1
|
Zheng M, Zhai Y, Yu Y, Shen J, Chu S, Focaccia E, Tian W, Wang S, Liu X, Yuan X, Wang Y, Li L, Feng B, Li Z, Guo X, Qiu J, Zhang C, Hou J, Sun Y, Yang X, Zuo X, Heikenwalder M, Li Y, Yuan D, Li S. TNF compromises intestinal bile-acid tolerance dictating colitis progression and limited infliximab response. Cell Metab 2024:S1550-4131(24)00233-X. [PMID: 38971153 DOI: 10.1016/j.cmet.2024.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 03/28/2024] [Accepted: 06/07/2024] [Indexed: 07/08/2024]
Abstract
The intestine constantly encounters and adapts to the external environment shaped by diverse dietary nutrients. However, whether and how gut adaptability to dietary challenges is compromised in ulcerative colitis is incompletely understood. Here, we show that a transient high-fat diet exacerbates colitis owing to inflammation-compromised bile acid tolerance. Mechanistically, excessive tumor necrosis factor (TNF) produced at the onset of colitis interferes with bile-acid detoxification through the receptor-interacting serine/threonine-protein kinase 1/extracellular signal-regulated kinase pathway in intestinal epithelial cells, leading to bile acid overload in the endoplasmic reticulum and consequent apoptosis. In line with the synergy of bile acids and TNF in promoting gut epithelial damage, high intestinal bile acids correlate with poor infliximab response, and bile acid clearance improves infliximab efficacy in experimental colitis. This study identifies bile acids as an "opportunistic pathogenic factor" in the gut that would represent a promising target and stratification criterion for ulcerative colitis prevention/therapy.
Collapse
Affiliation(s)
- Mengqi Zheng
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan 250012, China; Shandong Provincial Clinical Research Center for Digestive Diseases, Jinan, China
| | - Yunjiao Zhai
- Advanced Medical Research Institute, Shandong University, Jinan 250012, China
| | - Yanbo Yu
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan 250012, China; Shandong Provincial Clinical Research Center for Digestive Diseases, Jinan, China; Laboratory of Translational Gastroenterology, Qilu Hospital of Shandong University, Jinan 250012, China; Robot Engineering Laboratory for Precise Diagnosis and Therapy of GI Tumor, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Jing Shen
- Advanced Medical Research Institute, Shandong University, Jinan 250012, China
| | - Shuzheng Chu
- Advanced Medical Research Institute, Shandong University, Jinan 250012, China
| | - Enrico Focaccia
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Wenyu Tian
- Advanced Medical Research Institute, Shandong University, Jinan 250012, China
| | - Sui Wang
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Xuesong Liu
- Advanced Medical Research Institute, Shandong University, Jinan 250012, China
| | - Xi Yuan
- Advanced Medical Research Institute, Shandong University, Jinan 250012, China
| | - Yue Wang
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Lixiang Li
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan 250012, China; Shandong Provincial Clinical Research Center for Digestive Diseases, Jinan, China; Laboratory of Translational Gastroenterology, Qilu Hospital of Shandong University, Jinan 250012, China; Robot Engineering Laboratory for Precise Diagnosis and Therapy of GI Tumor, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Bingcheng Feng
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Zhen Li
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan 250012, China; Shandong Provincial Clinical Research Center for Digestive Diseases, Jinan, China; Laboratory of Translational Gastroenterology, Qilu Hospital of Shandong University, Jinan 250012, China; Robot Engineering Laboratory for Precise Diagnosis and Therapy of GI Tumor, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Xiaohuan Guo
- Institute for Immunology, School of Medicine, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory for Immunological Research on Chronic Diseases, Tsinghua University, Beijing 100084, China
| | - Ju Qiu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Cuijuan Zhang
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan 250012, China; Department of Pathology, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Jiajie Hou
- Cancer Centre, Faculty of Health Sciences University of Macau, Macau SAR, China; MOE Frontier Science Centre for Precision Oncology, University of Macau, Macau SAR, China
| | - Yiyuan Sun
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Xiaoyun Yang
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan 250012, China; Shandong Provincial Clinical Research Center for Digestive Diseases, Jinan, China; Laboratory of Translational Gastroenterology, Qilu Hospital of Shandong University, Jinan 250012, China; Robot Engineering Laboratory for Precise Diagnosis and Therapy of GI Tumor, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Xiuli Zuo
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan 250012, China; Shandong Provincial Clinical Research Center for Digestive Diseases, Jinan, China; Laboratory of Translational Gastroenterology, Qilu Hospital of Shandong University, Jinan 250012, China; Robot Engineering Laboratory for Precise Diagnosis and Therapy of GI Tumor, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Mathias Heikenwalder
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany; The M3 Research Center, Medical faculty, University Tübingen, Ottfried-Müller Strasse 37, Tübingen, Germany.
| | - Yanqing Li
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan 250012, China; Shandong Provincial Clinical Research Center for Digestive Diseases, Jinan, China; Laboratory of Translational Gastroenterology, Qilu Hospital of Shandong University, Jinan 250012, China; Robot Engineering Laboratory for Precise Diagnosis and Therapy of GI Tumor, Qilu Hospital of Shandong University, Jinan 250012, China.
| | - Detian Yuan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shandong University, Jinan 250012, China.
| | - Shiyang Li
- Department of Gastroenterology, Qilu Hospital of Shandong University, Jinan 250012, China; Shandong Provincial Clinical Research Center for Digestive Diseases, Jinan, China; Advanced Medical Research Institute, Shandong University, Jinan 250012, China; Key Laboratory for Experimental Teratology of Ministry of Education, Shandong University, Jinan 250012, China.
| |
Collapse
|
2
|
Wang C, Gu Y, Chu Q, Wang X, Ding Y, Qin X, Liu T, Wang S, Liu X, Wang B, Cao H. Gut microbiota and metabolites as predictors of biologics response in inflammatory bowel disease: A comprehensive systematic review. Microbiol Res 2024; 282:127660. [PMID: 38442454 DOI: 10.1016/j.micres.2024.127660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 02/02/2024] [Accepted: 02/19/2024] [Indexed: 03/07/2024]
Abstract
Nonresponse to biologic agents in patients with inflammatory bowel disease (IBD) poses a significant public health burden, and the prediction of response to biologics offers valuable insights for IBD management. Given the pivotal role of gut microbiota and their endogenous metabolites in IBD, we conducted a systematic review to investigate the potential of fecal microbiota and mucosal microbiota and endogenous metabolomic markers as predictors for biotherapy response in IBD patients. A total of 38 studies were included in the review. Following anti-TNF-α treatment, the bacterial community characteristics of IBD patients exhibited a tendency to resemble those observed in healthy controls, indicating an improved clinical response. The levels of endogenous metabolites butyrate and deoxycholic acid were significantly associated with clinical remission following anti-TNF-α therapy. IBD patients who responded well to vedolizumab treatment had higher levels of specific bacteria that produce butyrate, along with increased levels of metabolites such as butyrate, branched-chain amino acids and acetamide following vedolizumab treatment. Crohn's disease patients who responded positively to ustekinumab treatment showed higher levels of Faecalibacterium and lower levels of Escherichia/Shigella. In conclusion, fecal microbiota and mucosal microbiota as well as their endogenous metabolites could provide a predictive tool for assessing the response of IBD patients to various biological agents and serve as a valuable reference for precise drug selection in clinical IBD patients.
Collapse
Affiliation(s)
- Chen Wang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Yu Gu
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Qiao Chu
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Xin Wang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Yiyun Ding
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Xiali Qin
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Tianyu Liu
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Sinan Wang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Xiang Liu
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Bangmao Wang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Hailong Cao
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China.
| |
Collapse
|
3
|
Marinos G, Hamerich IK, Debray R, Obeng N, Petersen C, Taubenheim J, Zimmermann J, Blackburn D, Samuel BS, Dierking K, Franke A, Laudes M, Waschina S, Schulenburg H, Kaleta C. Metabolic model predictions enable targeted microbiome manipulation through precision prebiotics. Microbiol Spectr 2024; 12:e0114423. [PMID: 38230938 PMCID: PMC10846184 DOI: 10.1128/spectrum.01144-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 12/13/2023] [Indexed: 01/18/2024] Open
Abstract
While numerous health-beneficial interactions between host and microbiota have been identified, there is still a lack of targeted approaches for modulating these interactions. Thus, we here identify precision prebiotics that specifically modulate the abundance of a microbiome member species of interest. In the first step, we show that defining precision prebiotics by compounds that are only taken up by the target species but no other species in a community is usually not possible due to overlapping metabolic niches. Subsequently, we use metabolic modeling to identify precision prebiotics for a two-member Caenorhabditis elegans microbiome community comprising the immune-protective target species Pseudomonas lurida MYb11 and the persistent colonizer Ochrobactrum vermis MYb71. We experimentally confirm four of the predicted precision prebiotics, L-serine, L-threonine, D-mannitol, and γ-aminobutyric acid, to specifically increase the abundance of MYb11. L-serine was further assessed in vivo, leading to an increase in MYb11 abundance also in the worm host. Overall, our findings demonstrate that metabolic modeling is an effective tool for the design of precision prebiotics as an important cornerstone for future microbiome-targeted therapies.IMPORTANCEWhile various mechanisms through which the microbiome influences disease processes in the host have been identified, there are still only few approaches that allow for targeted manipulation of microbiome composition as a first step toward microbiome-based therapies. Here, we propose the concept of precision prebiotics that allow to boost the abundance of already resident health-beneficial microbial species in a microbiome. We present a constraint-based modeling pipeline to predict precision prebiotics for a minimal microbial community in the worm Caenorhabditis elegans comprising the host-beneficial Pseudomonas lurida MYb11 and the persistent colonizer Ochrobactrum vermis MYb71 with the aim to boost the growth of MYb11. Experimentally testing four of the predicted precision prebiotics, we confirm that they are specifically able to increase the abundance of MYb11 in vitro and in vivo. These results demonstrate that constraint-based modeling could be an important tool for the development of targeted microbiome-based therapies against human diseases.
Collapse
Affiliation(s)
- Georgios Marinos
- Research Group Medical Systems Biology, University Hospital Schleswig-Holstein Campus Kiel, Kiel University, Kiel, Schleswig-Holstein, Germany
| | - Inga K. Hamerich
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Schleswig-Holstein, Germany
| | - Reena Debray
- Department of Integrative Biology, University of California, Berkeley, California, USA
| | - Nancy Obeng
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Schleswig-Holstein, Germany
| | - Carola Petersen
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Schleswig-Holstein, Germany
| | - Jan Taubenheim
- Research Group Medical Systems Biology, University Hospital Schleswig-Holstein Campus Kiel, Kiel University, Kiel, Schleswig-Holstein, Germany
| | - Johannes Zimmermann
- Research Group Medical Systems Biology, University Hospital Schleswig-Holstein Campus Kiel, Kiel University, Kiel, Schleswig-Holstein, Germany
- Max-Planck Institute for Evolutionary Biology, Ploen, Schleswig-Holstein, Germany
| | - Dana Blackburn
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, Texas, USA
| | - Buck S. Samuel
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, Texas, USA
| | - Katja Dierking
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Schleswig-Holstein, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Schleswig-Holstein, Germany
| | - Matthias Laudes
- Institute of Diabetes and Clinical Metabolic Research, University Hospital Schleswig-Holstein Campus Kiel, Kiel, Schleswig-Holstein, Germany
| | - Silvio Waschina
- Nutriinformatics, Institute for Human Nutrition and Food Science, Kiel University, Kiel, Schleswig-Holstein, Germany
| | - Hinrich Schulenburg
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Schleswig-Holstein, Germany
- Max-Planck Institute for Evolutionary Biology, Ploen, Schleswig-Holstein, Germany
| | - Christoph Kaleta
- Research Group Medical Systems Biology, University Hospital Schleswig-Holstein Campus Kiel, Kiel University, Kiel, Schleswig-Holstein, Germany
| |
Collapse
|
4
|
Forero-Rodríguez J, Zimmermann J, Taubenheim J, Arias-Rodríguez N, Caicedo-Narvaez JD, Best L, Mendieta CV, López-Castiblanco J, Gómez-Muñoz LA, Gonzalez-Santos J, Arboleda H, Fernandez W, Kaleta C, Pinzón A. Changes in Bacterial Gut Composition in Parkinson's Disease and Their Metabolic Contribution to Disease Development: A Gut Community Reconstruction Approach. Microorganisms 2024; 12:325. [PMID: 38399728 PMCID: PMC10893096 DOI: 10.3390/microorganisms12020325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/08/2024] [Accepted: 01/10/2024] [Indexed: 02/25/2024] Open
Abstract
Parkinson's disease (PD) is a chronic and progressive neurodegenerative disease with the major symptoms comprising loss of movement coordination (motor dysfunction) and non-motor dysfunction, including gastrointestinal symptoms. Alterations in the gut microbiota composition have been reported in PD patients vs. controls. However, it is still unclear how these compositional changes contribute to disease etiology and progression. Furthermore, most of the available studies have focused on European, Asian, and North American cohorts, but the microbiomes of PD patients in Latin America have not been characterized. To address this problem, we obtained fecal samples from Colombian participants (n = 25 controls, n = 25 PD idiopathic cases) to characterize the taxonomical community changes during disease via 16S rRNA gene sequencing. An analysis of differential composition, diversity, and personalized computational modeling was carried out, given the fecal bacterial composition and diet of each participant. We found three metabolites that differed in dietary habits between PD patients and controls: carbohydrates, trans fatty acids, and potassium. We identified six genera that changed significantly in their relative abundance between PD patients and controls, belonging to the families Lachnospiraceae, Lactobacillaceae, Verrucomicrobioaceae, Peptostreptococcaceae, and Streptococcaceae. Furthermore, personalized metabolic modeling of the gut microbiome revealed changes in the predicted production of seven metabolites (Indole, tryptophan, fructose, phenylacetic acid, myristic acid, 3-Methyl-2-oxovaleric acid, and N-Acetylneuraminic acid). These metabolites are associated with the metabolism of aromatic amino acids and their consumption in the diet. Therefore, this research suggests that each individual's diet and intestinal composition could affect host metabolism. Furthermore, these findings open the door to the study of microbiome-host interactions and allow us to contribute to personalized medicine.
Collapse
Affiliation(s)
- Johanna Forero-Rodríguez
- Bioinformatics and Systems Biology Research Group, Genetic Institute, Universidad Nacional de Colombia, Bogotá 111321, Colombia; (J.F.-R.); (J.D.C.-N.); (J.L.-C.)
- Medical Systems Biology Research Group, Institute of Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24118 Kiel, Germany (J.T.)
| | - Johannes Zimmermann
- Medical Systems Biology Research Group, Institute of Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24118 Kiel, Germany (J.T.)
| | - Jan Taubenheim
- Medical Systems Biology Research Group, Institute of Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24118 Kiel, Germany (J.T.)
| | - Natalia Arias-Rodríguez
- Bioinformatics and Systems Biology Research Group, Genetic Institute, Universidad Nacional de Colombia, Bogotá 111321, Colombia; (J.F.-R.); (J.D.C.-N.); (J.L.-C.)
| | - Juan David Caicedo-Narvaez
- Bioinformatics and Systems Biology Research Group, Genetic Institute, Universidad Nacional de Colombia, Bogotá 111321, Colombia; (J.F.-R.); (J.D.C.-N.); (J.L.-C.)
- Neurosciences Research Group, Genetic Institute, Universidad Nacional de Colombia, Bogotá 111321, Colombia
| | - Lena Best
- Medical Systems Biology Research Group, Institute of Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24118 Kiel, Germany (J.T.)
| | - Cindy V. Mendieta
- PhD Program in Clinical Epidemiology, Department of Clinical Epidemiology and Biostatistics, Faculty of Medicine, Pontificia Universidad Javeriana, Bogotá 110231, Colombia;
- Department of Nutrition and Biochemistry, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
| | - Julieth López-Castiblanco
- Bioinformatics and Systems Biology Research Group, Genetic Institute, Universidad Nacional de Colombia, Bogotá 111321, Colombia; (J.F.-R.); (J.D.C.-N.); (J.L.-C.)
| | - Laura Alejandra Gómez-Muñoz
- Neurosciences Research Group, Genetic Institute, Universidad Nacional de Colombia, Bogotá 111321, Colombia
- Cell Death Research Group, Medical School and Genetic Institute, Universidad Nacional de Colombia, Bogotá 111321, Colombia
| | - Janneth Gonzalez-Santos
- Structural Biochemistry and Bioinformatics Laboratory, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
| | - Humberto Arboleda
- Cell Death Research Group, Medical School and Genetic Institute, Universidad Nacional de Colombia, Bogotá 111321, Colombia
| | - William Fernandez
- Neurosciences Research Group, Genetic Institute, Universidad Nacional de Colombia, Bogotá 111321, Colombia
- Cell Death Research Group, Medical School and Genetic Institute, Universidad Nacional de Colombia, Bogotá 111321, Colombia
| | - Christoph Kaleta
- Medical Systems Biology Research Group, Institute of Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24118 Kiel, Germany (J.T.)
| | - Andrés Pinzón
- Bioinformatics and Systems Biology Research Group, Genetic Institute, Universidad Nacional de Colombia, Bogotá 111321, Colombia; (J.F.-R.); (J.D.C.-N.); (J.L.-C.)
| |
Collapse
|
5
|
Blesl A, Wurm P, Waschina S, Gröchenig HP, Novacek G, Primas C, Reinisch W, Kutschera M, Illiasch C, Hennlich B, Steiner P, Koch R, Tillinger W, Haas T, Reicht G, Mayer A, Ludwiczek O, Miehsler W, Steidl K, Binder L, Reider S, Watschinger C, Fürst S, Kump P, Moschen A, Aden K, Gorkiewicz G, Högenauer C. Prediction of Response to Systemic Corticosteroids in Active UC by Microbial Composition-A Prospective Multicenter Study. Inflamm Bowel Dis 2024; 30:9-19. [PMID: 37463118 PMCID: PMC10769779 DOI: 10.1093/ibd/izad126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Indexed: 07/20/2023]
Abstract
BACKGROUND Corticosteroids are used for induction of remission in patients with moderately to severely active ulcerative colitis. However, up to one-third of patients fail to this therapy. We investigated if fecal microbial composition or its metabolic capacity are associated with response to systemic corticosteroids. METHODS In this prospective, multicenter study, patients with active ulcerative colitis (Lichtiger score ≥4) receiving systemic corticosteroids were eligible. Data were assessed and fecal samples collected before and after 4 weeks of treatment. Patients were divided into responders (decrease of Lichtiger Score ≥50%) and nonresponders. The fecal microbiome was assessed by the 16S rRNA gene marker and analyzed with QIIME 2. Microbial metabolic pathways were predicted using parsimonious flux balance analysis. RESULTS Among 93 included patients, 69 (74%) patients responded to corticosteroids after 4 weeks. At baseline, responders could not be distinguished from nonresponders by microbial diversity and composition, except for a subgroup of biologic-naïve patients. Within 4 weeks of treatment, responders experienced changes in beta diversity with enrichment of ascribed beneficial taxa, including Blautia, Anaerostipes, and Bifidobacterium, as well as an increase in predicted butyrate synthesis. Nonresponders had only minor longitudinal taxonomic changes with a significant increase of Streptococcus salivarius and a microbial composition shifting away from responders. CONCLUSION Baseline microbial diversity and composition seem to be of limited use to predict response to systemic corticosteroids in active ulcerative colitis. Response is longitudinally associated with restoration of microbial composition and its metabolic capacity.
Collapse
Affiliation(s)
- Andreas Blesl
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, Medical University of Graz, Graz, Austria
| | - Philipp Wurm
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, Medical University of Graz, Graz, Austria
- Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Silvio Waschina
- Christian-Albrechts-University Kiel, Institute for Human Nutrition and Food Science, Nutriinformatics, Kiel, Germany
| | | | - Gottfried Novacek
- Department of Internal Medicine III, Division of Gastroenterology and Hepatology, Medical University of Vienna, Vienna, Austria
| | - Christian Primas
- Department of Internal Medicine III, Division of Gastroenterology and Hepatology, Medical University of Vienna, Vienna, Austria
| | - Walter Reinisch
- Department of Internal Medicine III, Division of Gastroenterology and Hepatology, Medical University of Vienna, Vienna, Austria
| | - Maximilian Kutschera
- Department of Internal Medicine III, Division of Gastroenterology and Hepatology, Medical University of Vienna, Vienna, Austria
| | | | | | | | - Robert Koch
- Medical University of Innsbruck, Innsbruck, Austria
| | | | | | | | | | | | | | - Karin Steidl
- Brothers of Saint John of God Hospital, St. Veit an der Glan, Austria
| | - Lukas Binder
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, Medical University of Graz, Graz, Austria
| | - Simon Reider
- Department of Internal Medicine 2 (Gastroenterology and Hepatology), Faculty of Medicine, Kepler University Hospital, Johannes Kepler University, Linz, Austria
- Christian Doppler Laboratory for Mucosal Immunology, Johannes Kepler University Linz, Linz, Austria
| | - Christina Watschinger
- Department of Internal Medicine 2 (Gastroenterology and Hepatology), Faculty of Medicine, Kepler University Hospital, Johannes Kepler University, Linz, Austria
- Christian Doppler Laboratory for Mucosal Immunology, Johannes Kepler University Linz, Linz, Austria
| | - Stefan Fürst
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, Medical University of Graz, Graz, Austria
| | - Patrizia Kump
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, Medical University of Graz, Graz, Austria
| | - Alexander Moschen
- Department of Internal Medicine 2 (Gastroenterology and Hepatology), Faculty of Medicine, Kepler University Hospital, Johannes Kepler University, Linz, Austria
- Christian Doppler Laboratory for Mucosal Immunology, Johannes Kepler University Linz, Linz, Austria
| | - Konrad Aden
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany
- Department of Internal Medicine I, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany
| | | | - Christoph Högenauer
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, Medical University of Graz, Graz, Austria
| |
Collapse
|
6
|
Zhang Y, Xia Y, Sun J. Probiotics and microbial metabolites maintain barrier and neuromuscular functions and clean protein aggregation to delay disease progression in TDP43 mutation mice. Gut Microbes 2024; 16:2363880. [PMID: 38860943 PMCID: PMC11174066 DOI: 10.1080/19490976.2024.2363880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 05/29/2024] [Indexed: 06/12/2024] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a neuromuscular disease. The ALS mice expressing human mutant of transactive response DNA binding protein of 43 kDa (hmTDP43) showed intestinal dysfunction before neuromuscular symptoms. We hypothesize that restoring the intestinal and microbial homeostasis with a bacterial metabolite or probiotics delays the ALS disease onset. We investigate the pathophysiological changes in the intestine and neurons, intestinal and blood-brain barriers, and inflammation during the ALS progression. We then cultured enteric glial cells (EGCs) isolated from TDP43 mice for mechanistic studies. TDP43 mice had significantly decreased intestinal mobility, increased permeability, and weakened muscle, compared with the age-matched wild-type mice. We observed increased hmTDP43 and Glial fibrillary acidic protein (GFAP), and decreased expression of α-smooth muscle actin (α-SMA), tight junction proteins (ZO-1 and Claudin-5) in the colon, spinal cord, and brain in TDP43 mice. TDP43 mice had reduced Butyryl-coenzyme A CoA transferase, decreased butyrate-producing bacteria Butyrivibrio fibrisolvens, and increased Bacteroides fragilis, compared to the WT mice. Serum inflammation cytokines (IL-6, IL-17, and IFN-γ) and LPS were elevated in TDP43 mice. EGCs from TDP43 mice showed aggregation of hmTDP43 associated with increased GFAP and ionized calcium-binding adaptor molecule (IBA1, a microglia marker). TDP43 mice treated with butyrate or probiotic VSL#3 had significantly increased rotarod time, increased intestinal mobility and decreased permeability, compared to the untreated group. Butyrate or probiotics treatment decreased the expression of GFAP, TDP43, and increased α-SMA, ZO-1, and Claudin-5 in the colon, spinal cord, and brain. Also, butyrate or probiotics treatment enhanced the Butyryl-coenzyme A CoA transferase, Butyrivibrio fibrisolvens, and reduced inflammatory cytokines in TDP43 mice. The TDP43 EGCs treated with butyrate or probiotics showed reduced GFAP, IBA1, and TDP43 aggregation. Restoring the intestinal and microbial homeostasis by beneficial bacteria and metabolites provide a potential therapeutic strategy to treat ALS.
Collapse
Affiliation(s)
- Yongguo Zhang
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois Chicago, Chicago, IL, USA
| | - Yinglin Xia
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois Chicago, Chicago, IL, USA
- Jesse Brown VA Medical Center, Chicago, IL, USA
| | - Jun Sun
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois Chicago, Chicago, IL, USA
- Jesse Brown VA Medical Center, Chicago, IL, USA
| |
Collapse
|
7
|
Meade S, Liu Chen Kiow J, Massaro C, Kaur G, Squirell E, Bressler B, Lunken G. Gut microbiome-associated predictors as biomarkers of response to advanced therapies in inflammatory bowel disease: a systematic review. Gut Microbes 2023; 15:2287073. [PMID: 38044504 PMCID: PMC10730146 DOI: 10.1080/19490976.2023.2287073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 11/20/2023] [Indexed: 12/05/2023] Open
Abstract
Loss of response to therapy in inflammatory bowel disease (IBD) has led to a surge in research focusing on precision medicine. Three systematic reviews have been published investigating the associations between gut microbiota and disease activity or IBD therapy. We performed a systematic review to investigate the microbiome predictors of response to advanced therapy in IBD. Unlike previous studies, our review focused on predictors of response to therapy; so the included studies assessed microbiome predictors before the proposed time of response or remission. We also provide an update of the available data on mycobiomes and viromes. We highlight key themes in the literature that may serve as future biomarkers of treatment response: the abundance of fecal SCFA-producing bacteria and opportunistic bacteria, metabolic pathways related to butyrate synthesis, and non-butyrate metabolomic predictors, including bile acids (BAs), amino acids, and lipids, as well as mycobiome predictors of response.
Collapse
Affiliation(s)
- Susanna Meade
- Department of Medicine, University of British Columbia, Vancouver, Canada
- IBD Centre of BC, Vancouver, Canada
| | - Jeremy Liu Chen Kiow
- Department of Medicine, University of British Columbia, Vancouver, Canada
- IBD Centre of BC, Vancouver, Canada
| | - Cristian Massaro
- Department of Pediatrics, Univerisity of British Columbia, Vancouver, Canada
- BC Children’s Hospital Research Institute, Vancouver, Canada
| | - Gurpreet Kaur
- IBD Centre of BC, Vancouver, Canada
- Department of Pediatrics, Univerisity of British Columbia, Vancouver, Canada
| | - Elizabeth Squirell
- Department of Medicine, University of British Columbia, Vancouver, Canada
- IBD Centre of BC, Vancouver, Canada
| | - Brian Bressler
- Department of Medicine, University of British Columbia, Vancouver, Canada
- IBD Centre of BC, Vancouver, Canada
| | - Genelle Lunken
- IBD Centre of BC, Vancouver, Canada
- Department of Pediatrics, Univerisity of British Columbia, Vancouver, Canada
- BC Children’s Hospital Research Institute, Vancouver, Canada
| |
Collapse
|
8
|
Starke S, Harris DMM, Zimmermann J, Schuchardt S, Oumari M, Frank D, Bang C, Rosenstiel P, Schreiber S, Frey N, Franke A, Aden K, Waschina S. Amino acid auxotrophies in human gut bacteria are linked to higher microbiome diversity and long-term stability. THE ISME JOURNAL 2023; 17:2370-2380. [PMID: 37891427 PMCID: PMC10689445 DOI: 10.1038/s41396-023-01537-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 10/06/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023]
Abstract
Amino acid auxotrophies are prevalent among bacteria. They can govern ecological dynamics in microbial communities and indicate metabolic cross-feeding interactions among coexisting genotypes. Despite the ecological importance of auxotrophies, their distribution and impact on the diversity and function of the human gut microbiome remain poorly understood. This study performed the first systematic analysis of the distribution of amino acid auxotrophies in the human gut microbiome using a combined metabolomic, metagenomic, and metabolic modeling approach. Results showed that amino acid auxotrophies are ubiquitous in the colon microbiome, with tryptophan auxotrophy being the most common. Auxotrophy frequencies were higher for those amino acids that are also essential to the human host. Moreover, a higher overall abundance of auxotrophies was associated with greater microbiome diversity and stability, and the distribution of auxotrophs was found to be related to the human host's metabolome, including trimethylamine oxide, small aromatic acids, and secondary bile acids. Thus, our results suggest that amino acid auxotrophies are important factors contributing to microbiome ecology and host-microbiome metabolic interactions.
Collapse
Affiliation(s)
- Svenja Starke
- Institute of Human Nutrition and Food Science, Nutriinformatics, Kiel University, Kiel, Germany
| | - Danielle M M Harris
- Institute of Human Nutrition and Food Science, Nutriinformatics, Kiel University, Kiel, Germany
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Johannes Zimmermann
- Zoological Institute, Research Group Evolutionary Ecology and Genetics, Kiel University, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Sven Schuchardt
- Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM), Hanover, Germany
| | - Mhmd Oumari
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Derk Frank
- Department of Internal Medicine III, University Medical Center Schleswig-Holstein, Kiel, Germany
- German Centre for Cardiovascular Research (DZHK), Partner site Hamburg, Kiel, Lübeck, Germany
| | - Corinna Bang
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Norbert Frey
- Department of Internal Medicine III, University Medical Center Schleswig-Holstein, Kiel, Germany
- German Centre for Cardiovascular Research (DZHK), Partner site Hamburg, Kiel, Lübeck, Germany
- Department of Internal Medicine III, University Hospital Heidelberg, Heidelberg, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Konrad Aden
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany.
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Germany.
| | - Silvio Waschina
- Institute of Human Nutrition and Food Science, Nutriinformatics, Kiel University, Kiel, Germany.
| |
Collapse
|
9
|
Kaźmierczak-Siedlecka K, Bulman N, Ulasiński P, Sobocki BK, Połom K, Marano L, Kalinowski L, Skonieczna-Żydecka K. Pharmacomicrobiomics of cell-cycle specific anti-cancer drugs - is it a new perspective for personalized treatment of cancer patients? Gut Microbes 2023; 15:2281017. [PMID: 37985748 PMCID: PMC10730203 DOI: 10.1080/19490976.2023.2281017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 11/05/2023] [Indexed: 11/22/2023] Open
Abstract
Intestinal bacteria are equipped with an enzyme apparatus that is involved in the active biotransformation of xenobiotics, including drugs. Pharmacomicrobiomics, a new area of pharmacology, analyses interactions between bacteria and xenobiotics. However, there is another side to the coin. Pharmacotherapeutic agents can significantly modify the microbiota, which consequently affects their efficacy. In this review, we comprehensively gathered scientific evidence on the interplay between anticancer therapies and gut microbes. We also underlined how such interactions might impact the host response to a given therapy. We discuss the possibility of modulating the gut microbiota to increase the effectiveness/decrease the incidence of adverse events during tumor therapy. The anticipation of the future brings new evidence that gut microbiota is a target of interest to increase the efficacy of therapy.
Collapse
Affiliation(s)
- Karolina Kaźmierczak-Siedlecka
- Department of Medical Laboratory Diagnostics – Fahrenheit Biobank BBMRI.pl, Medical University of Gdansk, Gdańsk, Poland
| | - Nikola Bulman
- Department of Medical Laboratory Diagnostics – Fahrenheit Biobank BBMRI.pl, Medical University of Gdansk, Gdańsk, Poland
| | - Paweł Ulasiński
- Unit of Surgery with Unit of Oncological Surgery in Koscierzyna, Kościerzyna, Poland
| | - Bartosz Kamil Sobocki
- Department of Oncology and Radiotherapy, Medical University of Gdansk, Gdańsk, Poland
| | - Karol Połom
- Academy of Medical and Social Applied Sciences, Elbląg, Poland
| | - Luigi Marano
- Academy of Medical and Social Applied Sciences, Elbląg, Poland
| | - Leszek Kalinowski
- Department of Medical Laboratory Diagnostics – Fahrenheit Biobank BBMRI.pl, Medical University of Gdansk, Gdańsk, Poland
- BioTechMed Centre/Department of Mechanics of Materials and Structures, Gdansk University of Technology, Gdansk, Poland
| | | |
Collapse
|
10
|
Jin S, Xu J, Zou Y, Li X, Yu B, Han J, Wang X, Zhao L. Microbiome changes involves in mercaptopurine mediated anti-inflammatory response in acute lymphoblastic leukemia mice. Int Immunopharmacol 2023; 123:110782. [PMID: 37573688 DOI: 10.1016/j.intimp.2023.110782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/20/2023] [Accepted: 08/07/2023] [Indexed: 08/15/2023]
Abstract
BACKGROUND Inflammasome has been reported to play an important role in the pathogenesis and progression of hematologic malignancies. As one of the backbone drugs for treating acute lymphoblastic leukemia (ALL), the anti-inflammatory effect of mercaptopurine (6-MP) and the impact of gut microbiome changes caused by 6-MP on anti-inflammasome remain unclear. OBJECTIVE We aimed to explore the association between 6-MP therapeutic effects and microbiome-involved inflammatory responses in ALL mice models. STUDY DESIGN ALL murine model was built by i.v. injecting murine L1210 cells into DBA/2 mice (model group). Two weeks after cell injections, 6-MP was orally administrated for 14 days (6-MP group). Fecal samples of mice were collected at different time points. Cecum short-chain fatty acids (SCFAs) concentrations were determined by LC-MS/MS method. Serum cytokines were measured using a cytometric bead array. Gut microbiota composition in mice was explored using 16S rRNA gene sequencing. RESULTS The anti-tumor effect of 6-MP was proved in ALL mice models. The levels of pro-inflammatory factors IL-6 and TNFα significantly decreased after the administration of 6-MP. Cecum contents' acetate, propionate, and butyrate levels were negatively correlated with IL-6 (correlation coefficient: acetate, -0.24; propionate, -0.26; butyrate, -0.17) and TNFα (correlation coefficient: acetate, -0.45; propionate, -0.42; butyrate, -0.31) changes. Relative abundance changes of f_Lachnospiraceae.g_ASF356 and f_Peptococcaceae.g_uncultured were in accordance with the changes of butyrate levels and opposite to the changes of pro-inflammatory levels. CONCLUSION The anti-inflammatory response of 6-MP influenced by intestinal microbiota and its metabolites SCFAs, especially butyrate, played an essential role in improving ALL progression.
Collapse
Affiliation(s)
- Siyao Jin
- Department of Pharmacy, Beijing Children's Hospital, Capital Medical University, Beijing 100045, China
| | - Jiamin Xu
- Department of Pharmacy, Beijing Children's Hospital, Capital Medical University, Beijing 100045, China
| | - Yaru Zou
- Department of Pharmacy, Beijing Children's Hospital, Capital Medical University, Beijing 100045, China; Department of Pharmacy, Children's Hospital of Soochow University, Suzhou, Jiangsu, 215025, China
| | - Xiaona Li
- Department of Pharmacy, Peking University Third Hospital, Beijing 100191, China
| | - Boran Yu
- Department of Pharmacy, Beijing Children's Hospital, Capital Medical University, Beijing 100045, China
| | - Jiaqi Han
- Department of Pharmacy, Beijing Children's Hospital, Capital Medical University, Beijing 100045, China
| | - Xiaoling Wang
- Department of Pharmacy, Beijing Children's Hospital, Capital Medical University, Beijing 100045, China
| | - Libo Zhao
- Department of Pharmacy, Beijing Children's Hospital, Capital Medical University, Beijing 100045, China; Department of Pharmacy, Peking University Third Hospital, Beijing 100191, China.
| |
Collapse
|
11
|
O’Reilly C, Mills S, Rea MC, Lavelle A, Ghosh S, Hill C, Ross RP. Interplay between inflammatory bowel disease therapeutics and the gut microbiome reveals opportunities for novel treatment approaches. MICROBIOME RESEARCH REPORTS 2023; 2:35. [PMID: 37849974 PMCID: PMC7615213 DOI: 10.20517/mrr.2023.41] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 09/19/2023] [Accepted: 09/22/2023] [Indexed: 10/19/2023]
Abstract
Inflammatory bowel disease (IBD) is a complex heterogeneous disorder defined by recurring chronic inflammation of the gastrointestinal tract, attributed to a combination of factors including genetic susceptibility, altered immune response, a shift in microbial composition/microbial insults (infection/exposure), and environmental influences. Therapeutics generally used to treat IBD mainly focus on the immune response and include non-specific anti-inflammatory and immunosuppressive therapeutics and targeted therapeutics aimed at specific components of the immune system. Other therapies include exclusive enteral nutrition and emerging stem cell therapies. However, in recent years, scientists have begun to examine the interplay between these therapeutics and the gut microbiome, and we present this information here. Many of these therapeutics are associated with alterations to gut microbiome composition and functionality, often driving it toward a "healthier profile" and preclinical studies have revealed that such alterations can play an important role in therapeutic efficacy. The gut microbiome can also improve or hinder IBD therapeutic efficacy or generate undesirable metabolites. For certain IBD therapeutics, the microbiome composition, particularly before treatment, may serve as a biomarker of therapeutic efficacy. Utilising this information and manipulating the interactions between the gut microbiome and IBD therapeutics may enhance treatment outcomes in the future and bring about new opportunities for personalised, precision medicine.
Collapse
Affiliation(s)
- Catherine O’Reilly
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork P61C996, Ireland
- Microbiology Department, University College Cork, Co. Cork T12TP07, Ireland
- APC Microbiome Ireland, University College Cork, Co. Cork T12YT20, Ireland
- Authors contributed equally
| | - Susan Mills
- APC Microbiome Ireland, University College Cork, Co. Cork T12YT20, Ireland
- Authors contributed equally
| | - Mary C. Rea
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork P61C996, Ireland
- APC Microbiome Ireland, University College Cork, Co. Cork T12YT20, Ireland
| | - Aonghus Lavelle
- APC Microbiome Ireland, University College Cork, Co. Cork T12YT20, Ireland
| | - Subrata Ghosh
- APC Microbiome Ireland, University College Cork, Co. Cork T12YT20, Ireland
| | - Colin Hill
- Microbiology Department, University College Cork, Co. Cork T12TP07, Ireland
- APC Microbiome Ireland, University College Cork, Co. Cork T12YT20, Ireland
| | - R. Paul Ross
- Microbiology Department, University College Cork, Co. Cork T12TP07, Ireland
- APC Microbiome Ireland, University College Cork, Co. Cork T12YT20, Ireland
| |
Collapse
|
12
|
Zhu M, Song Y, Xu Y, Xu H. Manipulating Microbiota in Inflammatory Bowel Disease Treatment: Clinical and Natural Product Interventions Explored. Int J Mol Sci 2023; 24:11004. [PMID: 37446182 DOI: 10.3390/ijms241311004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/16/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a complex multifactorial chronic inflammatory disease, that includes Crohn's disease (CD) and ulcerative colitis (UC), having progressively increasing global incidence. Disturbed intestinal flora has been highlighted as an important feature of IBD and offers promising strategies for IBD remedies. A brief overview of the variations occurring in intestinal flora during IBD is presented, and the role of the gut microbiota in intestinal barrier maintenance, immune and metabolic regulation, and the absorption and supply of nutrients is reviewed. More importantly, we review drug research on gut microbiota in the past ten years, including research on clinical and natural drugs, as well as adjuvant therapies, such as Fecal Microbiota Transplantation and probiotic supplements. We also summarize the interventions and mechanisms of these drugs on gut microbiota.
Collapse
Affiliation(s)
- Mengjie Zhu
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Yijie Song
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Yu Xu
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Hongxi Xu
- Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| |
Collapse
|
13
|
Colman RJ, Mizuno T, Fukushima K, Haslam DB, Hyams JS, Boyle B, Noe JD, D’Haens GR, Limbergen JV, Chun K, Yang J, Denson LA, Ollberding NJ, Vinks AA, Minar P. Real world population pharmacokinetic study in children and young adults with inflammatory bowel disease discovers novel blood and stool microbial predictors of vedolizumab clearance. Aliment Pharmacol Ther 2023; 57:524-539. [PMID: 36314265 PMCID: PMC9931651 DOI: 10.1111/apt.17277] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/04/2022] [Accepted: 10/15/2022] [Indexed: 12/09/2022]
Abstract
BACKGROUND Vedolizumab for inflammatory bowel disease (IBD) is often intensified based on distinct pharmacokinetics in children. Prior adult-specific population pharmacokinetic models have identified limited covariates of drug clearance. AIMS To establish a population pharmacokinetic model for children and young adults to identify novel covariates of drug clearance to better account for paediatric-specific inter-patient variability in vedolizumab pharmacokinetics; a key secondary exploratory aim was to identify microbial signatures of pharmacokinetic outcomes in a subset of patients. METHODS The study included data from 463 observed vedolizumab concentrations (59 peaks and 404 troughs) from 74 patients with IBD (52 with Crohn's disease and 22 with ulcerative colitis or unclassified IBD, median age 16 years). Pharmacokinetic analysis was conducted with non-linear mixed effects modelling. For the evaluation of the exposure-response relationship, clinical outcomes were evaluated by trough levels, clearance and vedolizumab exposure. Whole-genome metagenomic sequencing was conducted at baseline and week 2. RESULTS A two-compartment population pharmacokinetic model was identified with a clear correlation between CL and weight, erythrocyte sedimentation rate, and hypoalbuminemia. Trough concentrations before infusion 3 (37 μg/ml) and before infusion 4 (20 μg/ml) best predicted steroid-free clinical remission at infusion 4. Using faecal metagenomics, we identified an early (baseline and week 2) abundance of butyrate-producing species and pathways that were associated with an infusion 4 trough concentration >20 μg/ml. CONCLUSIONS This novel paediatric vedolizumab pharmacokinetic model could inform precision dosing. While additional studies are needed, an abundance of faecal butyrate producers is associated with early response to vedolizumab, suggesting that microbial analysis may be beneficial to biological selection.
Collapse
Affiliation(s)
- Ruben J. Colman
- Division of Gastroenterology, Hepatology, and Nutrition, Cincinnati Children’s Hospital Medical Center
| | - Tomoyuki Mizuno
- Division of Clinical Pharmacology, Cincinnati Children’s Hospital Medical Center
- Department of Pediatrics, University of Cincinnati College of Medicine
| | - Keizo Fukushima
- Division of Clinical Pharmacology, Cincinnati Children’s Hospital Medical Center
| | - David B. Haslam
- Division of Infectious Diseases, Cincinnati Children’s Hospital Medical Center
- Department of Pediatrics, University of Cincinnati College of Medicine
| | - Jeffrey S. Hyams
- Division of Digestive Diseases, Hepatology and Nutrition, Connecticut Children’s Medical Center
| | - Brendan Boyle
- Division of Gastroenterology, Hepatology and Nutrition, Nationwide Children’s Hospital
| | - Joshua D. Noe
- Division of Gastroenterology, Hepatology and Nutrition, Children’s Hospital of Wisconsin
| | - Geert R. D’Haens
- Gastroenterology and Hepatology, Amsterdam University Medical Centers – location University of Amsterdam, Amsterdam, the Netherlands
| | - Johan Van Limbergen
- Department of Pediatric Gastroenterology and Nutrition, Amsterdam University Medical Centers – Location University of Amsterdam, Emma Children’s Hospital, Amsterdam, the Netherlands
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology Metabolism, University of Amsterdam, Amsterdam, Netherlands
| | | | | | - Lee A. Denson
- Division of Gastroenterology, Hepatology, and Nutrition, Cincinnati Children’s Hospital Medical Center
- Department of Pediatrics, University of Cincinnati College of Medicine
| | - Nicholas J. Ollberding
- Department of Pediatrics, University of Cincinnati College of Medicine
- Division of Biostatistics and Epidemiology, Cincinnati Children’s Hospital Medical Center
| | - Alexander A. Vinks
- Division of Clinical Pharmacology, Cincinnati Children’s Hospital Medical Center
- Department of Pediatrics, University of Cincinnati College of Medicine
| | - Phillip Minar
- Division of Gastroenterology, Hepatology, and Nutrition, Cincinnati Children’s Hospital Medical Center
- Department of Pediatrics, University of Cincinnati College of Medicine
| |
Collapse
|
14
|
Varga A, Makszin L, Bufa A, Sipos D, Kása P, Pál S, Rosenstiel P, Sommer F, Kocsis B, Péterfi Z. Efficacy of lyophilised bacteria-rich faecal sediment and supernatant with reduced bacterial count for treating patients with Clostridioides difficile Infection - A novel method for capsule faecal microbiota transfer. Front Cell Infect Microbiol 2023; 13:1041384. [PMID: 36756616 PMCID: PMC9899802 DOI: 10.3389/fcimb.2023.1041384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 01/03/2023] [Indexed: 01/24/2023] Open
Abstract
Background and aims Faecal microbiota transfer (FMT) has managed to earn its place in the Clostridioides difficile infection (CDI) guidelines by having comparable efficacy and recurrence rate of fidaxomicin. After more than 100 successful FMT administration through nasogastric tube, we started using hard gelatine capsules filled with lyophilised faecal sediment and supernatant. Our main question was whether uncoated capsules (containing faecal sediment or supernatant) are comparable to the widely used nasogastric tubes in CDI. We also investigated the effect of storage and time on the survival rate of bacteria in the samples. Methods We compared the efficacy of our capsules to other treatment options of CDI at the Department of Infectology at the University of Pécs (Hungary). For our study, stool was collected from a single donor. We treated 10 patients with relapsing CDI, 5 of them received supernatant, 5 received sediment. Donor samples were stored on 4 different temperatures and tested to determine the survival rates of bacteria. As pilot projects, we also assessed the changes of bacterial taxa, protein- and lipid compositions. Moreover, we selected 4 patients to compare their samples prior and after FMT by using microbiome (16S amplicon sequencing), protein, and lipid analyses. Results 4 out of the 5 patients who received supernatant became symptomless within 2 days after FMT. In the sediment group 3 out of 5 patients were cured from CDI. Comparing the supernatant to the sediment, we found significantly lower number of colony-forming units in the supernatant. We found that -80°C is the most suitable temperature to store the samples. The stool lipid profiles of recipients showed a more diverse composition after FMT, and changes in the stool protein profiles were observed as well. In the microbiome analysis, we observed an increase in the alpha diversity after FMT. Conclusions Our study of 10 patients showed good efficacy of lyophilised faecal supernatant using capsules. The single donor approach proved to be effective in our investigation. A significantly lower CFU number was sufficient for the effect, the separation can be achieved by widely available instruments. For storage temperature, -20°C was sufficient in our clinical practice.
Collapse
Affiliation(s)
- Adorján Varga
- 1stDepartment of Internal Medicine - Department of Infectology, University of Pécs, Medical School, Pécs, Hungary.,Department of Medical Microbiology and Immunology, University of Pécs, Medical School, Pécs, Hungary
| | - Lilla Makszin
- Institute of Bioanalysis, Medical School, and Szentágothai Research Center, University of Pécs, Pécs, Hungary
| | - Anita Bufa
- Institute of Bioanalysis, Medical School, and Szentágothai Research Center, University of Pécs, Pécs, Hungary
| | - Dávid Sipos
- 1stDepartment of Internal Medicine - Department of Infectology, University of Pécs, Medical School, Pécs, Hungary
| | - Péter Kása
- Institute of Pharmaceutical Technology and Biopharmacy, University of Pécs, Faculty of Pharmacy, Pécs, Hungary
| | - Szilárd Pál
- Institute of Pharmaceutical Technology and Biopharmacy, University of Pécs, Faculty of Pharmacy, Pécs, Hungary
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian Albrechts University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Felix Sommer
- Institute of Clinical Molecular Biology, Christian Albrechts University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Béla Kocsis
- Department of Medical Microbiology and Immunology, University of Pécs, Medical School, Pécs, Hungary
| | - Zoltán Péterfi
- 1stDepartment of Internal Medicine - Department of Infectology, University of Pécs, Medical School, Pécs, Hungary
| |
Collapse
|
15
|
Assessing the Relationship between the Gut Microbiota and Inflammatory Bowel Disease Therapeutics: A Systematic Review. Pathogens 2023; 12:pathogens12020262. [PMID: 36839534 PMCID: PMC9965214 DOI: 10.3390/pathogens12020262] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 02/10/2023] Open
Abstract
Current inflammatory bowel disease (IBD) treatments including non-biological, biological, and nutritional therapies aim to achieve remission and mucosal healing. Treatment efficacy, however, is highly variable, and there is growing evidence that the gut microbiota influences therapeutic efficacy. The aim of this study was to conduct a systematic review and meta-analysis to define changes in the gut microbiota following IBD treatment and to identify microbial predictors of treatment response. A systematic search using MEDLINE/Embase and PubMed was performed in July 2022. The review was conducted based on the Preferred Reporting Items for Systematic reviews and Meta-Analyses guidelines. Studies were included if they reported longitudinal microbiota analysis (>2 weeks) using next-generation sequencing or high-throughput sequencing of faecal/mucosal samples from IBD patients commencing treatment. Meta-analysis on alpha-diversity changes following infliximab treatment was conducted. Thirty-nine studies met the inclusion criteria, and four studies were included in the meta-analysis. An increase in alpha diversity was observed following treatment with 5-aminosalicylates, corticosteroids, and biological therapies in most studies. Characteristic signatures involving the enrichment of short-chain-fatty-acid-producing bacteria including Faecalibacterium prausnitzii and a reduction of pathogenic bacteria including various Proteobacteria were demonstrated following treatment with specific signatures identified based on treatment outcome. The meta-analysis demonstrated a statistically significant increase in bacterial richness following infliximab treatment (standardised mean difference -1.16 (-1.50, -0.83), p < 0.00001). Conclusion: Distinct microbial signatures are seen following treatment and are associated with treatment response. The interrogation of large longitudinal studies is needed to establish the link between the gut microbiota and IBD therapeutic outcomes.
Collapse
|
16
|
Liu XY, Tang H, Zhou QY, Zeng YL, Chen D, Xu H, Li Y, Tan B, Qian JM. Advancing the precision management of inflammatory bowel disease in the era of omics approaches and new technology. World J Gastroenterol 2023; 29:272-285. [PMID: 36687128 PMCID: PMC9846940 DOI: 10.3748/wjg.v29.i2.272] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 12/01/2022] [Accepted: 12/21/2022] [Indexed: 01/06/2023] Open
Abstract
There is great heterogeneity among inflammatory bowel disease (IBD) patients in terms of pathogenesis, clinical manifestation, response to treatment, and prognosis, which requires the individualized and precision management of patients. Many studies have focused on prediction biomarkers and models for assessing IBD disease type, activity, severity, and prognosis. During the era of biologics, how to predict the response and side effects of patients to different treatments and how to quickly recognize the loss of response have also become important topics. Multiomics is a promising area for investigating the complex network of IBD pathogenesis. Integrating numerous amounts of data requires the use of artificial intelligence.
Collapse
Affiliation(s)
- Xin-Yu Liu
- Department of Gastroenterology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Science, Beijing 100730, China
- Eight-year Medical Doctor Program, Peking Union Medical College & Chinese Academy of Medical Science, Beijing 100730, China
| | - Hao Tang
- Department of Internal Medicine, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Science, Beijing 100730, China
| | - Qing-Yang Zhou
- Department of Gastroenterology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Science, Beijing 100730, China
| | - Yan-Lin Zeng
- Department of Gastroenterology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Science, Beijing 100730, China
- School of Medicine, Tsinghua University, Beijing 100084, China
| | - Dan Chen
- Department of Gastroenterology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Science, Beijing 100730, China
| | - Hui Xu
- Department of Gastroenterology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Science, Beijing 100730, China
| | - Yue Li
- Department of Gastroenterology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Science, Beijing 100730, China
| | - Bei Tan
- Department of Gastroenterology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Science, Beijing 100730, China
| | - Jia-Ming Qian
- Department of Gastroenterology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Science, Beijing 100730, China
| |
Collapse
|
17
|
Lin Z, Mao D, Jin C, Wang J, Lai Y, Zhang Y, Zhou M, Ge Q, Zhang P, Sun Y, Xu K, Wang Y, Zhu H, Lai B, Wu H, Mu Q, Ouyang G, Sheng L. The gut microbiota correlate with the disease characteristics and immune status of patients with untreated diffuse large B-cell lymphoma. Front Immunol 2023; 14:1105293. [PMID: 36891300 PMCID: PMC9986463 DOI: 10.3389/fimmu.2023.1105293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 02/06/2023] [Indexed: 02/22/2023] Open
Abstract
Background Gut microbiota characteristics in patients with diffuse large B-cell lymphoma (DLBCL) are reportedly different when compared with the healthy population and it remains unclear if the gut microbiota affects host immunity and clinical disease features. This research investigated the gut microbiota in patients with untreated DLBCL and analyzed its correlation with patient clinical characteristics, humoral, and cell immune status. Methods Thirty-five patients with untreated DLBCL and 20 healthy controls (HCs) were recruited to this study and microbiota differences in stool samples were analyzed by 16S rDNA sequencing. Absolute ratios of immune cell subset counts in peripheral blood were detected by flow cytometry and peripheral blood cytokine levels were detected by enzyme-linked immunosorbent assay. Relationships between changes in patient microbiomes and clinical characteristics, such as clinical stage, international prognostic index (IPI) risk stratification, cell origin, organ involved and treatment responses were investigated and correlations between differential microbiota and host immune indices were analyzed. Results The alpha-diversity index of intestinal microecology in DLBCL patients was not significantly different when compared with HCs (P>0.05), nonetheless beta-diversity was significantly decreased (P=0.001). p_Proteobacteria were dominant in DLBCL, while p_Bacteroidetes abundance was significantly decreased when compared with HCs (P<0.05). Gut microbiota characteristics were identified that were associated with clinical features, such as tumor load, risk stratification and cell origin, and correlation analyses were performed between differential flora abundance associated with these clinical features and host immune status. The p_Firmicutes was positively correlated with absolute lymphocyte values, g_Prevotella_2 and s_un_g_Prevotella_2 were negatively correlated with absolute lymphocyte values, T cell counts and CD4 cell counts, while g_Pyramidobacter, s_un_g_Pyramidobacter, and f_Peptostreptococcaceae were negatively correlated with IgA. Conclusions Dominant gut microbiota, abundance, diversity, and structure in DLBCL were influenced by the disease, correlated with patient immune status and this suggested that the microecology-immune axis may be involved in regulating lymphoma development. In the future, it may be possible to improve immune function in patients with DLBCL by regulating the gut microbiota, improve treatment response rates and increase patient survival rates.
Collapse
Affiliation(s)
- Zhouning Lin
- School of Medicine, Ningbo University, Ningbo, Zhejiang, China.,Department of Hematology, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China
| | - Dan Mao
- School of Medicine, Ningbo University, Ningbo, Zhejiang, China.,Department of Ultrasound and Medicine, Ningbo Yinzhou People's Hospital, Ningbo, Zhejiang, China
| | - Changyu Jin
- School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Jiaping Wang
- Department of Hematology, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China
| | - Yanli Lai
- Department of Hematology, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China
| | - Yanli Zhang
- Department of Hematology, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China
| | - Miao Zhou
- Department of Hematology, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China
| | - Qunfang Ge
- Department of Hematology, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China
| | - Ping Zhang
- Department of Hematology, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China
| | - Yongcheng Sun
- Department of Hematology, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China
| | - Kaihong Xu
- Department of Hematology, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China
| | - Yi Wang
- Department of Hematology, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China
| | - Huiling Zhu
- Department of Hematology, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China
| | - Binbin Lai
- Department of Hematology, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China
| | - Hao Wu
- Department of Hematology, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China
| | - Qitian Mu
- Department of Hematology, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China
| | - Guifang Ouyang
- Department of Hematology, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China
| | - Lixia Sheng
- Department of Hematology, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China
| |
Collapse
|
18
|
Misra R, Sarafian M, Pechlivanis A, Ding N, Miguens-Blanco J, McDonald J, Holmes E, Marchesi J, Arebi N. Ethnicity Associated Microbial and Metabonomic Profiling in Newly Diagnosed Ulcerative Colitis. Clin Exp Gastroenterol 2022; 15:199-212. [PMID: 36505887 PMCID: PMC9733448 DOI: 10.2147/ceg.s371965] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 11/07/2022] [Indexed: 12/11/2022] Open
Abstract
Introduction Ulcerative colitis (UC) differs across geography and ethnic groups. Gut microbial diversity plays a pivotal role in disease pathogenesis and differs across ethnic groups. The functional diversity in microbial-driven metabolites may have a pathophysiologic role and offer new therapeutic avenues. Methods Demographics and clinical data were recorded from newly diagnosed UC patients. Blood, urine and faecal samples were collected at three time points over one year. Bacterial content was analysed by 16S rRNA sequencing. Bile acid profiles and polar molecules in three biofluids were measured using liquid-chromatography mass spectrometry (HILIC) and nuclear magnetic resonance spectroscopy. Results We studied 42 patients with a new diagnosis of UC (27 South Asians; 15 Caucasians) with 261 biosamples. There were significant differences in relative abundance of bacteria at the phylum, genus and species level. Relative concentrations of urinary metabolites in South Asians were significantly lower for hippurate (positive correlation for Ruminococcus) and 4-cresol sulfate (Clostridia) (p<0.001) with higher concentrations of lactate (negative correlation for Bifidobacteriaceae). Faecal conjugated and primary conjugated bile acids concentrations were significantly higher in South Asians (p=0.02 and p=0.03 respectively). Results were unaffected by diet, phenotype, disease severity and ongoing therapy. Comparison of time points at diagnosis and at 1 year did not reveal changes in microbial and metabolic profile. Conclusion Ethnic-related microbial metabolite associations were observed in South Asians with UC. This suggests a predisposition to UC may be influenced by environmental factors reflected in a distinct gene-environment interaction. The variations may serve as markers to identify risk factors for UC and modified to enhance therapeutic response.
Collapse
Affiliation(s)
- Ravi Misra
- Gastroenterology, St Mark’s Academic Institute, London, UK,Correspondence: Ravi Misra, St. Mark’s Academic Institute, Imperial College, St. Mark’s Hospital, Watford Road, London, United Kingdom, Tel +44 0208 235 4124, Email
| | - Magali Sarafian
- Division of Integrative Systems Medicine and Digestive Disease, Department of Surgery and Cancer, Imperial College, London, UK
| | | | - Nik Ding
- St Vincent’s Hospital, Inflammatory Bowel Disease Unit, Melbourne, Australia
| | - Jesus Miguens-Blanco
- Division of Integrative Systems Medicine and Digestive Disease, Department of Surgery and Cancer, Imperial College, London, UK
| | | | - Elaine Holmes
- Division of Integrative Systems Medicine and Digestive Disease, Department of Surgery and Cancer, Imperial College, London, UK,Health Futures Institute, Murdoch and Edith Cowan Universities, Murdoch, Australia
| | - Julian Marchesi
- Division of Integrative Systems Medicine and Digestive Disease, Department of Surgery and Cancer, Imperial College, London, UK,School of Biosciences, Cardiff University, Cardiff, UK,Centre for Gut Health, Imperial College, London, UK
| | - Naila Arebi
- Gastroenterology, St Mark’s Academic Institute, London, UK
| |
Collapse
|
19
|
Boix-Amorós A, Monaco H, Sambataro E, Clemente JC. Novel technologies to characterize and engineer the microbiome in inflammatory bowel disease. Gut Microbes 2022; 14:2107866. [PMID: 36104776 PMCID: PMC9481095 DOI: 10.1080/19490976.2022.2107866] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
We present an overview of recent experimental and computational advances in technology used to characterize the microbiome, with a focus on how these developments improve our understanding of inflammatory bowel disease (IBD). Specifically, we present studies that make use of flow cytometry and metabolomics assays to provide a functional characterization of microbial communities. We also describe computational methods for strain-level resolution, temporal series, mycobiome and virome data, co-occurrence networks, and compositional data analysis. In addition, we review novel techniques to therapeutically manipulate the microbiome in IBD. We discuss the benefits and drawbacks of these technologies to increase awareness of specific biases, and to facilitate a more rigorous interpretation of results and their potential clinical application. Finally, we present future lines of research to better characterize the relation between microbial communities and IBD pathogenesis and progression.
Collapse
Affiliation(s)
- Alba Boix-Amorós
- Department of Genetics and Genomic Sciences, Precision Immunology Institute, Icahn School of Medicine at Mount Sinai. New York, NY, USA
| | - Hilary Monaco
- Department of Genetics and Genomic Sciences, Precision Immunology Institute, Icahn School of Medicine at Mount Sinai. New York, NY, USA
| | - Elisa Sambataro
- Department of Biological Sciences, CUNY Hunter College, New York, NY, USA
| | - Jose C. Clemente
- Department of Genetics and Genomic Sciences, Precision Immunology Institute, Icahn School of Medicine at Mount Sinai. New York, NY, USA,CONTACT Jose C. Clemente Department of Genetics and Genomic Sciences, Precision Immunology Institute, Icahn School of Medicine at Mount Sinai. New York, NY10029USA
| |
Collapse
|
20
|
Distinct Longitudinal Changes in Immunoglobulin G N-Glycosylation Associate with Therapy Response in Chronic Inflammatory Diseases. Int J Mol Sci 2022; 23:ijms23158473. [PMID: 35955616 PMCID: PMC9368836 DOI: 10.3390/ijms23158473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/19/2022] [Accepted: 07/24/2022] [Indexed: 12/10/2022] Open
Abstract
Immunosuppressants and biologicals are widely used therapeutics for various chronic inflammatory diseases (CID). To gain more detailed insight into their downstream effects, we examined their impact on serum immunoglobulin G (IgG) glycosylation. We analyzed IgG subclass-specific fragment crystallizable (Fc) N-glycosylation in patients suffering from various CID using the LC-MS approach. Firstly, we compared IgG Fc N-glycosylation between 128 CID patients and 204 healthy controls. Our results replicated previously observed CID-related decrease in IgG Fc galactosylation (adjusted p-value range 1.70 × 10−2–5.95 × 10−22) and sialylation (adjusted p-value range 1.85 × 10−2–1.71 × 10−18). Secondly, to assess changes in IgG Fc N-glycosylation associated with therapy and remission status, we compared 139 CID patients receiving either azathioprine, infliximab, or vedolizumab therapy. We observed an increase in IgG Fc galactosylation (adjusted p-value range 1.98 × 10−2–1.30 × 10−15) and sialylation (adjusted p-value range 3.28 × 10−6–4.34 × 10−18) during the treatment. Furthermore, patients who reached remission displayed increased Fc galactosylation levels (p-value range 2.25 × 10−2–5.44 × 10−3) in comparison to patients with active disease. In conclusion, the alterations in IgG Fc glycosylation and the fact these changes are even more pronounced in patients who achieved remission, suggest modulation of IgG inflammatory potential associated with CID therapy.
Collapse
|
21
|
Jagt JZ, Verburgt CM, de Vries R, de Boer NKH, Benninga MA, de Jonge WJ, van Limbergen JE, de Meij TGJ. Faecal Metabolomics in Paediatric Inflammatory Bowel Disease: A Systematic Review. J Crohns Colitis 2022; 16:1777-1790. [PMID: 35679608 PMCID: PMC9683079 DOI: 10.1093/ecco-jcc/jjac079] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND AND AIMS Paediatric inflammatory bowel disease [IBD] is characterized by altered immunological and metabolic pathways. Metabolomics may therefore increase pathophysiological understanding and could develop into characterization of biomarkers for diagnosis and IBD treatment response. However, no uniform metabolomic profiles have been identified to date. This systematic review aimed to identify faecal metabolomic signatures in paediatric IBD vs controls, and to describe metabolites associated with disease activity and treatment response. METHODS A literature search was performed in Embase, Medline, Web of Science and Cochrane Library. Studies assessing faecal metabolomics in paediatric patients < 18 years with IBD [de novo, active, inactive] with comparative groups [IBD vs non-IBD; responders vs non-responders] were included. The quality of included studies was assessed according to the Newcastle-Ottawa Scale. RESULTS Nineteen studies were included [540 patients with IBD, 386 controls], assessing faecal short-chain fatty acids [SCFA] [five studies], amino acids [AA] [ten studies], bile acids [BA] [eight studies] and other metabolites [nine studies] using various methodologies. Significantly increased levels of AA [particularly phenylalanine], primary BA and lower levels of secondary BA were described in paediatric IBD compared to controls. Faecal SCFA results varied across studies. Additionally, responders and non-responders to exclusive enteral nutrition and infliximab showed differences in baseline faecal metabolites [based on BA, AA]. CONCLUSIONS This systematic review provides evidence for distinct faecal metabolomic profiles in paediatric IBD. However, results varied across studies, possibly due to differences in study design and applied analytical techniques. Faecal metabolomics could provide more insight into host-microbial interactions in IBD, but further studies with standardized methodologies and reporting are needed.
Collapse
Affiliation(s)
- Jasmijn Z Jagt
- Corresponding author: Jasmijn Zaza Jagt, Department of Paediatric Gastroenterology, Emma Children’s Hospital, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands. Tel.: +316-50063766; E-mail:
| | | | - Ralph de Vries
- Medical Library, Vrije Universiteit Amsterdam, HV Amsterdam, The Netherlands
| | - Nanne K H de Boer
- Department of Gastroenterology and Hepatology, Amsterdam Gastroenterology and Metabolism Research Institute (AGEM), Amsterdam University Medical Centre, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Marc A Benninga
- Department of Paediatric Gastroenterology and Nutrition, Amsterdam University Medical Centres – location University of Amsterdam, Emma Children’s Hospital, AZ Amsterdam, The Netherlands
| | - Wouter J de Jonge
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology Metabolism, University of Amsterdam, BK Amsterdam, The Netherlands,Department of Surgery, University of Bonn, Bonn, Germany
| | - Johan E van Limbergen
- Department of Paediatric Gastroenterology and Nutrition, Amsterdam University Medical Centres – location University of Amsterdam, Emma Children’s Hospital, AZ Amsterdam, The Netherlands,Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology Metabolism, University of Amsterdam, BK Amsterdam, The Netherlands,Department of Pediatrics, Dalhousie University, Halifax, NS, Canada
| | - Tim G J de Meij
- Department of Paediatric Gastroenterology, Emma Children’s Hospital, Amsterdam UMC, Vrije Universiteit Amsterdam, HV Amsterdam, The Netherlands,Department of Paediatric Gastroenterology and Nutrition, Amsterdam University Medical Centres – location University of Amsterdam, Emma Children’s Hospital, AZ Amsterdam, The Netherlands
| |
Collapse
|
22
|
Hong CJ, Chen SY, Hsu YH, Yen GC. Protective effect of fermented okara on the regulation of inflammation, the gut microbiota, and SCFA production in rats with TNBS-induced colitis. Food Res Int 2022; 157:111390. [DOI: 10.1016/j.foodres.2022.111390] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 05/12/2022] [Accepted: 05/18/2022] [Indexed: 12/18/2022]
|
23
|
Yuan TY, Rajesh R, Tan M. Oral faecal microbiota transplantation in ulcerative colitis. Lancet Gastroenterol Hepatol 2022; 7:286. [PMID: 35278395 DOI: 10.1016/s2468-1253(21)00469-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 12/06/2021] [Indexed: 06/14/2023]
Affiliation(s)
- Tan Yi Yuan
- Department of Gastroenterology and Hepatology, Singapore General Hospital, Singapore 169608, Singapore
| | - R Rajesh
- Department of Gastroenterology and Hepatology, Singapore General Hospital, Singapore 169608, Singapore
| | - Malcolm Tan
- Department of Gastroenterology and Hepatology, Singapore General Hospital, Singapore 169608, Singapore.
| |
Collapse
|
24
|
Cytotoxicity of Thiopurine Drugs in Patients with Inflammatory Bowel Disease. TOXICS 2022; 10:toxics10040151. [PMID: 35448412 PMCID: PMC9026123 DOI: 10.3390/toxics10040151] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/11/2022] [Accepted: 03/17/2022] [Indexed: 02/04/2023]
Abstract
The effectiveness of thiopurine drugs in inflammatory bowel disease (IBD) was confirmed more than a half-century ago. It was proven that these can be essential immunomodulatory medications. Since then, they have been used routinely to maintain remission of Crohn’s disease (CD) and ulcerative colitis (UC). The cytotoxic properties of thiopurines and the numerous adverse effects of the treatment are controversial. However, the research subject of their pharmacology, therapy monitoring, and the search for predictive markers are still very relevant. In this article, we provide an overview of the current knowledge and findings in the field of thiopurines in IBD, focusing on the aspect of their cytotoxicity. Due to thiopurines’ benefits in IBD therapy, it is expected that they will still constitute an essential part of the CD and UC treatment algorithm. More studies are still required on the modulation of the action of thiopurines in combination therapy and their interaction with the gut microbiota.
Collapse
|
25
|
Hou J, Tang Y, Chen Y, Chen D. The Role of the Microbiota in Graves' Disease and Graves' Orbitopathy. Front Cell Infect Microbiol 2022; 11:739707. [PMID: 35004341 PMCID: PMC8727912 DOI: 10.3389/fcimb.2021.739707] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Accepted: 12/01/2021] [Indexed: 02/05/2023] Open
Abstract
Graves' disease (GD) is a clinical syndrome with an enlarged and overactive thyroid gland, an accelerated heart rate, Graves' orbitopathy (GO), and pretibial myxedema (PTM). GO is the most common extrathyroidal complication of GD. GD/GO has a significant negative impact on the quality of life. GD is the most common systemic autoimmune disorder, mediated by autoantibodies to the thyroid-stimulating hormone receptor (TSHR). It is generally accepted that GD/GO results from complex interactions between genetic and environmental factors that lead to the loss of immune tolerance to thyroid antigens. However, the exact mechanism is still elusive. Systematic investigations into GD/GO animal models and clinical patients have provided important new insight into these disorders during the past 4 years. These studies suggested that gut microbiota may play an essential role in the pathogenesis of GD/GO. Antibiotic vancomycin can reduce disease severity, but fecal material transfer (FMT) from GD/GO patients exaggerates the disease in GD/GO mouse models. There are significant differences in microbiota composition between GD/GO patients and healthy controls. Lactobacillus, Prevotella, and Veillonella often increase in GD patients. The commonly used therapeutic agents for GD/GO can also affect the gut microbiota. Antigenic mimicry and the imbalance of T helper 17 cells (Th17)/regulatory T cells (Tregs) are the primary mechanisms proposed for dysbiosis in GD/GO. Interventions including antibiotics, probiotics, and diet modification that modulate the gut microbiota have been actively investigated in preclinical models and, to some extent, in clinical settings, such as probiotics (Bifidobacterium longum) and selenium supplements. Future studies will reveal molecular pathways linking gut and thyroid functions and how they impact orbital autoimmunity. Microbiota-targeting therapeutics will likely be an essential strategy in managing GD/GO in the coming years.
Collapse
Affiliation(s)
- Jueyu Hou
- The Research Laboratory of Ophthalmology and Vision Sciences, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China.,The Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, China
| | - Yunjing Tang
- The Research Laboratory of Ophthalmology and Vision Sciences, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China.,The Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, China
| | - Yongjiang Chen
- The School of Optometry and Vision Science, University of Waterloo, Waterloo, ON, Canada
| | - Danian Chen
- The Research Laboratory of Ophthalmology and Vision Sciences, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China.,The Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, China
| |
Collapse
|
26
|
Kordulewska NK, Topa J, Rozmus D, Jarmołowska B. Effects of Osthole on Inflammatory Gene Expression and Cytokine Secretion in Histamine-Induced Inflammation in the Caco-2 Cell Line. Int J Mol Sci 2021; 22:ijms222413634. [PMID: 34948440 PMCID: PMC8708099 DOI: 10.3390/ijms222413634] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 12/14/2021] [Accepted: 12/17/2021] [Indexed: 12/05/2022] Open
Abstract
Hyperactivity of the immune system in the gastrointestinal tract leads to the development of chronic, inflammation-associated disorders. Such diseases, including inflammatory bowel disease, are not completely curable, but the specific line of treatment may reduce its symptoms. However, the response to treatment varies among patients, creating a necessity to uncover the pathophysiological basis of immune-mediated diseases and apply novel therapeutic strategies. The present study describes the anti-inflammatory properties of osthole during histamine-induced inflammation in the intestinal Caco-2 cell line. Osthole reduced the secretion of cytokines (CKs) and the expression level of inflammation-associated genes, which were increased after a histamine treatment. We have shown that the secretion of pro-inflammatory CKs (IL-1β, IL-6, IL-8, and TNF-α) during inflammation may be mediated by NFκB, and, after osthole treatment, this signaling pathway was disrupted. Our results suggest a possible role for osthole in the protection against inflammation in the gastrointestinal tract; thus, osthole may be considered as an anti-inflammatory modulator.
Collapse
Affiliation(s)
- Natalia K. Kordulewska
- Department of Biochemistry, Faculty of Biology and Biotechnology, University of Warmia and Mazury, 10-719 Olsztyn, Poland; (D.R.); (B.J.)
- Correspondence: (N.K.K.); (J.T.); Tel.: +48-89-523-37-63 (N.K.K.); +48-58-349-14-38 (J.T.)
| | - Justyna Topa
- Laboratory of Translational Oncology, Intercollegiate Faculty of Biotechnology, Medical University of Gdansk, 80-211 Gdansk, Poland
- Correspondence: (N.K.K.); (J.T.); Tel.: +48-89-523-37-63 (N.K.K.); +48-58-349-14-38 (J.T.)
| | - Dominika Rozmus
- Department of Biochemistry, Faculty of Biology and Biotechnology, University of Warmia and Mazury, 10-719 Olsztyn, Poland; (D.R.); (B.J.)
| | - Beata Jarmołowska
- Department of Biochemistry, Faculty of Biology and Biotechnology, University of Warmia and Mazury, 10-719 Olsztyn, Poland; (D.R.); (B.J.)
| |
Collapse
|
27
|
Hinrichsen F, Hamm J, Westermann M, Schröder L, Shima K, Mishra N, Walker A, Sommer N, Klischies K, Prasse D, Zimmermann J, Kaiser S, Bordoni D, Fazio A, Marinos G, Laue G, Imm S, Tremaroli V, Basic M, Häsler R, Schmitz RA, Krautwald S, Wolf A, Stecher B, Schmitt-Kopplin P, Kaleta C, Rupp J, Bäckhed F, Rosenstiel P, Sommer F. Microbial regulation of hexokinase 2 links mitochondrial metabolism and cell death in colitis. Cell Metab 2021; 33:2355-2366.e8. [PMID: 34847376 DOI: 10.1016/j.cmet.2021.11.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 08/07/2021] [Accepted: 11/09/2021] [Indexed: 12/14/2022]
Abstract
Hexokinases (HK) catalyze the first step of glycolysis limiting its pace. HK2 is highly expressed in gut epithelium, contributes to immune responses, and is upregulated during inflammation. We examined the microbial regulation of HK2 and its impact on inflammation using mice lacking HK2 in intestinal epithelial cells (Hk2ΔIEC). Hk2ΔIEC mice were less susceptible to acute colitis. Analyzing the epithelial transcriptome from Hk2ΔIEC mice during colitis and using HK2-deficient intestinal organoids and Caco-2 cells revealed reduced mitochondrial respiration and epithelial cell death in the absence of HK2. The microbiota strongly regulated HK2 expression and activity. The microbially derived short-chain fatty acid (SCFA) butyrate repressed HK2 expression via histone deacetylase 8 (HDAC8) and reduced mitochondrial respiration in wild-type but not in HK2-deficient Caco-2 cells. Butyrate supplementation protected wild-type but not Hk2ΔIEC mice from colitis. Our findings define a mechanism how butyrate promotes intestinal homeostasis and suggest targeted HK2-inhibition as therapeutic avenue for inflammation.
Collapse
Affiliation(s)
- Finn Hinrichsen
- Institute of Clinical Molecular Biology, University of Kiel, 24105 Kiel, Germany
| | - Jacob Hamm
- Institute of Clinical Molecular Biology, University of Kiel, 24105 Kiel, Germany
| | - Magdalena Westermann
- Institute of Clinical Molecular Biology, University of Kiel, 24105 Kiel, Germany
| | - Lena Schröder
- Institute of Clinical Molecular Biology, University of Kiel, 24105 Kiel, Germany
| | - Kensuke Shima
- Department of Infectious Diseases and Microbiology, University of Lübeck, 23538 Lübeck, Germany
| | - Neha Mishra
- Institute of Clinical Molecular Biology, University of Kiel, 24105 Kiel, Germany
| | - Alesia Walker
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, German Research Centre for Environmental Health (GmbH), 85764 Neuherberg, Germany
| | - Nina Sommer
- Institute of Clinical Molecular Biology, University of Kiel, 24105 Kiel, Germany
| | - Kenneth Klischies
- Institute of Clinical Molecular Biology, University of Kiel, 24105 Kiel, Germany
| | - Daniela Prasse
- Institute of General Microbiology, University of Kiel, 24118 Kiel, Germany
| | | | - Sina Kaiser
- Institute of Clinical Molecular Biology, University of Kiel, 24105 Kiel, Germany
| | - Dora Bordoni
- Institute of Clinical Molecular Biology, University of Kiel, 24105 Kiel, Germany
| | - Antonella Fazio
- Institute of Clinical Molecular Biology, University of Kiel, 24105 Kiel, Germany
| | - Georgios Marinos
- Institute of Experimental Medicine, University of Kiel, 24105 Kiel, Germany
| | - Georg Laue
- Institute of Clinical Molecular Biology, University of Kiel, 24105 Kiel, Germany
| | - Simon Imm
- Institute of Clinical Molecular Biology, University of Kiel, 24105 Kiel, Germany
| | - Valentina Tremaroli
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, University of Gothenburg, 41345 Gothenburg, Sweden
| | - Marijana Basic
- Institute for Laboratory Animal Science, Hannover Medical School, 30625 Hannover, Germany
| | - Robert Häsler
- Institute of Clinical Molecular Biology, University of Kiel, 24105 Kiel, Germany; Department of Dermatology and Allergy, University Hospital Schleswig-Holstein, 24105 Kiel, Germany
| | - Ruth A Schmitz
- Institute of General Microbiology, University of Kiel, 24118 Kiel, Germany
| | - Stefan Krautwald
- Department of Nephrology and Hypertension, University Hospital Schleswig-Holstein, 24105 Kiel, Germany
| | - Andrea Wolf
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Bärbel Stecher
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Ludwig-Maximilians-University of Munich, 80336 Munich, Germany; German Center for Infection Research (DZIF), partner site LMU Munich, Munich Germany
| | - Philippe Schmitt-Kopplin
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, German Research Centre for Environmental Health (GmbH), 85764 Neuherberg, Germany
| | - Christoph Kaleta
- Institute of Experimental Medicine, University of Kiel, 24105 Kiel, Germany
| | - Jan Rupp
- Department of Infectious Diseases and Microbiology, University of Lübeck, 23538 Lübeck, Germany
| | - Fredrik Bäckhed
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, University of Gothenburg, 41345 Gothenburg, Sweden; Department of Clinical Physiology, Sahlgrenska University Hospital, Gothenburg, Sweden; Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, University of Kiel, 24105 Kiel, Germany
| | - Felix Sommer
- Institute of Clinical Molecular Biology, University of Kiel, 24105 Kiel, Germany.
| |
Collapse
|
28
|
Zaiatz Bittencourt V, Jones F, Doherty G, Ryan EJ. Targeting Immune Cell Metabolism in the Treatment of Inflammatory Bowel Disease. Inflamm Bowel Dis 2021; 27:1684-1693. [PMID: 33693743 PMCID: PMC8522790 DOI: 10.1093/ibd/izab024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Indexed: 12/17/2022]
Abstract
The cells of the immune system are highly dynamic, constantly sensing and adapting to changes in their surroundings. Complex metabolic pathways govern leukocytes' ability to fine-tune their responses to external threats. Mammalian target of rapamycin complex 1 and hypoxia inducible factor are important hubs of these pathways and play a critical role coordinating cell activation and proliferation and cytokine production. For this reason, these molecules are attractive therapeutic targets in inflammatory disease. Insight into perturbations in immune cell metabolic pathways and their impact on inflammatory bowel disease (IBD) progression are starting to emerge. However, it remains to be determined whether the aberrations in immune metabolism that occur in gut resident immune cells contribute to disease pathogenesis or are reflected in the peripheral blood of patients with IBD. In this review, we explore what is known about the metabolic profile of T cells, monocytes, macrophages, dendritic cells, and natural killer cells in IBD and discuss the potential of manipulating immune cell metabolism as a novel approach to treating IBD.
Collapse
Affiliation(s)
- Vanessa Zaiatz Bittencourt
- Centre for Colorectal Disease, St. Vincent’s University Hospital, School of Medicine, University College Dublin, Dublin, Ireland
| | - Fiona Jones
- Centre for Colorectal Disease, St. Vincent’s University Hospital, School of Medicine, University College Dublin, Dublin, Ireland
| | - Glen Doherty
- Centre for Colorectal Disease, St. Vincent’s University Hospital, School of Medicine, University College Dublin, Dublin, Ireland
| | - Elizabeth J Ryan
- Centre for Colorectal Disease, St. Vincent’s University Hospital, School of Medicine, University College Dublin, Dublin, Ireland
- Department of Biological Sciences, Health Research Institute, University of Limerick, Limerick, Ireland
| |
Collapse
|
29
|
Sultan S, El-Mowafy M, Elgaml A, Ahmed TAE, Hassan H, Mottawea W. Metabolic Influences of Gut Microbiota Dysbiosis on Inflammatory Bowel Disease. Front Physiol 2021; 12:715506. [PMID: 34646151 PMCID: PMC8502967 DOI: 10.3389/fphys.2021.715506] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/18/2021] [Indexed: 12/12/2022] Open
Abstract
Inflammatory bowel diseases (IBD) are chronic medical disorders characterized by recurrent gastrointestinal inflammation. While the etiology of IBD is still unknown, the pathogenesis of the disease results from perturbations in both gut microbiota and the host immune system. Gut microbiota dysbiosis in IBD is characterized by depleted diversity, reduced abundance of short chain fatty acids (SCFAs) producers and enriched proinflammatory microbes such as adherent/invasive E. coli and H2S producers. This dysbiosis may contribute to the inflammation through affecting either the immune system or a metabolic pathway. The immune responses to gut microbiota in IBD are extensively discussed. In this review, we highlight the main metabolic pathways that regulate the host-microbiota interaction. We also discuss the reported findings indicating that the microbial dysbiosis during IBD has a potential metabolic impact on colonocytes and this may underlie the disease progression. Moreover, we present the host metabolic defectiveness that adds to the impact of symbiont dysbiosis on the disease progression. This will raise the possibility that gut microbiota dysbiosis associated with IBD results in functional perturbations of host-microbiota interactions, and consequently modulates the disease development. Finally, we shed light on the possible therapeutic approaches of IBD through targeting gut microbiome.
Collapse
Affiliation(s)
- Salma Sultan
- Faculty of Health Sciences, School of Nutrition Sciences, University of Ottawa, Ottawa, ON, Canada
| | - Mohammed El-Mowafy
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Abdelaziz Elgaml
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt.,Department of Microbiology and Immunology, Faculty of Pharmacy, Horus University, New Damietta, Egypt
| | - Tamer A E Ahmed
- Faculty of Health Sciences, School of Nutrition Sciences, University of Ottawa, Ottawa, ON, Canada.,Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Hebatoallah Hassan
- Faculty of Health Sciences, School of Nutrition Sciences, University of Ottawa, Ottawa, ON, Canada.,Department of Biotechnology, Institute of Graduate Studies and Research, Alexandria University, Alexandria, Egypt
| | - Walid Mottawea
- Faculty of Health Sciences, School of Nutrition Sciences, University of Ottawa, Ottawa, ON, Canada.,Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| |
Collapse
|
30
|
Heinken A, Basile A, Hertel J, Thinnes C, Thiele I. Genome-Scale Metabolic Modeling of the Human Microbiome in the Era of Personalized Medicine. Annu Rev Microbiol 2021; 75:199-222. [PMID: 34314593 DOI: 10.1146/annurev-micro-060221-012134] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The human microbiome plays an important role in human health and disease. Meta-omics analyses provide indispensable data for linking changes in microbiome composition and function to disease etiology. Yet, the lack of a mechanistic understanding of, e.g., microbiome-metabolome links hampers the translation of these findings into effective, novel therapeutics. Here, we propose metabolic modeling of microbial communities through constraint-based reconstruction and analysis (COBRA) as a complementary approach to meta-omics analyses. First, we highlight the importance of microbial metabolism in cardiometabolic diseases, inflammatory bowel disease, colorectal cancer, Alzheimer disease, and Parkinson disease. Next, we demonstrate that microbial community modeling can stratify patients and controls, mechanistically link microbes with fecal metabolites altered in disease, and identify host pathways affected by the microbiome. Finally, we outline our vision for COBRA modeling combined with meta-omics analyses and multivariate statistical analyses to inform and guide clinical trials, yield testable hypotheses, and ultimately propose novel dietary and therapeutic interventions. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Almut Heinken
- School of Medicine, National University of Ireland, Galway, H91 TK33, Ireland;
| | - Arianna Basile
- Department of Biology, University of Padua, Padua 35121, Italy
| | - Johannes Hertel
- School of Medicine, National University of Ireland, Galway, H91 TK33, Ireland; .,Department of Psychiatry and Psychotherapy, University of Greifswald, 17489 Greifswald, Germany
| | - Cyrille Thinnes
- School of Medicine, National University of Ireland, Galway, H91 TK33, Ireland;
| | - Ines Thiele
- School of Medicine, National University of Ireland, Galway, H91 TK33, Ireland; .,Division of Microbiology, National University of Ireland, Galway, H91 TK33, Ireland.,APC Microbiome Ireland, University College Cork, Cork, T12 K8AF, Ireland
| |
Collapse
|
31
|
Heinken A, Hertel J, Thiele I. Metabolic modelling reveals broad changes in gut microbial metabolism in inflammatory bowel disease patients with dysbiosis. NPJ Syst Biol Appl 2021; 7:19. [PMID: 33958598 PMCID: PMC8102608 DOI: 10.1038/s41540-021-00178-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 04/07/2021] [Indexed: 12/26/2022] Open
Abstract
Inflammatory bowel diseases, such as Crohn's Disease, are characterised by an altered blood and faecal metabolome, and changes in gut microbiome composition. Here, we present an efficient, scalable, tractable systems biology framework to mechanistically link microbial strains and faecal metabolites. We retrieve strain-level relative abundances from metagenomics data from a cohort of paediatric Crohn's Disease patients with and without dysbiosis and healthy control children and construct and interrogate a personalised microbiome model for each sample. Predicted faecal secretion profiles and strain-level contributions to each metabolite vary broadly between healthy, dysbiotic, and non-dysbiotic microbiomes. The reduced microbial diversity in IBD results in reduced numbers of secreted metabolites, especially in sulfur metabolism. We demonstrate that increased potential to synthesise amino acids is linked to Proteobacteria contributions, in agreement with experimental observations. The established modelling framework yields testable hypotheses that may result in novel therapeutic and dietary interventions targeting the host-gut microbiome-diet axis.
Collapse
Affiliation(s)
- Almut Heinken
- School of Medicine, National University of Ireland, Galway, Ireland
- Ryan Institute, National University of Ireland, Galway, Ireland
| | - Johannes Hertel
- School of Medicine, National University of Ireland, Galway, Ireland
- Ryan Institute, National University of Ireland, Galway, Ireland
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
| | - Ines Thiele
- School of Medicine, National University of Ireland, Galway, Ireland.
- Ryan Institute, National University of Ireland, Galway, Ireland.
- Division of Microbiology, National University of Galway, Galway, Ireland.
- APC Microbiome Ireland, Cork, Ireland.
| |
Collapse
|
32
|
Franzin M, Stefančič K, Lucafò M, Decorti G, Stocco G. Microbiota and Drug Response in Inflammatory Bowel Disease. Pathogens 2021; 10:211. [PMID: 33669168 PMCID: PMC7919657 DOI: 10.3390/pathogens10020211] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 02/10/2021] [Accepted: 02/11/2021] [Indexed: 02/06/2023] Open
Abstract
A mutualistic relationship between the composition, function and activity of the gut microbiota (GM) and the host exists, and the alteration of GM, sometimes referred as dysbiosis, is involved in various immune-mediated diseases, including inflammatory bowel disease (IBD). Accumulating evidence suggests that the GM is able to influence the efficacy of the pharmacological therapy of IBD and to predict whether individuals will respond to treatment. Additionally, the drugs used to treat IBD can modualate the microbial composition. The review aims to investigate the impact of the GM on the pharmacological therapy of IBD and vice versa. The GM resulted in an increase or decrease in therapeutic responses to treatment, but also to biotransform drugs to toxic metabolites. In particular, the baseline GM composition can help to predict if patients will respond to the IBD treatment with biologic drugs. On the other hand, drugs can affect the GM by incrementing or reducing its diversity and richness. Therefore, the relationship between the GM and drugs used in the treatment of IBD can be either beneficial or disadvantageous.
Collapse
Affiliation(s)
- Martina Franzin
- Department of Medicine, Surgery and Health Sciences, University of Trieste, 34127 Trieste, Italy;
| | - Katja Stefančič
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (K.S.); (G.S.)
| | - Marianna Lucafò
- Institute for Maternal and Child Health—IRCCS “Burlo Garofolo”, 34137 Trieste, Italy;
| | - Giuliana Decorti
- Department of Medicine, Surgery and Health Sciences, University of Trieste, 34127 Trieste, Italy;
- Institute for Maternal and Child Health—IRCCS “Burlo Garofolo”, 34137 Trieste, Italy;
| | - Gabriele Stocco
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (K.S.); (G.S.)
| |
Collapse
|
33
|
Verburgt CM, Ghiboub M, Benninga MA, de Jonge WJ, Van Limbergen JE. Nutritional Therapy Strategies in Pediatric Crohn's Disease. Nutrients 2021; 13:212. [PMID: 33450982 PMCID: PMC7828385 DOI: 10.3390/nu13010212] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 01/07/2021] [Accepted: 01/09/2021] [Indexed: 12/12/2022] Open
Abstract
The increase in incidences of pediatric Crohn's Disease (CD) worldwide has been strongly linked with dietary shifts towards a Westernized diet, ultimately leading to altered gut microbiota and disturbance in intestinal immunity and the metabolome. Multiple clinical studies in children with CD have demonstrated the high efficacy of nutritional therapy with exclusive enteral nutrition (EEN) to induce remission with an excellent safety profile. However, EEN is poorly tolerated, limiting its compliance and clinical application. This has spiked an interest in the development of alternative and better-tolerated nutritional therapy strategies. Several nutritional therapies have now been designed not only to treat the nutritional deficiencies seen in children with active CD but also to correct dysbiosis and reduce intestinal inflammation. In this review, we report the most recent insights regarding nutritional strategies in children with active CD: EEN, partial enteral nutrition (PEN), Crohn's disease exclusive diet (CDED), and CD treatment-with-eating diet (CD-TREAT). We describe their setup, efficacy, safety, and (dis)advantages as well as some of their potential mechanisms of action and perspectives. A better understanding of different nutritional therapeutic options and their mechanisms will yield better and safer management strategies for children with CD and may address the barriers and limitations of current strategies in children.
Collapse
Affiliation(s)
- Charlotte M. Verburgt
- Department of Pediatric Gastroenterology and Nutrition, Emma Children’s Hospital, Amsterdam University Medical Centers, 1105 AZ Amsterdam, The Netherlands; (C.M.V.); (M.G.); (M.A.B.)
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers, University of Amsterdam, 1105 BK Amsterdam, The Netherlands;
| | - Mohammed Ghiboub
- Department of Pediatric Gastroenterology and Nutrition, Emma Children’s Hospital, Amsterdam University Medical Centers, 1105 AZ Amsterdam, The Netherlands; (C.M.V.); (M.G.); (M.A.B.)
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers, University of Amsterdam, 1105 BK Amsterdam, The Netherlands;
| | - Marc A. Benninga
- Department of Pediatric Gastroenterology and Nutrition, Emma Children’s Hospital, Amsterdam University Medical Centers, 1105 AZ Amsterdam, The Netherlands; (C.M.V.); (M.G.); (M.A.B.)
| | - Wouter J. de Jonge
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers, University of Amsterdam, 1105 BK Amsterdam, The Netherlands;
- Department of Surgery, University of Bonn, 53127 Bonn, Germany
| | - Johan E. Van Limbergen
- Department of Pediatric Gastroenterology and Nutrition, Emma Children’s Hospital, Amsterdam University Medical Centers, 1105 AZ Amsterdam, The Netherlands; (C.M.V.); (M.G.); (M.A.B.)
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers, University of Amsterdam, 1105 BK Amsterdam, The Netherlands;
- Department of Pediatrics, Dalhousie University, Halifax, NS B3K 6R8, Canada
| |
Collapse
|
34
|
Demetrowitsch TJ, Schlicht K, Knappe C, Zimmermann J, Jensen-Kroll J, Pisarevskaja A, Brix F, Brandes J, Geisler C, Marinos G, Sommer F, Schulte DM, Kaleta C, Andersen V, Laudes M, Schwarz K, Waschina S. Precision Nutrition in Chronic Inflammation. Front Immunol 2020; 11:587895. [PMID: 33329569 PMCID: PMC7719806 DOI: 10.3389/fimmu.2020.587895] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/22/2020] [Indexed: 12/11/2022] Open
Abstract
The molecular foundation of chronic inflammatory diseases (CIDs) can differ markedly between individuals. As our understanding of the biochemical mechanisms underlying individual disease manifestations and progressions expands, new strategies to adjust treatments to the patient's characteristics will continue to profoundly transform clinical practice. Nutrition has long been recognized as an important determinant of inflammatory disease phenotypes and treatment response. Yet empirical work demonstrating the therapeutic effectiveness of patient-tailored nutrition remains scarce. This is mainly due to the challenges presented by long-term effects of nutrition, variations in inter-individual gastrointestinal microbiota, the multiplicity of human metabolic pathways potentially affected by food ingredients, nutrition behavior, and the complexity of food composition. Historically, these challenges have been addressed in both human studies and experimental model laboratory studies primarily by using individual nutrition data collection in tandem with large-scale biomolecular data acquisition (e.g. genomics, metabolomics, etc.). This review highlights recent findings in the field of precision nutrition and their potential implications for the development of personalized treatment strategies for CIDs. It emphasizes the importance of computational approaches to integrate nutritional information into multi-omics data analysis and to predict which molecular mechanisms may explain how nutrients intersect with disease pathways. We conclude that recent findings point towards the unexhausted potential of nutrition as part of personalized medicine in chronic inflammation.
Collapse
Affiliation(s)
- Tobias J. Demetrowitsch
- Division of Food Technology, Institute of Human Nutrition and Food Science, Kiel University, Kiel, Germany
| | - Kristina Schlicht
- Division of Endocrinology, Diabetes and Clinical Nutrition, Department of Medicine 1, Kiel University, Kiel, Germany
| | - Carina Knappe
- Division of Endocrinology, Diabetes and Clinical Nutrition, Department of Medicine 1, Kiel University, Kiel, Germany
| | - Johannes Zimmermann
- Research Group Medical Systems Biology, Institute of Experimental Medicine, Kiel University, Kiel, Germany
| | - Julia Jensen-Kroll
- Division of Food Technology, Institute of Human Nutrition and Food Science, Kiel University, Kiel, Germany
| | - Alina Pisarevskaja
- Division of Food Technology, Institute of Human Nutrition and Food Science, Kiel University, Kiel, Germany
- Division of Nutriinformatics, Institute of Human Nutrition and Food Science, Kiel University, Kiel, Germany
| | - Fynn Brix
- Division of Food Technology, Institute of Human Nutrition and Food Science, Kiel University, Kiel, Germany
| | - Juliane Brandes
- Division of Endocrinology, Diabetes and Clinical Nutrition, Department of Medicine 1, Kiel University, Kiel, Germany
| | - Corinna Geisler
- Division of Endocrinology, Diabetes and Clinical Nutrition, Department of Medicine 1, Kiel University, Kiel, Germany
| | - Georgios Marinos
- Research Group Medical Systems Biology, Institute of Experimental Medicine, Kiel University, Kiel, Germany
| | - Felix Sommer
- Institute of Clinical Molecular Biology (IKMB), Kiel University, Kiel, Germany
| | - Dominik M. Schulte
- Division of Endocrinology, Diabetes and Clinical Nutrition, Department of Medicine 1, Kiel University, Kiel, Germany
| | - Christoph Kaleta
- Research Group Medical Systems Biology, Institute of Experimental Medicine, Kiel University, Kiel, Germany
| | - Vibeke Andersen
- Institute of Regional Research, University of Southern Denmark, Odense, Denmark
- Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
- Focused Research Unit for Molecular Diagnostic and Clinical Research, University Hospital of Southern Denmark, Aabenraa, Denmark
| | - Matthias Laudes
- Division of Endocrinology, Diabetes and Clinical Nutrition, Department of Medicine 1, Kiel University, Kiel, Germany
| | - Karin Schwarz
- Division of Food Technology, Institute of Human Nutrition and Food Science, Kiel University, Kiel, Germany
| | - Silvio Waschina
- Division of Nutriinformatics, Institute of Human Nutrition and Food Science, Kiel University, Kiel, Germany
| |
Collapse
|
35
|
Nutritional Targeting of the Microbiome as Potential Therapy for Malnutrition and Chronic Inflammation. Nutrients 2020; 12:nu12103032. [PMID: 33022941 PMCID: PMC7601849 DOI: 10.3390/nu12103032] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 09/29/2020] [Accepted: 10/01/2020] [Indexed: 12/16/2022] Open
Abstract
Homeostatic interactions with the microbiome are central for a healthy human physiology and nutrition is the main driving force shaping the microbiome. In the past decade, a wealth of preclinical studies mainly using gnotobiotic animal models demonstrated that malnutrition and chronic inflammation stress these homeostatic interactions and various microbial species and their metabolites or metabolic activities have been associated with disease. For example, the dysregulation of the bacterial metabolism of dietary tryptophan promotes an inflammatory environment and susceptibility to pathogenic infection. Clinical studies have now begun to evaluate the therapeutic potential of nutritional and probiotic interventions in malnutrition and chronic inflammation to ameliorate disease symptoms or even prevent pathogenesis. Here, we therefore summarize the recent progress in this field and propose to move further towards the nutritional targeting of the microbiome for malnutrition and chronic inflammation.
Collapse
|