic Biomarker in the Future: A Systematic Review. Int. J. Mol. Sci., 25.","DOI":"10.3390\/ijms25147937"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"1118","DOI":"10.1053\/j.gastro.2021.07.042","article-title":"Extraintestinal Manifestations of Inflammatory Bowel Disease: Current Concepts, Treatment, and Implications for Disease Management","volume":"161","author":"Rogler","year":"2021","journal-title":"Gastroenterology"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"399","DOI":"10.1038\/s41575-022-00593-y","article-title":"Multiomics to elucidate inflammatory bowel disease risk factors and pathways","volume":"19","author":"Agrawal","year":"2022","journal-title":"Nat. Rev. Gastroenterol. Hepatol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1016\/j.dld.2023.07.011","article-title":"Switching from VEDOlizumab intravenous to subcutaneous formulation in ulcerative colitis patients in clinical remission: The SVEDO Study, an IG-IBD study","volume":"56","author":"Ribaldone","year":"2024","journal-title":"Dig. Liver Dis."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"30","DOI":"10.15403\/jgld-4656","article-title":"Tissue and Circulating MicroRNA-31, MicroRNA-200b, and MicroRNA-200c Reflects Disease Activity in Crohn\u2019s Disease Patients: Results from the BIOMIR Study","volume":"32","author":"Tocia","year":"2023","journal-title":"J. Gastrointest. Liver Dis."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"5534","DOI":"10.3390\/cimb45070350","article-title":"Inflammation, Autoinflammation and Autoimmunity in Inflammatory Bowel Diseases","volume":"45","author":"Padoan","year":"2023","journal-title":"Curr. Issues Mol. Biol."},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Garc\u00eda, M.J., Pascual, M., Del Pozo, C., D\u00edaz-Gonz\u00e1lez, A., Castro, B., Rasines, L., Crespo, J., and Rivero, M. (2020). Impact of immune-mediated diseases in inflammatory bowel disease and implications in therapeutic approach. Sci. Rep., 10.","DOI":"10.1038\/s41598-020-67710-2"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"S365","DOI":"10.1016\/S0016-5085(10)61681-2","article-title":"M1255 Fecal Calprotectin in Diagnosis of Complicated Colonic Diverticular Disease","volume":"138","author":"Dumitru","year":"2010","journal-title":"Gastroenterology"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"4053","DOI":"10.3748\/wjg.v28.i30.4053","article-title":"Gut microbiota, inflammatory bowel disease and colorectal cancer","volume":"28","author":"Quaglio","year":"2022","journal-title":"World J. Gastroenterol."},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Ispas, S., Tuta, L.A., Botnarciuc, M., Ispas, V., Staicovici, S., Ali, S., Nelson-Twakor, A., Cojocaru, C., Herlo, A., and Petcu, A. (2023). Metabolic Disorders, the Microbiome as an Endocrine Organ, and Their Relations with Obesity: A Literature Review. J. Pers. Med., 13.","DOI":"10.3390\/jpm13111602"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"3668","DOI":"10.3748\/wjg.v12.i23.3668","article-title":"Family and twin studies in inflammatory bowel disease","volume":"12","author":"Halme","year":"2006","journal-title":"World J. Gastroenterol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1002\/ibd.21385","article-title":"Update on the heritability of inflammatory bowel disease: The importance of twin studies","volume":"17","author":"Brant","year":"2011","journal-title":"Inflamm. Bowel Dis."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"i011","DOI":"10.1093\/ecco-jcc\/jjab232.010","article-title":"OP11 Expanded genome-wide association study of Inflammatory Bowel Disease identifies 174 novel loci and directly implicates new genes in disease susceptibility","volume":"16","author":"Fachal","year":"2022","journal-title":"J. Crohn\u2019s Colitis"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"796","DOI":"10.1038\/s41588-023-01384-0","article-title":"Genetic architecture of the inflammatory bowel diseases across East Asian and European ancestries","volume":"55","author":"Liu","year":"2023","journal-title":"Nat. Genet."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"527","DOI":"10.1038\/s41586-020-2025-2","article-title":"Pathway paradigms revealed from the genetics of inflammatory bowel disease","volume":"578","author":"Graham","year":"2020","journal-title":"Nature"},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Borowitz, S.M. (2023). The epidemiology of inflammatory bowel disease: Clues to pathogenesis?. Front. Pediatr., 10.","DOI":"10.3389\/fped.2022.1103713"},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Clemente-Su\u00e1rez, V.J., Beltr\u00e1n-Velasco, A.I., Redondo-Fl\u00f3rez, L., Mart\u00edn-Rodr\u00edguez, A., and Tornero-Aguilera, J.F. (2023). Global Impacts of Western Diet and Its Effects on Metabolism and Health: A Narrative Review. Nutrients, 15.","DOI":"10.3390\/nu15122749"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1146\/annurev-med-042320-021020","article-title":"The Gut Microbiome and Inflammatory Bowel Diseases","volume":"73","author":"Shan","year":"2022","journal-title":"Annu. Rev. Med."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1016\/j.crohns.2013.09.009","article-title":"A tale of two diseases: The history of inflammatory bowel disease","volume":"8","author":"Mulder","year":"2014","journal-title":"J. Crohn\u2019s Colitis"},{"key":"ref_24","first-page":"270","article-title":"Dysbiosis of gut microbiota in inflammatory bowel disease: Current therapies and potential for microbiota-modulating therapeutic approaches","volume":"21","author":"Alshehri","year":"2021","journal-title":"Bosn. J. Basic Med. Sci."},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Bica, I.C., Pietro\u0219el, V.A., Salmen, T., Diaconu, C.T., Fierbinteanu Braticevici, C., Stoica, R.A., Suceveanu, A.I., and Pantea Stoian, A. (2023). The Effects of Cardioprotective Antidiabetic Therapy on Microbiota in Patients with Type 2 Diabetes Mellitus-A Systematic Review. Int. J. Mol. Sci., 24.","DOI":"10.3390\/ijms24087184"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"180","DOI":"10.1016\/j.imj.2022.08.004","article-title":"Correlation between human gut microbiome and diseases","volume":"1","author":"Madhogaria","year":"2022","journal-title":"Infect. Med."},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Rinninella, E., Raoul, P., Cintoni, M., Franceschi, F., Miggiano, G.A.D., Gasbarrini, A., and Mele, M.C. (2019). What is the Healthy Gut Microbiota Composition? A Changing Ecosystem across Age, Environment, Diet, and Diseases. Microorganisms, 7.","DOI":"10.3390\/microorganisms7010014"},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Khan, I., Ullah, N., Zha, L., Bai, Y., Khan, A., Zhao, T., Che, T., and Zhang, C. (2019). Alteration of Gut Microbiota in Inflammatory Bowel Disease (IBD): Cause or Consequence? IBD Treatment Targeting the Gut Microbiome. Pathogens, 8.","DOI":"10.3390\/pathogens8030126"},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Gyriki, D., Nikolaidis, C., Stavropoulou, E., Bezirtzoglou, I., Tsigalou, C., Vradelis, S., and Bezirtzoglou, E. (2024). Exploring the Gut Microbiome\u2019s Role in Inflammatory Bowel Disease: Insights and Interventions. J. Pers. Med., 14.","DOI":"10.3390\/jpm14050507"},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Mosca, A., Leclerc, M., and Hugot, J.P. (2016). Gut Microbiota Diversity and Human Diseases: Should We Reintroduce Key Predators in Our Ecosystem?. Front. Microbiol., 7.","DOI":"10.3389\/fmicb.2016.00455"},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Do, K.-H., Ko, S.-H., Kim, K.B., Seo, K., and Lee, W.-K. (2023). Comparative Study of Intestinal Microbiome in Patients with Ulcerative Colitis and Healthy Controls in Korea. Microorganisms, 11.","DOI":"10.3390\/microorganisms11112750"},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Oligschlaeger, Y., Yadati, T., Houben, T., Condello Olivan, C.M., and Shiri-Sverdlov, R. (2019). Inflammatory Bowel Disease: A Stressed \u201cGut\/Feeling\u201d. Cells, 8.","DOI":"10.3390\/cells8070659"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"2293","DOI":"10.12998\/wjcc.v12.i14.2293","article-title":"Bringing gut microbiota into the spotlight of clinical research and medical practice","volume":"12","author":"Davoutis","year":"2024","journal-title":"World J. Clin. Cases"},{"key":"ref_34","unstructured":"Bella, L. (2024, July 11). Revolutionary Mechanistic Link Found between Diet, Gut Microbes and IBD. Luxembourg Institute of Health. Available online: https:\/\/www.lih.lu\/en\/article\/revolutionary-mechanistic-link-found-between-diet-gut-microbes-and-ibd\/."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"420","DOI":"10.5195\/jmla.2018.345","article-title":"The impact of patient, intervention, comparison, outcome (PICO) as a search strategy tool on literature search quality: A systematic review","volume":"106","author":"Eriksen","year":"2018","journal-title":"J. Med. Libr. Assoc."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"n71","DOI":"10.1136\/bmj.n71","article-title":"The PRISMA 2020 statement: An updated guideline for reporting systematic reviews","volume":"372","author":"Page","year":"2021","journal-title":"Br. Med. J."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"eaap8914","DOI":"10.1126\/scitranslmed.aap8914","article-title":"Gut microbiota composition and functional changes in inflammatory bowel disease and irritable bowel syndrome","volume":"10","author":"Imhann","year":"2018","journal-title":"Sci. Transl. Med."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"603","DOI":"10.1016\/j.chom.2017.04.010","article-title":"Gut Microbiome Function Predicts Response to Anti-integrin Biologic Therapy in Inflammatory Bowel Diseases","volume":"21","author":"Ananthakrishnan","year":"2017","journal-title":"Cell Host Microbe"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1038\/s41564-018-0306-4","article-title":"Gut microbiome structure and metabolic activity in inflammatory bowel disease","volume":"4","author":"Franzosa","year":"2019","journal-title":"Nat. Microbiol."},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Sokol, H., Landman, C., Seksik, P., Berard, L., Montil, M., Nion-Larmurier, I., Bourrier, A., Le Gall, G., Lalande, V., and De Rougemont, A. (2020). Fecal microbiota transplantation to maintain remission in Crohn\u2019s disease: A pilot randomized controlled study. Microbiome, 8.","DOI":"10.1186\/s40168-020-0792-5"},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Huang, C., Hao, W., Wang, X., Zhou, R., and Lin, Q. (2023). Probiotics for the treatment of ulcerative colitis: A review of experimental research from 2018 to 2022. Front. Microbiol., 14.","DOI":"10.3389\/fmicb.2023.1211271"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"156","DOI":"10.1001\/jama.2018.20046","article-title":"Effect of fecal microbiota transplantation on 8-week remission in patients with ulcerative colitis: A randomized clinical trial","volume":"321","author":"Costello","year":"2019","journal-title":"J. Am. Med. Assoc."},{"key":"ref_43","doi-asserted-by":"crossref","unstructured":"Ribaldone, D.G., Caviglia, G.P., Abdulle, A., Pellicano, R., Ditto, M.C., Morino, M., Fusaro, E., Saracco, G.M., Bugianesi, E., and Astegiano, M. (2019). Adalimumab Therapy Improves Intestinal Dysbiosis in Crohn\u2019s Disease. J. Clin. Med., 8.","DOI":"10.3390\/jcm8101646"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"4722","DOI":"10.3748\/wjg.v27.i28.4722","article-title":"Relationship between clinical features and intestinal microbiota in Chinese patients with ulcerative colitis","volume":"27","author":"He","year":"2021","journal-title":"World J. Gastroenterol."},{"key":"ref_45","doi-asserted-by":"crossref","unstructured":"Crothers, J.W., Chu, N.D., Nguyen, L.T.T., Phillips, M., Collins, C., Fortner, K., Del Rio-Guerra, R., Lavoie, B., Callas, P., and Velez, M. (2021). Daily, oral FMT for long-term maintenance therapy in ulcerative colitis: Results of a single-center, prospective, randomized pilot study. BMC Gastroenterol., 21.","DOI":"10.1186\/s12876-021-01856-9"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1093\/ibd\/izaa107","article-title":"Bacterial Mucosa-Associated Microbiome in Inflamed and Proximal Noninflamed Ileum of Patients with Crohn\u2019s Disease","volume":"27","author":"Olaisen","year":"2021","journal-title":"Inflamm. Bowel Dis."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"655","DOI":"10.1038\/s41586-019-1237-9","article-title":"Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases","volume":"569","author":"Arze","year":"2019","journal-title":"Nature"},{"key":"ref_48","doi-asserted-by":"crossref","unstructured":"Coufal, S., Galanova, N., Bajer, L., Gajdarova, Z., Schierova, D., Jiraskova Zakostelska, Z., Kostovcikova, K., Jackova, Z., Stehlikova, Z., and Drastich, P. (2019). Inflammatory Bowel Disease Types Differ in Markers of Inflammation, Gut Barrier and in Specific Anti-Bacterial Response. Cells, 8.","DOI":"10.3390\/cells8070719"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"930","DOI":"10.1053\/j.gastro.2019.11.294","article-title":"Differences in Gut Microbiota in Patients with vs without Inflammatory Bowel Diseases: A Systematic Review","volume":"158","author":"Pittayanon","year":"2020","journal-title":"Gastroenterology"},{"key":"ref_50","doi-asserted-by":"crossref","unstructured":"Forbes, J.D., Chen, C.Y., Knox, N.C., Marrie, R.A., El-Gabalawy, H., de Kievit, T., Alfa, M., Bernstein, C.N., and Van Domselaar, G. (2018). A comparative study of the gut microbiota in immune-mediated inflammatory diseases-does a common dysbiosis exist?. Microbiome, 6.","DOI":"10.1186\/s40168-018-0603-4"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"1504","DOI":"10.1053\/j.gastro.2017.08.028","article-title":"Increased Tryptophan Metabolism Is Associated with Activity of Inflammatory Bowel Diseases","volume":"153","author":"Nikolaus","year":"2017","journal-title":"Gastroenterology"},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"486","DOI":"10.1038\/s41564-019-0655-7","article-title":"Growth Effects of N-Acylethanolamines on Gut Bacteria Reflect Altered Bacterial Abundances in Inflammatory Bowel Disease","volume":"5","author":"Fornelos","year":"2020","journal-title":"Nat. Microbiol."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"1118","DOI":"10.1093\/ibd\/izad004","article-title":"Microbial Dynamics in Newly Diagnosed and Treatment Na\u00efve IBD Patients in the Mediterranean","volume":"29","author":"Rausch","year":"2023","journal-title":"Inflamm. Bowel Dis."},{"key":"ref_54","doi-asserted-by":"crossref","unstructured":"Fusco, W., Lorenzo, M.B., Cintoni, M., Porcari, S., Rinninella, E., Kaitsas, F., Lener, E., Mele, M.C., Gasbarrini, A., and Collado, M.C. (2023). Short-Chain Fatty-Acid-Producing Bacteria: Key Components of the Human Gut Microbiota. Nutrients, 15.","DOI":"10.3390\/nu15092211"},{"key":"ref_55","doi-asserted-by":"crossref","unstructured":"Lobionda, S., Sittipo, P., Kwon, H.Y., and Lee, Y.K. (2019). The Role of Gut Microbiota in Intestinal Inflammation with Respect to Diet and Extrinsic Stressors. Microorganisms, 7.","DOI":"10.3390\/microorganisms7080271"},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"2261477","DOI":"10.1080\/07853890.2023.2261477","article-title":"Multi-omics analysis reveals the interaction of gut microbiome and host microRNAs in ulcerative colitis","volume":"55","author":"Ma","year":"2023","journal-title":"Ann. Med."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"115804","DOI":"10.1016\/j.psychres.2024.115804","article-title":"Integrated multi-omics analysis reveals gut microbiota dysbiosis and systemic disturbance in major depressive disorder","volume":"334","author":"Xie","year":"2024","journal-title":"Psychiatry Res."},{"key":"ref_58","doi-asserted-by":"crossref","unstructured":"Venkova, T., Yeo, C.C., and Espinosa, M. (2018). Editorial: The Good, The Bad, and The Ugly: Multiple Roles of Bacteria in Human Life. Front. Microbiol., 9.","DOI":"10.3389\/fmicb.2018.01702"},{"key":"ref_59","doi-asserted-by":"crossref","unstructured":"Zegad\u0142o, K., Giero\u0144, M., \u017barnowiec, P., Durlik-Popi\u0144ska, K., Kr\u0119cisz, B., Kaca, W., and Czerwonka, G. (2023). Bacterial Motility and Its Role in Skin and Wound Infections. Int. J. Mol. Sci., 24.","DOI":"10.3390\/ijms24021707"},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1038\/s41392-022-00974-4","article-title":"Microbiota in health and diseases","volume":"7","author":"Hou","year":"2022","journal-title":"Signal Transduct. Target. Ther."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"k2179","DOI":"10.1136\/bmj.k2179","article-title":"Role of the gut microbiota in nutrition and health","volume":"361","author":"Valdes","year":"2018","journal-title":"Br. Med. J."},{"key":"ref_62","doi-asserted-by":"crossref","unstructured":"Beliz\u00e1rio, J.E., and Napolitano, M. (2015). Human microbiomes and their roles in dysbiosis, common diseases, and novel therapeutic approaches. Front. Microbiol., 6.","DOI":"10.3389\/fmicb.2015.01050"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"1294","DOI":"10.1016\/j.chom.2021.06.019","article-title":"Multi-omics reveal microbial determinants impacting responses to biologic therapies in inflammatory bowel disease","volume":"29","author":"Lee","year":"2021","journal-title":"Cell Host Microbe"},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"1019","DOI":"10.1093\/ecco-jcc\/jjaa252","article-title":"Bacterial and Fungal Profiles as Markers of Infliximab Drug Response in Inflammatory Bowel Disease","volume":"15","author":"Eberl","year":"2021","journal-title":"J. Crohn\u2019s Colitis"},{"key":"ref_65","doi-asserted-by":"crossref","unstructured":"Ojima, M.N., Gotoh, A., Takada, H., Odamaki, T., Xiao, J.Z., Katoh, T., and Katayama, T. (2020). Bifidobacterium bifidum Suppresses Gut Inflammation Caused by Repeated Antibiotic Disturbance without Recovering Gut Microbiome Diversity in Mice. Front. Microbiol., 11.","DOI":"10.3389\/fmicb.2020.01349"},{"key":"ref_66","doi-asserted-by":"crossref","unstructured":"Baldelli, V., Scaldaferri, F., Putignani, L., and Del Chierico, F. (2021). The Role of Enterobacteriaceae in Gut Microbiota Dysbiosis in Inflammatory Bowel Diseases. Microorganisms, 9.","DOI":"10.3390\/microorganisms9040697"},{"key":"ref_67","doi-asserted-by":"crossref","unstructured":"Mindrescu, N.M., Guja, C., Jinga, V., Ispas, S., Curici, A., Nelson Twakor, A., and Pantea Stoian, A.M. (2024). Interactions between Gut Microbiota and Oral Antihyperglycemic Drugs: A Systematic Review. Int. J. Mol. Sci., 25.","DOI":"10.3390\/ijms25063540"},{"key":"ref_68","doi-asserted-by":"crossref","unstructured":"Dahal, R.H., Kim, S., Kim, Y.K., Kim, E.S., and Kim, J. (2023). Insight into gut dysbiosis of patients with inflammatory bowel disease and ischemic colitis. Front. Microbiol., 14.","DOI":"10.3389\/fmicb.2023.1174832"},{"key":"ref_69","doi-asserted-by":"crossref","unstructured":"Santana, P.T., Rosas, S.L.B., Ribeiro, B.E., Marinho, Y., and de Souza, H.S.P. (2022). Dysbiosis in Inflammatory Bowel Disease: Pathogenic Role and Potential Therapeutic Targets. Int. J. Mol. Sci., 23.","DOI":"10.3390\/ijms23073464"},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"15","DOI":"10.5217\/ir.2023.00080","article-title":"Gut microbiota in pathophysiology, diagnosis, and therapeutics of inflammatory bowel disease","volume":"22","author":"Pandey","year":"2024","journal-title":"Intest. Res."},{"key":"ref_71","doi-asserted-by":"crossref","unstructured":"Crost, E.H., Coletto, E., Bell, A., and Juge, N. (2023). Ruminococcus gnavus: Friend or foe for human health. FEMS Microbiol. Rev., 47.","DOI":"10.1093\/femsre\/fuad014"},{"key":"ref_72","doi-asserted-by":"crossref","unstructured":"Wang, R. (2023). Clostridioides difficile infection: Microbe-microbe interactions and live biotherapeutics. Front. Microbiol., 14.","DOI":"10.3389\/fmicb.2023.1182612"},{"key":"ref_73","unstructured":"English|World Gastroenterology Organisation. (n.d.), and World Gastroenterology Organisation (WGO) (2024, June 27). Probiotics and Prebiotics. Available online: https:\/\/www.worldgastroenterology.org\/guidelines\/probiotics-and-prebiotics\/probiotics-and-prebiotics-english."},{"key":"ref_74","first-page":"CD006634","article-title":"Probiotics for induction of remission in Crohn\u2019s disease","volume":"7","author":"Limketkai","year":"2020","journal-title":"Cochrane Database Syst. Rev."},{"key":"ref_75","first-page":"CD005573","article-title":"Probiotics for induction of remission in ulcerative colitis","volume":"3","author":"Kaur","year":"2020","journal-title":"Cochrane Database Syst. Rev."},{"key":"ref_76","doi-asserted-by":"crossref","unstructured":"Singh, V., Lee, G., Son, H., Koh, H., Kim, E.S., Unno, T., and Shin, J.H. (2023). Butyrate producers, \u201cThe Sentinel of Gut\u201d: Their intestinal significance with and beyond butyrate, and prospective use as microbial therapeutics. Front. Microbiol., 13.","DOI":"10.3389\/fmicb.2022.1103836"},{"key":"ref_77","doi-asserted-by":"crossref","unstructured":"Mart\u00edn, R., Rios-Covian, D., Huillet, E., Auger, S., Khazaal, S., Berm\u00fadez-Humar\u00e1n, L.G., Sokol, H., Chatel, J.M., and Langella, P. (2023). Faecalibacterium: A bacterial genus with promising human health applications. FEMS Microbiol. Rev., 47.","DOI":"10.1093\/femsre\/fuad039"},{"key":"ref_78","doi-asserted-by":"crossref","unstructured":"Halaweish, H.F., Boatman, S., and Staley, C. (2022). Encapsulated Fecal Microbiota Transplantation: Development, Efficacy, and Clinical Application. Front. Cell. Infect. Microbiol., 12.","DOI":"10.3389\/fcimb.2022.826114"},{"key":"ref_79","doi-asserted-by":"crossref","unstructured":"Mayorga, L., Serrano-G\u00f3mez, G., Xie, Z., Borruel, N., and Manichanh, C. (2022). Intercontinental Gut Microbiome Variances in IBD. Int. J. Mol. Sci., 23.","DOI":"10.3390\/ijms231810868"},{"key":"ref_80","doi-asserted-by":"crossref","unstructured":"Li, Q., Zheng, T., Ding, H., Chen, J., Li, B., Zhang, Q., Yang, S., Zhang, S., and Guan, W. (2023). Exploring the Benefits of Probiotics in Gut Inflammation and Diarrhea\u2014From an Antioxidant Perspective. Antioxidants, 12.","DOI":"10.3390\/antiox12071342"},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"1192","DOI":"10.3748\/wjg.v20.i5.1192","article-title":"Role of the gut microbiota in inflammatory bowel disease pathogenesis: What have we learnt in the past 10 years?","volume":"20","author":"Hold","year":"2014","journal-title":"World J. Gastroenterol."},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1053\/j.gastro.2023.09.019","article-title":"Pathobionts in Inflammatory Bowel Disease: Origins, Underlying Mechanisms, and Implications for Clinical Care","volume":"166","author":"Gilliland","year":"2024","journal-title":"Gastroenterology"},{"key":"ref_83","doi-asserted-by":"crossref","unstructured":"Khorsand, B., Asadzadeh Aghdaei, H., Nazemalhosseini-Mojarad, E., Nadalian, B., Nadalian, B., and Houri, H. (2022). Overrepresentation of Enterobacteriaceae and Escherichia coli is the major gut microbiome signature in Crohn\u2019s disease and ulcerative colitis; A comprehensive metagenomic analysis of IBDMDB datasets. Front. Cell. Infect. Microbiol., 12.","DOI":"10.3389\/fcimb.2022.1015890"},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"920","DOI":"10.1093\/ecco-jcc\/jjad204","article-title":"The Impact of Dietary Interventions on the Microbiota in Inflammatory Bowel Disease: A Systematic Review","volume":"18","author":"Nieva","year":"2024","journal-title":"J. Crohn\u2019s Colitis."},{"key":"ref_85","doi-asserted-by":"crossref","unstructured":"Sorboni, S.G., Moghaddam, H.S., Jafarzadeh-Esfehani, R., and Soleimanpour, S. (2022). A Comprehensive Review on the Role of the Gut Microbiome in Human Neurological Disorders. Clin. Microbiol. Rev., 35.","DOI":"10.1128\/CMR.00338-20"},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"448","DOI":"10.1038\/s41586-020-2881-9","article-title":"Host variables confound gut microbiota studies of human disease","volume":"587","author":"Sklar","year":"2020","journal-title":"Nature"}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/25\/15\/8451\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T15:28:55Z","timestamp":1760110135000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/25\/15\/8451"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,8,2]]},"references-count":86,"journal-issue":{"issue":"15","published-online":{"date-parts":[[2024,8]]}},"alternative-id":["ijms25158451"],"URL":"https:\/\/doi.org\/10.3390\/ijms25158451","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,8,2]]}}}