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It involves numerous physiological processes impacting host health, mainly via immune system modulation. A balanced microbiome contributes to the gut\u2019s barrier function, preventing the invasion of pathogens and maintaining the integrity of the gut lining. Dysbiosis, or an imbalance in the gut microbiome\u2019s composition and function, disrupts essential processes and contributes to various diseases. This narrative review summarizes key findings related to the gut microbiota in modern multifactorial inflammatory conditions such as ulcerative colitis or Crohn\u2019s disease. It addresses the challenges posed by antibiotic-driven dysbiosis, particularly in the context of C. difficile infections, and the development of novel therapies like fecal microbiota transplantation and biotherapeutic drugs to combat these infections. An emphasis is given to restoration of the healthy gut microbiome through dietary interventions, probiotics, prebiotics, and novel approaches for managing gut-related diseases.<\/jats:p>","DOI":"10.3390\/ijms25179715","type":"journal-article","created":{"date-parts":[[2024,9,9]],"date-time":"2024-09-09T05:59:08Z","timestamp":1725861548000},"page":"9715","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":110,"title":["Insights into Gut Dysbiosis: Inflammatory Diseases, Obesity, and Restoration Approaches"],"prefix":"10.3390","volume":"25","author":[{"given":"Andy","family":"Acevedo-Rom\u00e1n","sequence":"first","affiliation":[{"name":"Microbiology Department, University of Puerto Rico Medical Sciences Campus, San Juan 00936, Puerto Rico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Natalia","family":"Pag\u00e1n-Zayas","sequence":"additional","affiliation":[{"name":"Microbiology Department, University of Puerto Rico Medical Sciences Campus, San Juan 00936, Puerto Rico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liz I.","family":"Vel\u00e1zquez-Rivera","sequence":"additional","affiliation":[{"name":"Microbiology Department, University of Puerto Rico Medical Sciences Campus, San Juan 00936, Puerto Rico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aryanne C.","family":"Torres-Ventura","sequence":"additional","affiliation":[{"name":"Microbiology Department, University of Puerto Rico Medical Sciences Campus, San Juan 00936, Puerto Rico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1880-0498","authenticated-orcid":false,"given":"Filipa","family":"Godoy-Vitorino","sequence":"additional","affiliation":[{"name":"Microbiology Department, University of Puerto Rico Medical Sciences Campus, San Juan 00936, Puerto Rico"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2024,9,8]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"342","DOI":"10.21037\/atm.2019.06.56","article-title":"Human Microbial Ecology and the Rising New Medicine","volume":"7","year":"2019","journal-title":"Ann. Transl. Med."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1108","DOI":"10.1136\/gutjnl-2018-317503","article-title":"Role of the Microbiome in Human Development","volume":"68","author":"Knight","year":"2019","journal-title":"Gut"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/j.jcmgh.2019.07.006","article-title":"The Structure and Function of the Human Small Intestinal Microbiota: Current Understanding and Future Directions","volume":"9","author":"Kastl","year":"2020","journal-title":"Cell Mol. Gastroenterol. Hepatol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"e31134","DOI":"10.1016\/j.heliyon.2024.e31134","article-title":"Prevotella Enterotype Associates with Diets Supporting Acidic Faecal pH and Production of Propionic Acid by Microbiota","volume":"10","author":"Adamberg","year":"2024","journal-title":"Heliyon"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"7046","DOI":"10.1080\/21655979.2021.1972077","article-title":"The Gut Microbial Diversity of Colon Cancer Patients and the Clinical Significance","volume":"12","author":"He","year":"2021","journal-title":"Bioengineered"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"577","DOI":"10.1038\/s41577-024-01014-8","article-title":"Short-Chain Fatty Acids: Linking Diet, the Microbiome and Immunity","volume":"24","author":"Mann","year":"2024","journal-title":"Nat. Rev. Immunol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"782","DOI":"10.1002\/ccr3.2096","article-title":"The Efficacy of Fecal Microbiota Transplantation for Patients with Chronic Pouchitis: A Case Series","volume":"7","author":"Nishida","year":"2019","journal-title":"Clin. Case Rep."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"760","DOI":"10.1177\/0884533615606898","article-title":"Microbiota in Inflammatory Bowel Disease Pathogenesis and Therapy: Is It All About Diet?","volume":"30","author":"Serban","year":"2015","journal-title":"Nutr. Clin. Prac."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1053\/j.gastro.2007.04.005","article-title":"The Fecal Microbiota of Irritable Bowel Syndrome Patients Differs Significantly from That of Healthy Subjects","volume":"133","author":"Kassinen","year":"2007","journal-title":"Gastroenterology"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"501","DOI":"10.1089\/chi.2018.0040","article-title":"Childhood Obesity and Firmicutes\/Bacteroidetes Ratio in the Gut Microbiota: A Systematic Review","volume":"14","author":"Indiani","year":"2018","journal-title":"Child Obes."},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Guo, Y., Xie, J.-P., Deng, K., Li, X., Yuan, Y., Xuan, Q., Xie, J., He, X.-M., Wang, Q., and Li, J.-J. (2019). Prophylactic Effects of Bifidobacterium Adolescentis on Anxiety and Depression-Like Phenotypes After Chronic Stress: A Role of the Gut Microbiota-Inflammation Axis. Front. Behav. Neurosci., 13.","DOI":"10.3389\/fnbeh.2019.00126"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"113","DOI":"10.25122\/jml-2018-0075","article-title":"A Review of the Diagnosis, Prevention, and Treatment Methods of Inflammatory Bowel Disease","volume":"12","author":"Seyedian","year":"2019","journal-title":"J. Med. Life"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1001\/jama.2020.18936","article-title":"Management of Crohn Disease: A Review","volume":"325","author":"Cushing","year":"2021","journal-title":"JAMA"},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Zhou, J.-L., Bao, J.-C., Liao, X.-Y., Chen, Y.-J., Wang, L.-W., Fan, Y.-Y., Xu, Q.-Y., Hao, L.-X., Li, K.-J., and Liang, M.-X. (2023). Trends and Projections of Inflammatory Bowel Disease at the Global, Regional and National Levels, 1990\u20132050: A Bayesian Age-Period-Cohort Modeling Study. BMC Public Health, 23.","DOI":"10.1186\/s12889-023-17431-8"},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Kaczmarek-Ry\u015b, M., Hryhorowicz, S.T., Lis, E., Banasiewicz, T., Paszkowski, J., Borejsza-Wysocki, M., Walkowiak, J., Cichy, W., Krokowicz, P., and Czkwianianc, E. (2021). Crohn\u2019s Disease Susceptibility and Onset Are Strongly Related to Three NOD2 Gene Haplotypes. J. Clin. Med., 10.","DOI":"10.3390\/jcm10173777"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1053\/j.gastro.2016.10.020","article-title":"Understanding and Preventing the Global Increase of Inflammatory Bowel Disease","volume":"152","author":"Kaplan","year":"2017","journal-title":"Gastroenterology"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"3764","DOI":"10.1038\/s41467-024-48106-6","article-title":"Diet-Omics in the Study of Urban and Rural Crohn Disease Evolution (SOURCE) Cohort","volume":"15","author":"Braun","year":"2024","journal-title":"Nat. Commun."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"4322","DOI":"10.1038\/s41467-020-17956-1","article-title":"Integrated Microbiota and Metabolite Profiles Link Crohn\u2019s Disease to Sulfur Metabolism","volume":"11","author":"Metwaly","year":"2020","journal-title":"Nat. Commun."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"2660","DOI":"10.12998\/wjcc.v10.i9.2660","article-title":"Role of Metabolites Derived from Gut Microbiota in Inflammatory Bowel Disease","volume":"10","author":"Zheng","year":"2022","journal-title":"World J. Clin. Cases"},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Candelli, M., Franza, L., Pignataro, G., Ojetti, V., Covino, M., Piccioni, A., Gasbarrini, A., and Franceschi, F. (2021). Interaction between Lipopolysaccharide and Gut Microbiota in Inflammatory Bowel Diseases. Int. J. Mol. Sci., 22.","DOI":"10.3390\/ijms22126242"},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Markowiak-Kope\u0107, P., and \u015ali\u017cewska, K. (2020). The Effect of Probiotics on the Production of Short-Chain Fatty Acids by Human Intestinal Microbiome. Nutrients, 12.","DOI":"10.3390\/nu12041107"},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Shin, Y., Han, S., Kwon, J., Ju, S., Choi, T.G., Kang, I., and Kim, S.S. (2023). Roles of Short-Chain Fatty Acids in Inflammatory Bowel Disease. Nutrients, 15.","DOI":"10.3390\/nu15204466"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"196","DOI":"10.6026\/97320630016196","article-title":"Linking Gut Microbiota with the Human Diseases","volume":"16","author":"Vandana","year":"2020","journal-title":"Bioinformation"},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Vakadaris, G., Stefanis, C., Giorgi, E., Brouvalis, M., Voidarou, C., Kourkoutas, Y., Tsigalou, C., and Bezirtzoglou, E. (2023). The Role of Probiotics in Inducing and Maintaining Remission in Crohn\u2019s Disease and Ulcerative Colitis: A Systematic Review of the Literature. Biomedicines, 11.","DOI":"10.3390\/biomedicines11020494"},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Virk, M.S., Virk, M.A., He, Y., Tufail, T., Gul, M., Qayum, A., Rehman, A., Rashid, A., Ekumah, J.-N., and Han, X. (2024). The Anti-Inflammatory and Curative Exponent of Probiotics: A Comprehensive and Authentic Ingredient for the Sustained Functioning of Major Human Organs. Nutrients, 16.","DOI":"10.3390\/nu16040546"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"6809","DOI":"10.3748\/wjg.v21.i22.6809","article-title":"Exclusive Enteral Nutrition in Children with Crohn\u2019s Disease","volume":"21","author":"Day","year":"2015","journal-title":"World J. Gastroenterol."},{"key":"ref_27","first-page":"31","article-title":"Update on Fecal Microbiota Transplantation for the Treatment of Inflammatory Bowel Disease","volume":"17","author":"Allegretti","year":"2021","journal-title":"Gastroenterol. Hepatol."},{"key":"ref_28","unstructured":"Kahn, S.A. (2024, May 24). A Phase I\/II, Double Blinded, Placebo Controlled, Single-Center Study of Fecal Microbiota Transplant (FMT) for the Treatment of Active Pediatric Ulcerative Colitis and Pediatric Active Crohn\u2019s Colitis, Available online: https:\/\/clinicaltrials.gov\/."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"716","DOI":"10.1001\/jama.2023.23814","article-title":"What Is Ulcerative Colitis?","volume":"331","author":"Voelker","year":"2024","journal-title":"JAMA"},{"key":"ref_30","unstructured":"(2020). Definition & Facts of Ulcerative Colitis\u2014NIDDK, National Institute of Diabetes and Digestive and Kidney Diseases."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"1067","DOI":"10.1177\/2050640620957138","article-title":"Oral Health and Salivary Function in Ulcerative Colitis Patients","volume":"8","author":"Goldinova","year":"2020","journal-title":"United Eur. Gastroenterol. J."},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Zhu, L., Qiao, L., Dou, X., Song, X., Chang, J., Zeng, X., and Xu, C. (2023). Lactobacillus Casei ATCC 393 Combined with Vasoactive Intestinal Peptide Alleviates Dextran Sodium Sulfate-Induced Ulcerative Colitis in C57BL\/6 Mice via NF-\u03baB and Nrf2 Signaling Pathways. Biomed. Pharmacother., 165.","DOI":"10.1016\/j.biopha.2023.115033"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"3609","DOI":"10.3748\/wjg.v27.i24.3609","article-title":"Altered Profiles of Fecal Bile Acids Correlate with Gut Microbiota and Inflammatory Responses in Patients with Ulcerative Colitis","volume":"27","author":"Yang","year":"2021","journal-title":"World J. Gastroenterol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1186\/s13099-024-00612-0","article-title":"Constituents of Stable Commensal Microbiota Imply Diverse Colonic Epithelial Cell Reactivity in Patients with Ulcerative Colitis","volume":"16","author":"Inciuraite","year":"2024","journal-title":"Gut Pathog."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"108","DOI":"10.1136\/gutjnl-2016-312135","article-title":"The Interplay of Host Genetics and the Gut Microbiota Underlying the Onset and Clinical Presentation of Inflammatory Bowel Disease","volume":"67","author":"Imhann","year":"2019","journal-title":"Gut"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"1132","DOI":"10.4014\/jmb.2002.02044","article-title":"Fecal Microbiota Transplantation (FMT) Alleviates Experimental Colitis in Mice by Gut Microbiota Regulation","volume":"30","author":"Zhang","year":"2020","journal-title":"J. Microbiol. Biotechnol."},{"key":"ref_37","doi-asserted-by":"crossref","unstructured":"Sun, S., Xu, X., Liang, L., Wang, X., Bai, X., Zhu, L., He, Q., Liang, H., Xin, X., and Wang, L. (2021). Lactic Acid-Producing Probiotic Saccharomyces Cerevisiae Attenuates Ulcerative Colitis via Suppressing Macrophage Pyroptosis and Modulating Gut Microbiota. Front. Immunol., 12.","DOI":"10.3389\/fimmu.2021.777665"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"7135","DOI":"10.1038\/s41467-023-42788-0","article-title":"Microbiome and Metabolome Features in Inflammatory Bowel Disease via Multi-Omics Integration Analyses across Cohorts","volume":"14","author":"Ning","year":"2023","journal-title":"Nat. Commun."},{"key":"ref_39","doi-asserted-by":"crossref","unstructured":"Cheng, H., Liu, J., Zhang, D., Wang, J., Tan, Y., Feng, W., and Peng, C. (2022). Ginsenoside Rg1 Alleviates Acute Ulcerative Colitis by Modulating Gut Microbiota and Microbial Tryptophan Metabolism. Front. Immunol., 13.","DOI":"10.3389\/fimmu.2022.817600"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"2145843","DOI":"10.1080\/19490976.2022.2145843","article-title":"Lactobacillus Johnsonii Alleviates Colitis by TLR1\/2-STAT3 Mediated CD206+ macrophagesIL-10 Activation","volume":"14","author":"Jia","year":"2022","journal-title":"Gut Microbes"},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Sovran, B., Planchais, J., Jegou, S., Straube, M., Lamas, B., Natividad, J.M., Agus, A., Dupraz, L., Glodt, J., and Da Costa, G. (2018). Enterobacteriaceae Are Essential for the Modulation of Colitis Severity by Fungi. Microbiome, 6.","DOI":"10.1186\/s40168-018-0538-9"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"104978","DOI":"10.1016\/j.phrs.2020.104978","article-title":"Evodiamine Has Therapeutic Efficacy in Ulcerative Colitis by Increasing Lactobacillus Acidophilus Levels and Acetate Production","volume":"159","author":"Wang","year":"2020","journal-title":"Pharmacol. Res."},{"key":"ref_43","doi-asserted-by":"crossref","unstructured":"Wan, J., Zhang, Y., He, W., Tian, Z., Lin, J., Liu, Z., Li, Y., Chen, M., Han, S., and Liang, J. (2022). Gut Microbiota and Metabolite Changes in Patients With Ulcerative Colitis and Clostridioides difficile Infection. Front. Microbiol., 13.","DOI":"10.3389\/fmicb.2022.802823"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1186\/s13568-022-01411-z","article-title":"Bifidobacterium BLa80 Mitigates Colitis by Altering Gut Microbiota and Alleviating Inflammation","volume":"12","author":"Dong","year":"2022","journal-title":"AMB Express"},{"key":"ref_45","first-page":"25","article-title":"Administration of Live, but Not Inactivated, Faecalibacterium Prausnitzii Has a Preventive Effect on Dextran Sodium Sulfate-induced Colitis in Mice","volume":"20","author":"Kawade","year":"2019","journal-title":"Mol. Med. Rep."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"fuad039","DOI":"10.1093\/femsre\/fuad039","article-title":"Faecalibacterium: A Bacterial Genus with Promising Human Health Applications","volume":"47","author":"Huillet","year":"2023","journal-title":"FEMS Microbiol. Rev."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"262","DOI":"10.1038\/s41564-021-01050-3","article-title":"Multi-Omics Analyses of the Ulcerative Colitis Gut Microbiome Link Bacteroides Vulgatus Proteases with Disease Severity","volume":"7","author":"Mills","year":"2022","journal-title":"Nat. Microbiol."},{"key":"ref_48","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_49","doi-asserted-by":"crossref","first-page":"793","DOI":"10.1186\/s12967-023-04687-2","article-title":"Muc2 Mucin O-Glycosylation Interacts with Enteropathogenic Escherichia Coli to Influence the Development of Ulcerative Colitis Based on the NF-kB Signaling Pathway","volume":"21","author":"Wei","year":"2023","journal-title":"J. Transl. Med."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"100549","DOI":"10.1016\/j.genrep.2019.100549","article-title":"Citrobacter Rodentium Infection Inhibits Colonic P-Glycoprotein Expression","volume":"18","author":"Patel","year":"2020","journal-title":"Gene Rep."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"188","DOI":"10.3892\/mmr.2022.12704","article-title":"Protection against Ulcerative Colitis and Colorectal Cancer by Evodiamine via Anti-Inflammatory Effects","volume":"25","author":"Zhang","year":"2022","journal-title":"Mol. Med. Rep."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"S70","DOI":"10.1053\/j.gastro.2021.12.150","article-title":"The Synthetic Glycan KB295 Optimizes Microbiome Composition and Function in Ulcerative Colitis\u2014Results from a Proof of Principle Human Study","volume":"162","author":"Meisner","year":"2022","journal-title":"Gastroenterology"},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"566","DOI":"10.1038\/s42255-020-0243-4","article-title":"Lactate: The Ugly Duckling of Energy Metabolism","volume":"2","author":"Rabinowitz","year":"2020","journal-title":"Nat. Metab."},{"key":"ref_54","doi-asserted-by":"crossref","unstructured":"Luzentales-Simpson, M., Pang, Y.C.F., Zhang, A., Sousa, J.A., and Sly, L.M. (2021). Vedolizumab: Potential Mechanisms of Action for Reducing Pathological Inflammation in Inflammatory Bowel Diseases. Front. Cell Dev. Biol., 9.","DOI":"10.3389\/fcell.2021.612830"},{"key":"ref_55","doi-asserted-by":"crossref","unstructured":"Eun, C.S., Kwak, M.-J., Han, D.S., Lee, A.R., Park, D.I., Yang, S.-K., Kim, Y.S., and Kim, J.F. (2016). Does the Intestinal Microbial Community of Korean Crohn\u2019s Disease Patients Differ from That of Western Patients?. BMC Gastroenterol., 16.","DOI":"10.1186\/s12876-016-0437-0"},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1136\/gutjnl-2014-308341","article-title":"Geographical Patterns of the Standing and Active Human Gut Microbiome in Health and IBD","volume":"65","author":"Rehman","year":"2016","journal-title":"Gut"},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1159\/000477205","article-title":"Gut Microbiota in Health, Diverticular Disease, Irritable Bowel Syndrome, and Inflammatory Bowel Diseases: Time for Microbial Marker of Gastrointestinal Disorders","volume":"36","author":"Lopetuso","year":"2017","journal-title":"Dig. Dis."},{"key":"ref_58","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_59","doi-asserted-by":"crossref","unstructured":"Santoru, M.L., Piras, C., Murgia, A., Palmas, V., Camboni, T., Liggi, S., Ibba, I., Lai, M.A., Orr\u00f9, S., and Blois, S. (2017). Cross Sectional Evaluation of the Gut-Microbiome Metabolome Axis in an Italian Cohort of IBD Patients. Sci. Rep., 7.","DOI":"10.1038\/s41598-017-10034-5"},{"key":"ref_60","doi-asserted-by":"crossref","unstructured":"Martinez, E., Crevecoeur, S., Thirion, C., Grandjean, J., Fall, P.A., Hayette, M.-P., Michel, M., Taminiau, B., Louis, E., and Daube, G. (2023). Gut Microbiota Associated with Clostridioides difficile Carriage in Three Clinical Groups (Inflammatory Bowel Disease, C. difficile Infection and Healthcare Workers) in Hospital Field. Microorganisms, 11.","DOI":"10.3390\/microorganisms11102527"},{"key":"ref_61","doi-asserted-by":"crossref","unstructured":"Nobili, A., Pane, M., Skvortsova, M., Salem, M.B., Morgenthaler, S., Jamieson, E., Stefano, M.D., Bathrellou, E., Mamalaki, E., and Ramos-Garcia, V. (2024). Innovative Biomarkers for Obesity and Type 1 Diabetes Based on Bifidobacterium and Metabolomic Profiling. Microorganisms, 12.","DOI":"10.3390\/microorganisms12050931"},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"1017","DOI":"10.1016\/j.clnu.2013.02.008","article-title":"Faecal Levels of Bifidobacterium and Clostridium Coccoides but Not Plasma Lipopolysaccharide Are Inversely Related to Insulin and HOMA Index in Women","volume":"32","author":"Teixeira","year":"2013","journal-title":"Clin. Nutr."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1016\/j.chom.2014.12.009","article-title":"MyD88 Signaling in T Cells Directs IgA-Mediated Control of the Microbiota to Promote Health","volume":"17","author":"Kubinak","year":"2015","journal-title":"Cell Host Microbe"},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1264\/jsme2.ME14054","article-title":"Intestinal Colonization by a Lachnospiraceae Bacterium Contributes to the Development of Diabetes in Obese Mice","volume":"29","author":"Kameyama","year":"2014","journal-title":"Microbes Env."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"1004","DOI":"10.1002\/mnfr.201400780","article-title":"Contrasting Effects of Fresh and Fermented Kimchi Consumption on Gut Microbiota Composition and Gene Expression Related to Metabolic Syndrome in Obese Korean Women","volume":"59","author":"Han","year":"2015","journal-title":"Mol. Nutr. Food Res."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"65","DOI":"10.3164\/jcbn.15-152","article-title":"Comparison of the Gut Microbial Community between Obese and Lean Peoples Using 16S Gene Sequencing in a Japanese Population","volume":"59","author":"Andoh","year":"2016","journal-title":"J. Clin. Biochem. Nutr."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"406","DOI":"10.1016\/j.tim.2014.04.003","article-title":"Clostridium Difficile Spore Biology: Sporulation, Germination, and Spore Structural Proteins","volume":"22","author":"Shen","year":"2014","journal-title":"Trends Microbiol."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1128\/CMR.1.1.1","article-title":"Clostridium Difficile: Its Disease and Toxins","volume":"1","author":"Lyerly","year":"1988","journal-title":"Clin. Microbiol. Rev."},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"15","DOI":"10.4161\/gmic.26854","article-title":"Clostridium Difficile Binary Toxin CDT: Mechanism, Epidemiology, and Potential Clinical Importance","volume":"5","author":"Gerding","year":"2014","journal-title":"Gut Microbes"},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"ofac001","DOI":"10.1093\/ofid\/ofac001","article-title":"Binary Toxin Expression by Clostridioides difficile Is Associated With Worse Disease","volume":"9","author":"Young","year":"2022","journal-title":"Open Forum Infect. Dis."},{"key":"ref_71","doi-asserted-by":"crossref","unstructured":"Wan, S., You, P., Shi, Q., Hu, H., Zhang, L., Chen, L., Wu, Z., Lin, S., Song, X., and Luo, Y. (2024). Gut Microbiome Changes in Mouse, Mongolian Gerbil, and Hamster Models Following Clostridioides difficile Challenge. Front. Microbiol., 15.","DOI":"10.3389\/fmicb.2024.1368194"},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"1403","DOI":"10.1001\/jama.2019.3849","article-title":"Diagnosis and Treatment of Clostridioides ( Clostridium ) Difficile Infection in Adults in 2020","volume":"323","author":"Rao","year":"2020","journal-title":"JAMA"},{"key":"ref_73","first-page":"319","article-title":"Clostridioides difficile Infection: Landscape and Microbiome Therapeutics","volume":"19","author":"Gawey","year":"2023","journal-title":"Gastroenterol. Hepatol."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"1320","DOI":"10.1056\/NEJMoa1910215","article-title":"Trends in U.S. Burden of Clostridioides difficile Infection and Outcomes","volume":"382","author":"Guh","year":"2020","journal-title":"N. Engl. J. Med."},{"key":"ref_75","first-page":"231","article-title":"Current Diagnostic and Treatment Approach of Clostridioides difficile Infection","volume":"55","author":"Yunita","year":"2023","journal-title":"Acta Medica Indones."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"S194","DOI":"10.1093\/infdis\/jiaa408","article-title":"Mechanisms of Colonization Resistance Against Clostridioides difficile","volume":"223","author":"Pike","year":"2020","journal-title":"J. Infect. Dis."},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"wrae114","DOI":"10.1093\/ismejo\/wrae114","article-title":"Island Biogeography Theory Provides a Plausible Explanation for Why Larger Vertebrates and Taller Humans Have More Diverse Gut Microbiomes","volume":"18","author":"Sarmiento","year":"2024","journal-title":"ISME J."},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"1241214","DOI":"10.1126\/science.1241214","article-title":"Gut Microbiota from Twins Discordant for Obesity Modulate Metabolism in Mice","volume":"341","author":"Ridaura","year":"2013","journal-title":"Science"},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"514","DOI":"10.1007\/s13679-023-00527-y","article-title":"Update on the Obesity Epidemic: After the Sudden Rise, Is the Upward Trajectory Beginning to Flatten?","volume":"12","author":"Koliaki","year":"2023","journal-title":"Curr. Obes. Rep."},{"key":"ref_80","doi-asserted-by":"crossref","unstructured":"Stanislawski, M.A., Dabelea, D., Lange, L.A., Wagner, B.D., and Lozupone, C.A. (2019). Gut Microbiota Phenotypes of Obesity. NPJ Biofilms Microbiomes, 5.","DOI":"10.1038\/s41522-019-0091-8"},{"key":"ref_81","doi-asserted-by":"crossref","unstructured":"Rohm, T.V., Fuchs, R., M\u00fcller, R.L., Keller, L., Baumann, Z., Bosch, A.J.T., Schneider, R., Labes, D., Langer, I., and Pilz, J.B. (2021). Obesity in Humans Is Characterized by Gut Inflammation as Shown by Pro-Inflammatory Intestinal Macrophage Accumulation. Front. Immunol., 12.","DOI":"10.3389\/fimmu.2021.668654"},{"key":"ref_82","first-page":"239","article-title":"Health Impacts of Obesity","volume":"31","author":"Djalalinia","year":"2015","journal-title":"Pak. J. Med. Sci."},{"key":"ref_83","first-page":"11788","article-title":"Bacteroides Uniformis CECT 7771 Alleviates Inflammation within the Gut-adipose Tissue Axis Involving TLR5 Signaling in Obese Mice","volume":"11","author":"Fabersani","year":"2021","journal-title":"Nat. Portf."},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"228","DOI":"10.1126\/science.1179721","article-title":"Metabolic Syndrome and Altered Gut Microbiota in Mice Lacking Toll-Like Receptor 5","volume":"328","author":"Aitken","year":"2010","journal-title":"Science"},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"eaat9351","DOI":"10.1126\/science.aat9351","article-title":"T Cell\u2013Mediated Regulation of the Microbiota Protects against Obesity","volume":"365","author":"Petersen","year":"2019","journal-title":"Science"},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"3650","DOI":"10.1038\/s41467-019-11370-y","article-title":"Gut-Associated IgA+ Immune Cells Regulate Obesity-Related Insulin Resistance","volume":"10","author":"Luck","year":"2019","journal-title":"Nat. Commun."},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"5650","DOI":"10.1038\/s41467-019-13538-y","article-title":"Flagellin-Elicited Adaptive Immunity Suppresses Flagellated Microbiota and Vaccinates against Chronic Inflammatory Diseases","volume":"10","author":"Tran","year":"2019","journal-title":"Nat. Commun."},{"key":"ref_88","doi-asserted-by":"crossref","unstructured":"Mafra, D., Borges, N.A., Baptista, B.G., Martins, L.F., Borland, G., Shiels, P.G., and Stenvinkel, P. (2024). What Can the Gut Microbiota of Animals Teach Us about the Relationship between Nutrition and Burden of Lifestyle Diseases?. Nutrients, 16.","DOI":"10.3390\/nu16111789"},{"key":"ref_89","doi-asserted-by":"crossref","first-page":"2559","DOI":"10.1038\/s41396-018-0166-1","article-title":"Factors Influencing Bacterial Microbiome Composition in a Wild Non-Human Primate Community in Ta\u00ef National Park, C\u00f4te d\u2019Ivoire","volume":"12","author":"Gogarten","year":"2018","journal-title":"ISME J."},{"key":"ref_90","doi-asserted-by":"crossref","first-page":"690","DOI":"10.1093\/icb\/icx090","article-title":"The Effects of Captivity on the Mammalian Gut Microbiome","volume":"57","author":"McKenzie","year":"2017","journal-title":"Integr. Comp. Biol."},{"key":"ref_91","unstructured":"Clavel, T., Lagkouvardos, I., Blaut, M., and Stecher, B. (2024, August 29). The Mouse Gut Microbiome Revisited: From Complex Diversity to Model Ecosystems\u2014ClinicalKey. Available online: https:\/\/www.clinicalkey.com\/#!\/content\/playContent\/1-s2.0-S1438422116300170?returnurl=null&referrer=null."},{"key":"ref_92","doi-asserted-by":"crossref","unstructured":"Pei, L., Ke, Y., Zhao, H., Wang, L., Jia, C., Liu, W., Fu, Q., Shi, M., Cui, J., and Li, S. (2019). Role of Colonic Microbiota in the Pathogenesis of Ulcerative Colitis. BMC Gastroenterol., 19.","DOI":"10.1186\/s12876-019-0930-3"},{"key":"ref_93","doi-asserted-by":"crossref","first-page":"694","DOI":"10.1016\/0016-5085(90)90290-H","article-title":"A Novel Method in the Induction of Reliable Experimental Acute and Chronic Ulcerative Colitis in Mice","volume":"98","author":"Okayasu","year":"1990","journal-title":"Gastroenterology"},{"key":"ref_94","doi-asserted-by":"crossref","unstructured":"Gray, S.M., Moss, A.D., Herzog, J.W., Kashiwagi, S., Liu, B., Young, J.B., Sun, S., Bhatt, A.P., Fodor, A.A., and Balfour Sartor, R. (2024). Mouse Adaptation of Human Inflammatory Bowel Diseases Microbiota Enhances Colonization Efficiency and Alters Microbiome Aggressiveness Depending on the Recipient Colonic Inflammatory Environment. Microbiome, 12.","DOI":"10.1186\/s40168-024-01857-2"},{"key":"ref_95","doi-asserted-by":"crossref","unstructured":"Rashed, R., Valcheva, R., and Dieleman, L.A. (2022). Manipulation of Gut Microbiota as a Key Target for Crohn\u2019s Disease. Front. Med., 9.","DOI":"10.3389\/fmed.2022.887044"},{"key":"ref_96","doi-asserted-by":"crossref","unstructured":"N\u00fa\u00f1ez-S\u00e1nchez, M.A., Melgar, S., O\u2019Donoghue, K., Mart\u00ednez-S\u00e1nchez, M.A., Fern\u00e1ndez-Ruiz, V.E., Ferrer-G\u00f3mez, M., Ruiz-Alcaraz, A.J., and Ramos-Molina, B. (2022). Crohn\u2019s Disease, Host\u2013Microbiota Interactions, and Immunonutrition: Dietary Strategies Targeting Gut Microbiome as Novel Therapeutic Approaches. Int. J. Mol. Sci., 23.","DOI":"10.3390\/ijms23158361"},{"key":"ref_97","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1136\/gutjnl-2015-309333","article-title":"Dysbiotic Gut Microbiota Causes Transmissible Crohn\u2019s Disease-like Ileitis Independent of Failure in Antimicrobial Defence","volume":"65","author":"Schaubeck","year":"2016","journal-title":"Gut"},{"key":"ref_98","doi-asserted-by":"crossref","first-page":"62","DOI":"10.1128\/IAI.05496-11","article-title":"Profound Alterations of Intestinal Microbiota Following a Single Dose of Clindamycin Results in Sustained Susceptibility to Clostridium Difficile-Induced Colitis","volume":"80","author":"Buffie","year":"2012","journal-title":"Infect. Immun."},{"key":"ref_99","doi-asserted-by":"crossref","first-page":"2367","DOI":"10.1128\/IAI.01520-08","article-title":"Reproducible Community Dynamics of the Gastrointestinal Microbiota Following Antibiotic Perturbation","volume":"77","author":"Antonopoulos","year":"2009","journal-title":"Infect. Immun."},{"key":"ref_100","doi-asserted-by":"crossref","unstructured":"Piccioni, A., Rosa, F., Manca, F., Pignataro, G., Zanza, C., Savioli, G., Covino, M., Ojetti, V., Gasbarrini, A., and Franceschi, F. (2022). Gut Microbiota and Clostridium Difficile: What We Know and the New Frontiers. Int. J. Mol. Sci., 23.","DOI":"10.3390\/ijms232113323"},{"key":"ref_101","doi-asserted-by":"crossref","first-page":"1756284821994736","DOI":"10.1177\/1756284821994736","article-title":"Gut Microbiome and Clostridioides difficile Infection: A Closer Look at the Microscopic Interface","volume":"14","author":"Sehgal","year":"2021","journal-title":"Ther. Adv. Gastroenterol."},{"key":"ref_102","doi-asserted-by":"crossref","first-page":"17562848221115320","DOI":"10.1177\/17562848221115320","article-title":"Recent Insights into the Role of Microbiome in the Pathogenesis of Obesity","volume":"15","author":"Levin","year":"2022","journal-title":"Ther. Adv. Gastroenterol."},{"key":"ref_103","doi-asserted-by":"crossref","first-page":"4112","DOI":"10.1111\/febs.16298","article-title":"Innate Immunity and Inflammophagy: Balancing the Defence and Immune Homeostasis","volume":"289","author":"Chauhan","year":"2022","journal-title":"FEBS J."},{"key":"ref_104","doi-asserted-by":"crossref","first-page":"515","DOI":"10.1097\/MCO.0000000000000209","article-title":"Influence of High-Fat Diet on Gut Microbiota: A Driving Force for Chronic Disease Risk","volume":"18","author":"Murphy","year":"2015","journal-title":"Curr. Opin. Clin. Nutr. Metab. Care"},{"key":"ref_105","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1007\/s40121-023-00907-w","article-title":"Efficacy and Health-Related Quality of Life Impact of Fecal Microbiota, Live-Jslm: A Post Hoc Analysis of PUNCH CD3 Patients at First Recurrence of Clostridioides difficile Infection","volume":"13","author":"Feuerstadt","year":"2024","journal-title":"Infect. Dis. Ther."},{"key":"ref_106","doi-asserted-by":"crossref","unstructured":"Binyamin, D., Nitzan, O., Azrad, M., Hamo, Z., Koren, O., and Peretz, A. (2021). The Microbial Diversity Following Antibiotic Treatment of Clostridioides difficile Infection. BMC Gastroenterol., 21.","DOI":"10.1186\/s12876-021-01754-0"},{"key":"ref_107","doi-asserted-by":"crossref","first-page":"354","DOI":"10.1097\/MCG.0b013e3181c87e02","article-title":"Changes in the Composition of the Human Fecal Microbiome After Bacteriotherapy for Recurrent Clostridium Difficile-Associated Diarrhea","volume":"44","author":"Khoruts","year":"2010","journal-title":"J. Clin. Gastroenterol."},{"key":"ref_108","doi-asserted-by":"crossref","first-page":"935","DOI":"10.1007\/s40121-020-00339-w","article-title":"Faecal Microbiota Transplantation Is Effective for the Initial Treatment of Clostridium Difficile Infection: A Retrospective Clinical Review","volume":"9","author":"Roshan","year":"2020","journal-title":"Infect. Dis. Ther."},{"key":"ref_109","doi-asserted-by":"crossref","unstructured":"Zou, B., Liu, S., Li, X., He, J., Dong, C., Ruan, M., Huang, Z., and Shu, S. (2023). Repeated and Multiple Fecal Microbiota Transplantations plus Partial Enteral Nutrition as the First-Line Treatment in Active Pediatric Crohn\u2019s Disease. Front. Cell. Infect. Microbiol., 13.","DOI":"10.3389\/fcimb.2023.1083236"},{"key":"ref_110","doi-asserted-by":"crossref","unstructured":"Wilson, B.C., Vatanen, T., Cutfield, W.S., and O\u2019Sullivan, J.M. (2019). The Super-Donor Phenomenon in Fecal Microbiota Transplantation. Front. Cell. Infect. Microbiol., 9.","DOI":"10.3389\/fcimb.2019.00002"},{"key":"ref_111","doi-asserted-by":"crossref","first-page":"1527","DOI":"10.1007\/s40265-022-01797-x","article-title":"Efficacy and Safety of RBX2660 in PUNCH CD3, a Phase III, Randomized, Double-Blind, Placebo-Controlled Trial with a Bayesian Primary Analysis for the Prevention of Recurrent Clostridioides difficile Infection","volume":"82","author":"Khanna","year":"2022","journal-title":"Drugs"},{"key":"ref_112","doi-asserted-by":"crossref","first-page":"17562848231174277","DOI":"10.1177\/17562848231174277","article-title":"Safety of Fecal Microbiota, Live-Jslm (REBYOTATM) in Individuals with Recurrent Clostridioides difficile Infection: Data from Five Prospective Clinical Trials","volume":"16","author":"Lee","year":"2023","journal-title":"Ther. Adv. Gastroenterol."},{"key":"ref_113","doi-asserted-by":"crossref","first-page":"220","DOI":"10.1056\/NEJMoa2106516","article-title":"SER-109, an Oral Microbiome Therapy for Recurrent Clostridioides difficile Infection","volume":"386","author":"Feuerstadt","year":"2022","journal-title":"N. Engl. J. Med."},{"key":"ref_114","doi-asserted-by":"crossref","first-page":"1504","DOI":"10.1093\/cid\/ciad448","article-title":"Prevalence of Comorbid Factors in Patients With Recurrent Clostridioides difficile Infection in ECOSPOR III, a Randomized Trial of an Oral Microbiota\u2013Based Therapeutic","volume":"77","author":"Berenson","year":"2023","journal-title":"Clin. Infect. Dis."},{"key":"ref_115","doi-asserted-by":"crossref","first-page":"1103","DOI":"10.1007\/s10096-023-04644-3","article-title":"High Carriage Rate of Extended-Spectrum Beta-Lactamase Enterobacterales and Diarrheagenic Escherichia Coli in Healthy Donor Screening for Fecal Microbiota Transplantation","volume":"42","author":"Chuang","year":"2023","journal-title":"Eur. J. Clin. Microbiol. Infect. Dis."},{"key":"ref_116","first-page":"150","article-title":"Adverse Events in Fecal Microbiota Transplantation: A Systematic Review and Meta-Analysis","volume":"35","author":"Rapoport","year":"2022","journal-title":"Ann. Gastroenterol."},{"key":"ref_117","doi-asserted-by":"crossref","first-page":"100069","DOI":"10.1016\/j.infpip.2020.100069","article-title":"Regulation, Risk and Safety of Faecal Microbiota Transplant","volume":"2","author":"Merrick","year":"2020","journal-title":"Infect. Prev. Prac."},{"key":"ref_118","doi-asserted-by":"crossref","unstructured":"Dwiyanto, J., Hussain, M.H., Reidpath, D., Ong, K.S., Qasim, A., Lee, S.W.H., Lee, S.M., Foo, S.C., Chong, C.W., and Rahman, S. (2021). Ethnicity Influences the Gut Microbiota of Individuals Sharing a Geographical Location: A Cross-Sectional Study from a Middle-Income Country. Sci. Rep., 11.","DOI":"10.1038\/s41598-021-82311-3"},{"key":"ref_119","doi-asserted-by":"crossref","unstructured":"van Leeuwen, P.T., Brul, S., Zhang, J., and Wortel, M.T. (2023). Synthetic Microbial Communities (SynComs) of the Human Gut: Design, Assembly, and Applications. FEMS Microbiol. Rev., 47.","DOI":"10.1093\/femsre\/fuad012"},{"key":"ref_120","doi-asserted-by":"crossref","first-page":"6061","DOI":"10.1002\/anie.202014052","article-title":"Targeted Delivery of Persulfides to the Gut: Effects on the Microbiome","volume":"60","author":"Dillon","year":"2021","journal-title":"Angew. Chem. Int. Ed. Engl."},{"key":"ref_121","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1128\/msystems.00013-20","article-title":"Stable Neutralization of a Virulence Factor in Bacteria Using Temperate Phage in the Mammalian Gut","volume":"5","author":"Hsu","year":"2020","journal-title":"mSystems"},{"key":"ref_122","unstructured":"Metchnikoff, E. (1907). The Prolongation of Life: Optimistic Studies, Heinemann. English translation edited by P. Chalmers Mitchell."},{"key":"ref_123","doi-asserted-by":"crossref","first-page":"1406","DOI":"10.1016\/j.cell.2018.08.047","article-title":"Post-Antibiotic Gut Mucosal Microbiome Reconstitution Is Impaired by Probiotics and Improved by Autologous FMT","volume":"174","author":"Suez","year":"2018","journal-title":"Cell"},{"key":"ref_124","first-page":"27","article-title":"Probiotics Are Effective at Preventing Clostridium Difficile-Associated Diarrhea: A Systematic Review and Meta-Analysis","volume":"9","author":"Lau","year":"2016","journal-title":"Int. J. Gen. Med."},{"key":"ref_125","doi-asserted-by":"crossref","first-page":"eaax4905","DOI":"10.1126\/scitranslmed.aax4905","article-title":"A Probiotic Yeast-Based Immunotherapy against Clostridioides difficile Infection","volume":"12","author":"Chen","year":"2020","journal-title":"Sci. Transl. Med."},{"key":"ref_126","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1007\/5584_2018_321","article-title":"Probiotics in Functional Gastrointestinal Disorders","volume":"1125","author":"Hojsak","year":"2019","journal-title":"Adv. Exp. Med. Biol."},{"key":"ref_127","doi-asserted-by":"crossref","first-page":"533","DOI":"10.1097\/MCG.0000000000002002","article-title":"World Gastroenterology Organisation Global Guidelines: Probiotics and Prebiotics","volume":"58","author":"Guarner","year":"2024","journal-title":"J. Clin. Gastroenterol."},{"key":"ref_128","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_129","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1186\/s12964-024-01611-z","article-title":"The Development of Probiotics and Prebiotics Therapy to Ulcerative Colitis: A Therapy That Has Gained Considerable Momentum","volume":"22","author":"Guo","year":"2024","journal-title":"Cell Commun. Signal"},{"key":"ref_130","doi-asserted-by":"crossref","first-page":"2211","DOI":"10.1016\/j.fshw.2023.03.041","article-title":"Stachyose Modulates Gut Microbiota and Alleviates DSS-Induced Ulcerative Colitis in Mice","volume":"12","author":"Wang","year":"2023","journal-title":"Food Sci. Hum. Wellness"},{"key":"ref_131","doi-asserted-by":"crossref","unstructured":"Guarino, M.P.L., Altomare, A., Emerenziani, S., Di Rosa, C., Ribolsi, M., Balestrieri, P., Iovino, P., Rocchi, G., and Cicala, M. (2020). Mechanisms of Action of Prebiotics and Their Effects on Gastro-Intestinal Disorders in Adults. Nutrients, 12.","DOI":"10.3390\/nu12041037"},{"key":"ref_132","doi-asserted-by":"crossref","unstructured":"Bacha, A.A., Suhail, M., Awwad, F.A., Ismail, E.A.A., and Ahmad, H. (2024). Role of Dietary Fiber and Lifestyle Modification in Gut Health and Sleep Quality. Front. Nutr., 11.","DOI":"10.3389\/fnut.2024.1324793"},{"key":"ref_133","doi-asserted-by":"crossref","unstructured":"Jalanka, J., Major, G., Murray, K., Singh, G., Nowak, A., Kurtz, C., Silos-Santiago, I., Johnston, J.M., de Vos, W.M., and Spiller, R. (2019). The Effect of Psyllium Husk on Intestinal Microbiota in Constipated Patients and Healthy Controls. Int. J. Mol. Sci., 20.","DOI":"10.3390\/ijms20020433"},{"key":"ref_134","doi-asserted-by":"crossref","first-page":"436","DOI":"10.1016\/j.nutres.2011.05.011","article-title":"Fermented Kimchi Reduces Body Weight and Improves Metabolic Parameters in Overweight and Obese Patients","volume":"31","author":"Kim","year":"2011","journal-title":"Nutr. Res."},{"key":"ref_135","doi-asserted-by":"crossref","unstructured":"Hassan, N.E., El-Masry, S.A., Shebini, S.M.E., Ahmed, N.H., Mehanna, N.S., Wahed, M.M.A., Amine, D., Hashish, A., Selim, M., and Afify, M.A.S. (2024). Effect of Weight Loss Program Using Prebiotics and Probiotics on Body Composition, Physique, and Metabolic Products: Longitudinal Intervention Study. Sci. Rep., 14.","DOI":"10.1038\/s41598-024-61130-2"},{"key":"ref_136","doi-asserted-by":"crossref","unstructured":"Kanazawa, A., Aida, M., Yoshida, Y., Kaga, H., Katahira, T., Suzuki, L., Tamaki, S., Sato, J., Goto, H., and Azuma, K. (2021). Effects of Synbiotic Supplementation on Chronic Inflammation and the Gut Microbiota in Obese Patients with Type 2 Diabetes Mellitus: A Randomized Controlled Study. Nutrients, 13.","DOI":"10.3390\/nu13020558"},{"key":"ref_137","doi-asserted-by":"crossref","first-page":"356","DOI":"10.1007\/s12519-022-00664-9","article-title":"Effects of Synbiotic Supplementation on Anthropometric Indices and Body Composition in Overweight or Obese Children and Adolescents: A Randomized, Double-Blind, Placebo-Controlled Clinical Trial","volume":"19","author":"Atazadegan","year":"2023","journal-title":"World J. Pediatr. WJP"},{"key":"ref_138","doi-asserted-by":"crossref","first-page":"111802","DOI":"10.1016\/j.nut.2022.111802","article-title":"Specially Designed Yogurt Supplemented with Combination of Pro- and Prebiotics Relieved Constipation in Mice and Humans","volume":"103\u2013104","author":"Li","year":"2022","journal-title":"Nutrition"},{"key":"ref_139","doi-asserted-by":"crossref","unstructured":"Rivero-Pino, F., Casquete, M., Castro, M.J., Redondo Del Rio, P., Gutierrez, E., Mayo-Iscar, A., Nocito, M., and Corell, A. (2024). Prospective, Randomized, Double-Blind Parallel Group Nutritional Study to Evaluate the Effects of Routine Intake of Fresh vs. Pasteurized Yogurt on the Immune System in Healthy Adults. Nutrients, 16.","DOI":"10.3390\/nu16121969"},{"key":"ref_140","first-page":"58","article-title":"Microbial Community of Kefir and Its Impact on the Gastrointestinal Microbiome in Health and Disease","volume":"74","author":"Lazda","year":"2020","journal-title":"Proc. Latv. Acad. Sci. Sect. B. Nat. Exact Appl. Sci."},{"key":"ref_141","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1017\/S0007114520002743","article-title":"Kefir Microbial Composition Is a Deciding Factor in the Physiological Impact of Kefir in a Mouse Model of Obesity","volume":"125","author":"Bourrie","year":"2021","journal-title":"Br. J. Nutr."},{"key":"ref_142","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1016\/j.jff.2018.04.039","article-title":"Traditional Kefir Reduces Weight Gain and Improves Plasma and Liver Lipid Profiles More Successfully than a Commercial Equivalent in a Mouse Model of Obesity","volume":"46","author":"Bourrie","year":"2018","journal-title":"J. Funct. Foods"},{"key":"ref_143","doi-asserted-by":"crossref","unstructured":"Gupta, V.K., Rajendraprasad, S., Ozkan, M., Ramachandran, D., Ahmad, S., Bakken, J.S., Laudanski, K., Gajic, O., Bauer, B., and Zec, S. (2024). Safety, Feasibility, and Impact on the Gut Microbiome of Kefir Administration in Critically Ill Adults. BMC Med., 22.","DOI":"10.1186\/s12916-024-03299-x"},{"key":"ref_144","doi-asserted-by":"crossref","first-page":"3771","DOI":"10.3168\/jds.2017-13539","article-title":"Exploring the Influence of Culture Conditions on Kefir\u2019s Anticancer Properties","volume":"101","author":"Hatmal","year":"2018","journal-title":"J. Dairy Sci."},{"key":"ref_145","doi-asserted-by":"crossref","unstructured":"Fraiz, G.M., Costa, M.A.C., Cardoso, R.R., H\u00e9bert, J.R., Zhao, L., Corich, V., Giacomini, A., Milagro, F.I., and Barros, F.A.R. (2024). Fermentation | Free Full-Text | Black Tea Kombucha Consumption: Effect on Cardiometabolic Parameters and Diet Quality of Individuals with and without Obesity. Fermentation, 10.","DOI":"10.3390\/fermentation10080384"},{"key":"ref_146","doi-asserted-by":"crossref","first-page":"976","DOI":"10.4315\/0362-028X-63.7.976","article-title":"Kombucha, the Fermented Tea: Microbiology, Composition, and Claimed Health Effects","volume":"63","author":"Greenwalt","year":"2000","journal-title":"J. Food Prot."},{"key":"ref_147","doi-asserted-by":"crossref","unstructured":"Jakubczyk, K., Ka\u0142du\u0144ska, J., Kochman, J., and Janda, K. (2020). Chemical Profile and Antioxidant Activity of the Kombucha Beverage Derived from White, Green, Black and Red Tea. Antioxidants, 9.","DOI":"10.3390\/antiox9050447"},{"key":"ref_148","doi-asserted-by":"crossref","unstructured":"Kim, J., Bhattarai, U., and Adhikari, K. (2022). The Healthy Eater\u2019s Idea and Related Behavior of a Healthy Diet\u2014A Case Study with Kombucha Drinkers. Beverages, 8.","DOI":"10.3390\/beverages8020025"},{"key":"ref_149","doi-asserted-by":"crossref","unstructured":"Antolak, H., Piechota, D., and Kucharska, A. (2021). Kombucha Tea\u2014A Double Power of Bioactive Compounds from Tea and Symbiotic Culture of Bacteria and Yeasts (SCOBY). Antioxidants, 10.","DOI":"10.3390\/antiox10101541"},{"key":"ref_150","first-page":"604","article-title":"The Protective Role of Kombucha Extract on the Normal Intestinal Microflora, High-Cholesterol Diet Caused Hypercholesterolemia, and Histological Structures Changes in New Zealand White Rabbits","volume":"10","author":"Alaei","year":"2020","journal-title":"Avicenna J. Phytomed."},{"key":"ref_151","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1007\/s10068-018-0433-y","article-title":"Effect of Kombucha on Gut-Microbiota in Mouse Having Non-Alcoholic Fatty Liver Disease","volume":"28","author":"Jung","year":"2018","journal-title":"Food Sci. Biotechnol."},{"key":"ref_152","doi-asserted-by":"crossref","unstructured":"Bamigbade, G.B., Subhash, A.J., Kamal-Eldin, A., Nystr\u00f6m, L., and Ayyash, M. (2022). An Updated Review on Prebiotics: Insights on Potentials of Food Seeds Waste as Source of Potential Prebiotics. Molecules, 27.","DOI":"10.3390\/molecules27185947"},{"key":"ref_153","doi-asserted-by":"crossref","first-page":"2500","DOI":"10.1021\/acs.jafc.8b06604","article-title":"Spent Coffee Grounds Extract, Rich in Mannooligosaccharides, Promotes a Healthier Gut Microbial Community in a Dose-Dependent Manner","volume":"67","author":"Pastoriza","year":"2019","journal-title":"J. Agric. Food Chem."},{"key":"ref_154","unstructured":"Godoy-Vitorino, F., and Vilanova-Cuevas, B. (2019). Probiotic Microbiota of Fermented Tropical Wood Drinks: Mauby and Tepache, ResearchGate."},{"key":"ref_155","unstructured":"de la Fuente-Salcido, N., Casta\u00f1eda-Ramirez, J., Garc\u00eda-Almend\u00e1rez, B., Bideshi, D., Salcedo-Hern\u00e1ndez, R., and Barbosa-Corona, J. (2024, August 27). Isolation and Characterization of Bacteriocinogenic Lactic Bacteria from M-Tuba and Tepache, Two Traditional Fermented Beverages in M\u00e9xico. Available online: https:\/\/onlinelibrary.wiley.com\/doi\/epdf\/10.1002\/fsn3.236."},{"key":"ref_156","first-page":"18572","article-title":"Kiwifruit (Actinidia Deliciosa) Changes Intestinal Microbial Profile","volume":"23","author":"Lee","year":"2012","journal-title":"Microb. Ecol. Health Dis."},{"key":"ref_157","doi-asserted-by":"crossref","unstructured":"You, S., Ma, Y., Yan, B., Pei, W., Wu, Q., Ding, C., and Huang, C. (2022). The Promotion Mechanism of Prebiotics for Probiotics: A Review. Front. Nutr., 9.","DOI":"10.3389\/fnut.2022.1000517"},{"key":"ref_158","doi-asserted-by":"crossref","first-page":"1800636","DOI":"10.1002\/mnfr.201800636","article-title":"Dietary Black Raspberries Impact the Colonic Microbiome and Phytochemical Metabolites in Mice","volume":"63","author":"Gu","year":"2019","journal-title":"Mol. Nutr. Food Res."},{"key":"ref_159","doi-asserted-by":"crossref","unstructured":"Chandrasekaran, P., Weiskirchen, S., and Weiskirchen, R. (2024). Effects of Probiotics on Gut Microbiota: An Overview. Int. J. Mol. Sci., 25.","DOI":"10.3390\/ijms25116022"},{"key":"ref_160","doi-asserted-by":"crossref","first-page":"96","DOI":"10.1016\/j.molmet.2019.01.012","article-title":"Synbiotic-Driven Improvement of Metabolic Disturbances Is Associated with Changes in the Gut Microbiome in Diet-Induced Obese Mice","volume":"22","author":"Ke","year":"2019","journal-title":"Mol. Metab."}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/25\/17\/9715\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T15:51:32Z","timestamp":1760111492000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/25\/17\/9715"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,9,8]]},"references-count":160,"journal-issue":{"issue":"17","published-online":{"date-parts":[[2024,9]]}},"alternative-id":["ijms25179715"],"URL":"https:\/\/doi.org\/10.3390\/ijms25179715","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,9,8]]}}}