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Bauset C, Carda-Diéguez M, Cejudo-Garcés A, Buetas E, Seco-Cervera M, Macias-Ceja DC, Navarro-Vicente F, Esplugues JV, Calatayud S, Mira Á, Ortiz-Masiá D, Barrachina MD, Cosín-Roger J. A disturbed metabolite-GPCR axis is associated with microbial dysbiosis in IBD patients: Potential role of GPR109A in macrophages. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167489. [PMID: 39233260 DOI: 10.1016/j.bbadis.2024.167489] [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: 01/31/2024] [Revised: 06/20/2024] [Accepted: 08/26/2024] [Indexed: 09/06/2024]
Abstract
Inflammatory Bowel Disease (IBD) is a chronic inflammatory disorder of the gastrointestinal tract characterized by disrupted immune function. Indeed, gut microbiota dysbiosis and metabolomic profile alterations, are hallmarks of IBD. In this scenario, metabolite-sensing G-protein coupled receptors (GPCRs), involved in several biological processes, have emerged as pivotal players in the pathophysiology of IBD. The aim of this study was to characterize the axis microbiota-metabolite-GPCR in intestinal surgical resections from IBD patients. Results showed that UC patients had a lower microbiota richness and bacterial load, with a higher proportion of the genus Cellulosimicrobium and a reduced proportion of Escherichia, whereas CD patients showed a decreased abundance of Enterococcus. Furthermore, metabolomic analysis revealed alterations in carboxylic acids, fatty acids, and amino acids in UC and CD samples. These patients also exhibited upregulated expression of most metabolite-sensing GPCRs analysed, which positively correlated with pro-inflammatory and pro-fibrotic markers. The role of GPR109A was studied in depth and increased expression of this receptor was detected in epithelial cells and cells from lamina propria, including CD68+ macrophages, in IBD patients. The treatment with β-hydroxybutyrate increased gene expression of GPR109A, CD86, IL1B and NOS2 in U937-derived macrophages. Besides, when GPR109A was transiently silenced, the mRNA expression and secretion of IL-1β, IL-6 and TNF-α were impaired in M1 macrophages. Finally, the secretome from siGPR109A M1 macrophages reduced the gene and protein expression of COL1A1 and COL3A1 in intestinal fibroblasts. A better understanding of metabolite-sensing GPCRs, such as GPR109A, could establish their potential as therapeutic targets for managing IBD.
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Affiliation(s)
- Cristina Bauset
- Departamento de Farmacología, Facultad de Medicina, Universidad de Valencia, Valencia, Spain
| | | | - Andrea Cejudo-Garcés
- Departamento de Farmacología, Facultad de Medicina, Universidad de Valencia, Valencia, Spain
| | - Elena Buetas
- Genomics & Health Department, FISABIO Foundation, Valencia, Spain
| | | | | | | | - Juan Vicente Esplugues
- Departamento de Farmacología, Facultad de Medicina, Universidad de Valencia, Valencia, Spain; CIBERehd (Centro de Investigaciones en Red Enfermedad Hepática y Digestiva), Madrid, Spain
| | - Sara Calatayud
- Departamento de Farmacología, Facultad de Medicina, Universidad de Valencia, Valencia, Spain; CIBERehd (Centro de Investigaciones en Red Enfermedad Hepática y Digestiva), Madrid, Spain
| | - Álex Mira
- Genomics & Health Department, FISABIO Foundation, Valencia, Spain; CIBER Center for Epidemiology and Public Health, Madrid, Spain
| | - Dolores Ortiz-Masiá
- CIBERehd (Centro de Investigaciones en Red Enfermedad Hepática y Digestiva), Madrid, Spain; Departamento de Medicina, Facultad de Medicina, Universidad de Valencia, Valencia, Spain.
| | - María Dolores Barrachina
- Departamento de Farmacología, Facultad de Medicina, Universidad de Valencia, Valencia, Spain; CIBERehd (Centro de Investigaciones en Red Enfermedad Hepática y Digestiva), Madrid, Spain.
| | - Jesús Cosín-Roger
- Departamento de Farmacología, Facultad de Medicina, Universidad de Valencia, Valencia, Spain; CIBERehd (Centro de Investigaciones en Red Enfermedad Hepática y Digestiva), Madrid, Spain
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2
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Yuan Y, Fu X, Deng Y, Sun Y. Exploring the role of genetics, gut microbiota and blood metabolites in IBD. Gut 2024:gutjnl-2024-333611. [PMID: 39366724 DOI: 10.1136/gutjnl-2024-333611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2024] [Accepted: 09/27/2024] [Indexed: 10/06/2024]
Affiliation(s)
- Yiwen Yuan
- State Key Laboratory of Swine and Poultry Breeding Industry, South China Agricultural University, Guangzhou, Guangdong, People's Republic of China
- Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, People's Republic of China
- Guangdong Provincial Key Laboratory for the Development Biology and Environmental Adaptation of Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, People's Republic of China
| | - Xi Fu
- Guangdong Provincial Engineering Research Center of Public Health Detection and Assessment, NMPA Key Laboratory for Technology Research and Evaluation of Pharmacovigilance, School of Public Health, Guangdong Pharmaceutical University, Guangzhou, Guangdong, People's Republic of China
| | - Yiqun Deng
- State Key Laboratory of Swine and Poultry Breeding Industry, South China Agricultural University, Guangzhou, Guangdong, People's Republic of China
- Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, People's Republic of China
- Guangdong Provincial Key Laboratory for the Development Biology and Environmental Adaptation of Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, People's Republic of China
| | - Yu Sun
- State Key Laboratory of Swine and Poultry Breeding Industry, South China Agricultural University, Guangzhou, Guangdong, People's Republic of China
- Guangdong Provincial Key Laboratory for the Development Biology and Environmental Adaptation of Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, People's Republic of China
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3
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Oh HN, Shin SY, Kim JH, Baek J, Kim HJ, Lee KM, Park SJ, Kim SY, Choi HK, Kim W, Sul WJ, Choi CH. Dynamic changes in the gut microbiota composition during adalimumab therapy in patients with ulcerative colitis: implications for treatment response prediction and therapeutic targets. Gut Pathog 2024; 16:44. [PMID: 39187879 PMCID: PMC11346184 DOI: 10.1186/s13099-024-00637-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 08/16/2024] [Indexed: 08/28/2024] Open
Abstract
BACKGROUND While significant research exists on gut microbiota changes after anti-tumor necrosis factor-alpha (anti TNF-α) therapy for ulcerative colitis, little is known about the longitudinal changes related to the effects of anti TNF-α. This study aimed to investigate the dynamics of gut microbiome changes during anti TNF-α (adalimumab) therapy in patients with ulcerative colitis (UC). RESULTS The microbiota composition was affected by the disease severity and extent in patients with UC. Regardless of clinical remission status at each time point, patients with UC exhibited microbial community distinctions from healthy controls. Distinct amplicon sequence variants (ASVs) differences were identified throughout the course of Adalimumab (ADA) treatment at each time point. A notable reduction in gut microbiome dissimilarity was observed only in remitters. Remitters demonstrated a decrease in the relative abundances of Burkholderia-Caballeronia-Paraburkholderia and Staphylococcus as the treatment progressed. Additionally, there was an observed increase in the relative abundances of Bifidobacterium and Dorea. Given the distribution of the 48 ASVs with high or low relative abundances in the pre-treatment samples according to clinical remission at week 8, a clinical remission at week 8 with a sensitivity and specificity of 72.4% and 84.3%, respectively, was predicted on the receiver operating characteristic curve (area under the curve, 0.851). CONCLUSIONS The gut microbiota undergoes diverse changes according to the treatment response during ADA treatment. These changes provide insights into predicting treatment responses to ADA and offer new therapeutic targets for UC.
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Affiliation(s)
- Han Na Oh
- Department of Systems Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea
- Inflamm-Aging Translational Research Center, Ajou University Medical Center, Suwon, Republic of Korea
| | - Seung Yong Shin
- Department of Internal Medicine, Chung-Ang University College of Medicine, 102 Heukseok-Ro, Dongjak-Gu, Seoul, Republic of Korea, 06973
| | - Jong-Hwa Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Jihye Baek
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Hyo Jong Kim
- Department of Gastroenterology, Kyung Hee University Hospital, Seoul, Republic of Korea
| | - Kang-Moon Lee
- Department of Gastroenterology, The Catholic University of Korea St. Vincent's Hospital, Suwon, Republic of Korea
| | - Soo Jung Park
- Department of Internal Medicine and Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Seok-Young Kim
- College of Pharmacy, Chung-Ang University, Seoul, Republic of Korea
| | - Hyung-Kyoon Choi
- College of Pharmacy, Chung-Ang University, Seoul, Republic of Korea
| | - Wonyong Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Woo Jun Sul
- Department of Systems Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea.
| | - Chang Hwan Choi
- Department of Internal Medicine, Chung-Ang University College of Medicine, 102 Heukseok-Ro, Dongjak-Gu, Seoul, Republic of Korea, 06973.
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Baines JF, Baldus CD, Bertels F, Brüggemann M, Kaleta C, Laudes M, Mueller FJ, Odenthal-Hesse L, Poyet M, Rainey PB, Rosenstiel P, Scheffold A, Sebens S, Thiery J, Traulsen A. Advancing evolutionary medicine in Northern Germany: Collaboration between Kiel University's Medical Faculty and the Max Planck Institute for Evolutionary Biology. Evol Med Public Health 2024; 12:117-121. [PMID: 39114444 PMCID: PMC11304943 DOI: 10.1093/emph/eoae013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 07/10/2024] [Indexed: 08/10/2024] Open
Affiliation(s)
- John F Baines
- Section of Evolutionary Medicine, Institute of Experimental Medicine, Kiel University, Kiel, Germany
- Guest Group Evolutionary Medicine, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Claudia D Baldus
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
- University Cancer Center Schleswig-Holstein (UCCSH), University Hospital Schleswig-Holstein, Kiel, Germany
| | - Frederic Bertels
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Monika Brüggemann
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
- University Cancer Center Schleswig-Holstein (UCCSH), University Hospital Schleswig-Holstein, Kiel, Germany
| | - Christoph Kaleta
- Research Group Medical Systems Biology, Institute of Experimental Medicine, Kiel University, Kiel, Germany
| | - Matthias Laudes
- Institute of Diabetes and Clinical Metabolic Research, University Hospital Schleswig-Holstein Campus Kiel, Kiel, Germany
| | - Franz-Josef Mueller
- Department of Psychiatry and Psychotherapy, Kiel University and University Hospital Schleswig-Holstein, Kiel, Germany
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Linda Odenthal-Hesse
- Research Group Meiotic Recombination and Genome Instability, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Mathilde Poyet
- Section of Evolutionary Medicine, Institute of Experimental Medicine, Kiel University, Kiel, Germany
| | - Paul B Rainey
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Laboratory of Biophysics and Evolution, ESPCI, Université Paris Sciences et Lettres, Paris, France
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Kiel University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Alexander Scheffold
- Institute of Immunology, Kiel University and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Susanne Sebens
- Institute for Experimental Cancer Research, Kiel University, University Hospital Schleswig-Holstein (UKSH), Kiel, Germany
| | - Joachim Thiery
- Faculty of Medicine, Kiel University and University Hospital Schleswig-Holstein (UKSH), Kiel, Germany
| | - Arne Traulsen
- Department of Theoretical Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
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5
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Menezes Nascimento Filho H, Kum AST, Bestetti AM, da Silva PHVA, Gallegos MMM, Damião AOMC, Navaneethan U, de Moura EGH. Patient-Related Factors Associated With Long-Term Outcomes After Successful Endoscopic Balloon Dilation For Crohn's Disease-Associated Ileo-Colic Strictures: A Systematic Review and Meta-analysis. CROHN'S & COLITIS 360 2024; 6:otae041. [PMID: 39175792 PMCID: PMC11339545 DOI: 10.1093/crocol/otae041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Indexed: 08/24/2024] Open
Abstract
Background Successful Crohn's disease (CD) therapy relies on timely and precise management strategies. Endoscopic balloon dilation (EBD) has been applied as a first-line treatment for symptomatic CD-associated strictures due to its minimally invasive nature and the possibility of preserving intestinal length. Objective The aim of the present study was to determine patient-related predictive factors associated with the need for surgery for CD-associated ileocolic strictures after technically successful EBD. Methods All original studies published before December 2023 that reported the outcomes of patients treated with EBD for ileocolic strictures secondary to CD and described follow-up for at least 1 year were included. The difference in risk of needing surgery was calculated for 8 different patient characteristics (Sex, smoking habit, previous surgery, biologic therapy, steroids, immunosuppressors, nature of the stricture, and endoscopic disease activity). Results There were significant differences in the risk of needing surgery after EBD among patients who underwent surgery and patients without a history of surgery (RD: -0.20 [-0.31, -0.08]), patients with endoscopic mucosal activity and patients in remission at the time of EBD (RD: 0.19 [0.04, 0.34]), patients using biologics at the time of EBD and patients not using biologics (RD: -0.09 [-0.16, -0.03]), and patients using steroids and those not using steroids at the time of EBD (RD: 0.16 [0.07, 0.26]). Conclusions The use of biologics and endoscopic disease remission at the time of EBD were protective factors against the need for surgery. No previous surgery or use of steroids at the time of EBD was associated with the need for surgery during follow-up.
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Affiliation(s)
- Hiram Menezes Nascimento Filho
- Gastrointestinal Endoscopy Unit, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Angelo So Taa Kum
- Gastrointestinal Endoscopy Unit, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Alexandre Moraes Bestetti
- Gastrointestinal Endoscopy Unit, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | | | - Megui Marilia Mansilla Gallegos
- Gastrointestinal Endoscopy Unit, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Adérson Omar Mourão Cintra Damião
- Department of Gastroenterology and Hepatology, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Udayakumar Navaneethan
- Orlando Health Digestive Health Institute Center for Advanced Endoscopy, Research and Education, Orlando, USA
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6
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Atreya R, Neurath MF. Biomarkers for Personalizing IBD Therapy: The Quest Continues. Clin Gastroenterol Hepatol 2024; 22:1353-1364. [PMID: 38320679 DOI: 10.1016/j.cgh.2024.01.026] [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: 08/30/2023] [Revised: 01/13/2024] [Accepted: 01/16/2024] [Indexed: 02/08/2024]
Abstract
Despite recent advances in the understanding of the pathogenesis of inflammatory bowel diseases (IBD) and advent of multiple targeted therapies, approximately one-third of patients are primary non-responders to initiated treatment, and half of patients lose response over time. There is currently a lack of available biomarkers that would prognosticate therapeutic effectiveness of these advanced therapies. This is partly explained by insufficient characterization of the functional roles assumed by the chosen molecular targets during disease treatment. There is a dire need for validated objective biomarkers, which could be indicators of a biological process, that can be applied in clinical practice to assist us in assigning therapies to patients with the highest probability of response. An appropriate molecular and cellular characterization that accounts for the interindividual differences in drug efficacy and potential side effects would help to guide clinicians in the management of patients with IBD and represent a major step to tailor a more personalized approach to treatment. An appropriate combination of complementing biomarkers should ideally incorporate a multimodal analysis in which genetic, microbial, transcriptional, proteomic, metabolic, and immunologic data are combined to enable a truly personalized approach. This would classify patients into disease subgroups according to molecular characteristics, which would enable us to initiate the most appropriate therapeutic substance. Emergence of single-cell technologies to map the intestinal cellular landscape and multiomic approaches have helped to further dissect the pathogenic mechanisms of mucosal inflammation, but the clinical translation of potential biomarkers remains cumbersome, and an ongoing concerted effort by the IBD community is required.
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Affiliation(s)
- Raja Atreya
- First Department of Medicine, Erlangen University Hospital, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany; Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany.
| | - Markus F Neurath
- First Department of Medicine, Erlangen University Hospital, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany; Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
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7
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Benvenuti L, Di Salvo C, Bellini G, Seguella L, Rettura F, Esposito G, Antonioli L, Ceravolo R, Bernardini N, Pellegrini C, Fornai M. Gut-directed therapy in Parkinson's disease. Front Pharmacol 2024; 15:1407925. [PMID: 38974034 PMCID: PMC11224490 DOI: 10.3389/fphar.2024.1407925] [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: 03/27/2024] [Accepted: 05/17/2024] [Indexed: 07/09/2024] Open
Abstract
Parkinson's disease (PD) is a common and slow-progressing neurodegenerative disorder characterized by motor and non-motor symptoms, including gastrointestinal (GI) dysfunctions. Over the last years, the microbiota-gut-brain (MGB) axis is emerging as a bacterial-neuro-immune ascending pathway that contributes to the progression of PD. Indeed, PD patients are characterized by changes in gut microbiota composition, alterations of intestinal epithelial barrier (IEB) and enteric neurogenic/inflammatory responses that, besides determining intestinal disturbances, contribute to brain pathology. In this context, despite the causal relationship between gut dysbiosis, impaired MGB axis and PD remains to be elucidated, emerging evidence shows that MGB axis modulation can represent a suitable therapeutical strategy for the treatment of PD. This review provides an overview of the available knowledge about the beneficial effects of gut-directed therapies, including dietary interventions, prebiotics, probiotics, synbiotics and fecal microbiota transplantation (FMT), in both PD patients and animal models. In this context, particular attention has been devoted to the mechanisms by which the modulation of MGB axis could halt or slow down PD pathology and, most importantly, how these approaches can be included in the clinical practice.
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Affiliation(s)
- Laura Benvenuti
- Unit of Pharmacology and Pharmacovigilance, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Clelia Di Salvo
- Unit of Pharmacology and Pharmacovigilance, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Gabriele Bellini
- Unit of Neurology, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Luisa Seguella
- Department of Physiology and Pharmacology “V.Erspamer”, Sapienza University of Rome, Rome, Italy
| | - Francesco Rettura
- Unit of Gastroenterology, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Giuseppe Esposito
- Department of Physiology and Pharmacology “V.Erspamer”, Sapienza University of Rome, Rome, Italy
| | - Luca Antonioli
- Unit of Pharmacology and Pharmacovigilance, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Roberto Ceravolo
- Unit of Neurology, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Nunzia Bernardini
- Unit of Histology and Medical Embryology, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Carolina Pellegrini
- Unit of Histology and Medical Embryology, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Matteo Fornai
- Unit of Pharmacology and Pharmacovigilance, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
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8
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Lange E, Kranert L, Krüger J, Benndorf D, Heyer R. Microbiome modeling: a beginner's guide. Front Microbiol 2024; 15:1368377. [PMID: 38962127 PMCID: PMC11220171 DOI: 10.3389/fmicb.2024.1368377] [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: 01/10/2024] [Accepted: 05/27/2024] [Indexed: 07/05/2024] Open
Abstract
Microbiomes, comprised of diverse microbial species and viruses, play pivotal roles in human health, environmental processes, and biotechnological applications and interact with each other, their environment, and hosts via ecological interactions. Our understanding of microbiomes is still limited and hampered by their complexity. A concept improving this understanding is systems biology, which focuses on the holistic description of biological systems utilizing experimental and computational methods. An important set of such experimental methods are metaomics methods which analyze microbiomes and output lists of molecular features. These lists of data are integrated, interpreted, and compiled into computational microbiome models, to predict, optimize, and control microbiome behavior. There exists a gap in understanding between microbiologists and modelers/bioinformaticians, stemming from a lack of interdisciplinary knowledge. This knowledge gap hinders the establishment of computational models in microbiome analysis. This review aims to bridge this gap and is tailored for microbiologists, researchers new to microbiome modeling, and bioinformaticians. To achieve this goal, it provides an interdisciplinary overview of microbiome modeling, starting with fundamental knowledge of microbiomes, metaomics methods, common modeling formalisms, and how models facilitate microbiome control. It concludes with guidelines and repositories for modeling. Each section provides entry-level information, example applications, and important references, serving as a valuable resource for comprehending and navigating the complex landscape of microbiome research and modeling.
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Affiliation(s)
- Emanuel Lange
- Multidimensional Omics Data Analysis, Department for Bioanalytics, Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany
- Graduate School Digital Infrastructure for the Life Sciences, Bielefeld Institute for Bioinformatics Infrastructure (BIBI), Faculty of Technology, Bielefeld University, Bielefeld, Germany
| | - Lena Kranert
- Institute for Automation Engineering, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Jacob Krüger
- Engineering of Software-Intensive Systems, Department of Mathematics and Computer Science, Eindhoven University of Technology, Eindhoven, Netherlands
| | - Dirk Benndorf
- Applied Biosciences and Bioprocess Engineering, Anhalt University of Applied Sciences, Köthen, Germany
| | - Robert Heyer
- Multidimensional Omics Data Analysis, Department for Bioanalytics, Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany
- Graduate School Digital Infrastructure for the Life Sciences, Bielefeld Institute for Bioinformatics Infrastructure (BIBI), Faculty of Technology, Bielefeld University, Bielefeld, Germany
- Multidimensional Omics Data Analysis, Faculty of Technology, Bielefeld University, Bielefeld, Germany
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9
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Zhang Z, Hu Y, Zhang N, Li J, Lu J, Wei H. Dietary supplementation with non-digestible isomaltooligosaccharide and Lactiplantibacillus plantarum ZDY2013 ameliorates DSS-induced colitis via modulating intestinal barrier integrity and the gut microbiota. Food Funct 2024; 15:5908-5920. [PMID: 38738338 DOI: 10.1039/d4fo00421c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Abstract
Non-digestible oligosaccharides have attracted attention due to their critical role in maintaining the balance of a host's gut microbiota. Lactiplantibacillus plantarum ZDY2013 was isolated from traditional fermented acid beans, which could metabolize many complex carbohydrates and had intestinal immunomodulatory effects. In our study, the ameliorative effect of a combination of non-digestible isomaltooligosaccharide (IMO) and L. plantarum ZDY2013 was investigated in dextran sulfate sodium (DSS)-induced colitis mice. The results showed that IMO could specifically promote L. plantarum ZDY2013 intestinal colonization after five days of gavage and ameliorate the symptoms of colitis (survival rate, DAI score, colon length, etc.) as well as colon tissue integrity. IMO combined with L. plantarum ZDY2013 increased the levels of intestinal tight junction proteins (ZO-1 and claudin) and mucin (MUC-2), followed by alleviation of inflammatory responses (decreased the expression of IL-1β, TNF-α, and IL-6 and increased the expression of IL-10 and IL-22) and the level of oxidative stress (decreased the level of COX-2 and iNOS and increased the expression of T-AOC and SOD). Furthermore, the combination increased the diversity of the gut microbiota and modulated the microbial structural component (decreased the abundance of Escherichia and Helicobacter and increased the abundance of Lactobacillus and SCFA-producing related species). Taken together, our results suggested that the consumption of IMO and L. plantarum ZDY2013 could improve the symptoms of colitis in mice by improving the intestinal barrier along with regulating the composition and metabolites of the gut microbiota.
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Affiliation(s)
- Zhihong Zhang
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China
- Sino-German Joint Research Institute, Nanchang University, 235 Nanjing East Road, Nanchang 330047, China.
- Chongqing Research Institute, Nanchang University, Chongqing 402660, China
| | - Yingsheng Hu
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China
| | - Na Zhang
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China
| | - Jinmei Li
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China
| | - Jinlin Lu
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China
| | - Hua Wei
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China
- Sino-German Joint Research Institute, Nanchang University, 235 Nanjing East Road, Nanchang 330047, China.
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10
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Syed S, Boland BS, Bourke LT, Chen LA, Churchill L, Dobes A, Greene A, Heller C, Jayson C, Kostiuk B, Moss A, Najdawi F, Plung L, Rioux JD, Rosen MJ, Torres J, Zulqarnain F, Satsangi J. Challenges in IBD Research 2024: Precision Medicine. Inflamm Bowel Dis 2024; 30:S39-S54. [PMID: 38778628 DOI: 10.1093/ibd/izae084] [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: 03/15/2024] [Indexed: 05/25/2024]
Abstract
Precision medicine is part of 5 focus areas of the Challenges in IBD Research 2024 research document, which also includes preclinical human IBD mechanisms, environmental triggers, novel technologies, and pragmatic clinical research. Building on Challenges in IBD Research 2019, the current Challenges aims to provide a comprehensive overview of current gaps in inflammatory bowel diseases (IBDs) research and deliver actionable approaches to address them with a focus on how these gaps can lead to advancements in interception, remission, and restoration for these diseases. The document is the result of multidisciplinary input from scientists, clinicians, patients, and funders, and represents a valuable resource for patient-centric research prioritization. In particular, the precision medicine section is focused on the main research gaps in elucidating how to bring the best care to the individual patient in IBD. Research gaps were identified in biomarker discovery and validation for predicting disease progression and choosing the most appropriate treatment for each patient. Other gaps were identified in making the best use of existing patient biosamples and clinical data, developing new technologies to analyze large datasets, and overcoming regulatory and payer hurdles to enable clinical use of biomarkers. To address these gaps, the Workgroup suggests focusing on thoroughly validating existing candidate biomarkers, using best-in-class data generation and analysis tools, and establishing cross-disciplinary teams to tackle regulatory hurdles as early as possible. Altogether, the precision medicine group recognizes the importance of bringing basic scientific biomarker discovery and translating it into the clinic to help improve the lives of IBD patients.
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Affiliation(s)
- Sana Syed
- Department of Pediatrics, University of Virginia, Charlottesville, VA, USA
- Patient representative for Crohn's & Colitis Foundation, New York, NY, USA
| | - Brigid S Boland
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Lauren T Bourke
- Precision Medicine Drug Development, Early Respiratory and Immunology, AstraZeneca, Boston, MA, USA
| | - Lea Ann Chen
- Division of Gastroenterology, Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Laurie Churchill
- Leona M. and Harry B. Helmsley Charitable Trust, New York, NY, USA
| | | | - Adam Greene
- Department of Pediatrics, University of Virginia, Charlottesville, VA, USA
| | | | | | | | - Alan Moss
- Crohn's & Colitis Foundation, New York, NY, USA
| | | | - Lori Plung
- Patient representative for Crohn's & Colitis Foundation, New York, NY, USA
| | - John D Rioux
- Research Center, Montreal Heart Institute, Université de Montréal, Montréal, Québec, Canada
| | - Michael J Rosen
- Division of Pediatric Gastroenterology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Joana Torres
- Division of Gastroenterology, Hospital Beatriz Ângelo, Hospital da Luz, Lisbon, Portugal
- Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Fatima Zulqarnain
- Department of Pediatrics, University of Virginia, Charlottesville, VA, USA
| | - Jack Satsangi
- Translational Gastroenterology Unit, Experimental Medicine Division, Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
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11
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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.
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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.
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12
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Stallmach A, Quickert S, Puta C, Reuken PA. The gastrointestinal microbiota in the development of ME/CFS: a critical view and potential perspectives. Front Immunol 2024; 15:1352744. [PMID: 38605969 PMCID: PMC11007072 DOI: 10.3389/fimmu.2024.1352744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 03/18/2024] [Indexed: 04/13/2024] Open
Abstract
Like other infections, a SARS-CoV-2 infection can also trigger Post-Acute Infection Syndromes (PAIS), which often progress into myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). ME/CFS, characterized by post-exercise malaise (PEM), is a severe multisystemic disease for which specific diagnostic markers or therapeutic concepts have not been established. Despite numerous indications of post-infectious neurological, immunological, endocrinal, and metabolic deviations, the exact causes and pathophysiology remain unclear. To date, there is a paucity of data, that changes in the composition and function of the gastrointestinal microbiota have emerged as a potential influencing variable associated with immunological and inflammatory pathways, shifts in ME/CFS. It is postulated that this dysbiosis may lead to intestinal barrier dysfunction, translocation of microbial components with increased oxidative stress, and the development or progression of ME/CFS. In this review, we detailed discuss the findings regarding alterations in the gastrointestinal microbiota and its microbial mediators in ME/CFS. When viewed critically, there is currently no evidence indicating causality between changes in the microbiota and the development of ME/CFS. Most studies describe associations within poorly defined patient populations, often combining various clinical presentations, such as irritable bowel syndrome and fatigue associated with ME/CFS. Nevertheless, drawing on analogies with other gastrointestinal diseases, there is potential to develop strategies aimed at modulating the gut microbiota and/or its metabolites as potential treatments for ME/CFS and other PAIS. These strategies should be further investigated in clinical trials.
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Affiliation(s)
- Andreas Stallmach
- Department of Internal Medicine IV (Gastroenterology, Hepatology, and Infectious Diseases), Jena University Hospital, Jena, Germany
| | - Stefanie Quickert
- Department of Internal Medicine IV (Gastroenterology, Hepatology, and Infectious Diseases), Jena University Hospital, Jena, Germany
| | - Christian Puta
- Department of Sports Medicine and Health Promotion, Friedrich-Schiller-University Jena, Jena, Germany
- Center for Sepsis Control and Care (CSCC), Jena University Hospital/Friedrich-Schiller-University Jena, Jena, Germany
- Center for Interdisciplinary Prevention of Diseases Related to Professional Activities, Jena, Germany
| | - Philipp A. Reuken
- Department of Internal Medicine IV (Gastroenterology, Hepatology, and Infectious Diseases), Jena University Hospital, Jena, Germany
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13
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Kumar M, Murugesan S, Ibrahim N, Elawad M, Al Khodor S. Predictive biomarkers for anti-TNF alpha therapy in IBD patients. J Transl Med 2024; 22:284. [PMID: 38493113 PMCID: PMC10943853 DOI: 10.1186/s12967-024-05058-1] [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: 01/11/2024] [Accepted: 03/04/2024] [Indexed: 03/18/2024] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic gastrointestinal condition characterized by severe gut inflammation, commonly presenting as Crohn's disease, ulcerative colitis or categorized as IBD- unclassified. While various treatments have demonstrated efficacy in adult IBD patients, the advent of anti-TNF therapies has significantly revolutionized treatment outcomes and clinical management. These therapies have played a pivotal role in achieving clinical and endoscopic remission, promoting mucosal healing, averting disease progression, and diminishing the necessity for surgery. Nevertheless, not all patients exhibit positive responses to these therapies, and some may experience a loss of responsiveness over time. This review aims to present a comprehensive examination of predictive biomarkers for monitoring the therapeutic response to anti-TNF therapy in IBD patients. It will explore their limitations and clinical utilities, paving the way for a more personalized and effective therapeutic approach.
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Affiliation(s)
- Manoj Kumar
- Research Department, Sidra Medicine, Doha, Qatar
| | | | - Nazira Ibrahim
- Division of Gastroenterology, Hepatology and Nutrition, Sidra Medicine, Doha, Qatar
| | - Mamoun Elawad
- Division of Gastroenterology, Hepatology and Nutrition, Sidra Medicine, Doha, Qatar
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14
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Sugihara K, Kamada N. Metabolic network of the gut microbiota in inflammatory bowel disease. Inflamm Regen 2024; 44:11. [PMID: 38443988 PMCID: PMC10913301 DOI: 10.1186/s41232-024-00321-w] [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: 12/07/2023] [Accepted: 02/07/2024] [Indexed: 03/07/2024] Open
Abstract
Gut dysbiosis is closely linked to the pathogenesis of inflammatory bowel disease (IBD). Emerging studies highlight the relationship between host metabolism and the modulation of gut microbiota composition through regulating the luminal microenvironment. In IBD, various disease-associated factors contribute to the significant perturbation of host metabolism. Such disturbance catalyzes the selective proliferation of specific microbial populations, particularly pathobionts such as adherent invasive Escherichia coli and oral-derived bacteria. Pathobionts employ various strategies to adapt better to the disease-associated luminal environments. In addition to the host-microbe interaction, recent studies demonstrate that the metabolic network between commensal symbionts and pathobionts facilitates the expansion of pathobionts in the inflamed gut. Understanding the metabolic network among the host, commensal symbionts, and pathobionts provides new insights into the pathogenesis of IBD and novel avenues for treating IBD.
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Affiliation(s)
- Kohei Sugihara
- WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan
| | - Nobuhiko Kamada
- WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan.
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, 1150 W. Medical Center Drive, Ann Arbor, MI, 48109, USA.
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA.
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15
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Caenepeel C, Falony G, Machiels K, Verstockt B, Goncalves PJ, Ferrante M, Sabino J, Raes J, Vieira-Silva S, Vermeire S. Dysbiosis and Associated Stool Features Improve Prediction of Response to Biological Therapy in Inflammatory Bowel Disease. Gastroenterology 2024; 166:483-495. [PMID: 38096956 DOI: 10.1053/j.gastro.2023.11.304] [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: 08/26/2021] [Revised: 11/13/2023] [Accepted: 11/25/2023] [Indexed: 01/09/2024]
Abstract
BACKGROUND & AIMS Dysbiosis of the gut microbiota is considered a key contributor to inflammatory bowel disease (IBD) etiology. Here, we investigated potential associations between microbiota composition and the outcomes to biological therapies. METHODS The study prospectively recruited 296 patients with active IBD (203 with Crohn's disease, 93 with ulcerative colitis) initiating biological therapy. Quantitative microbiome profiles of pretreatment and posttreatment fecal samples were obtained combining flow cytometry with 16S amplicon sequencing. Therapeutic response was assessed by endoscopy, patient-reported outcomes, and changes in fecal calprotectin. The effect of therapy on microbiome variation was evaluated using constrained ordination methods. Prediction of therapy outcome was performed using logistic regression with 5-fold cross-validation. RESULTS At baseline, 65.9% of patients carried the dysbiotic Bacteroides2 (Bact2) enterotype, with a significantly higher prevalence among patients with ileal involvement (76.8%). Microbiome variation was associated with the choice of biological therapy rather than with therapeutic outcome. Only anti-tumor necrosis factor-α treatment resulted in a microbiome shift away from Bact2, concomitant with an increase in microbial load and butyrogen abundances and a decrease in potentially opportunistic Veillonella. Remission rates for patients hosting Bact2 at baseline were significantly higher with anti-tumor necrosis factor-α than with vedolizumab (65.1% vs 35.2%). A prediction model, based on anthropometrics and clinical data, stool features (microbial load, moisture, and calprotectin), and Bact2 detection predicted treatment outcome with 73.9% accuracy for specific biological therapies. CONCLUSION Fecal characterization based on microbial load, moisture content, calprotectin concentration, and enterotyping may aid in the therapeutic choice of biological therapy in IBD.
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Affiliation(s)
- Clara Caenepeel
- Translational Research Center for Gastrointestinal Disorders (TARGID), Katholieke Universiteit Leuven, Leuven, Belgium; Department of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium
| | - Gwen Falony
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium; Center for Microbiology, Vlaams Instituut voor Biotechnologie (VIB), Leuven, Belgium; Institute of Medical Microbiology and Hygiene and Research Center for Immunotherapy (FZI), University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Kathleen Machiels
- Translational Research Center for Gastrointestinal Disorders (TARGID), Katholieke Universiteit Leuven, Leuven, Belgium; Pfizer Biopharmaceuticals, Brussels, Belgium
| | - Bram Verstockt
- Translational Research Center for Gastrointestinal Disorders (TARGID), Katholieke Universiteit Leuven, Leuven, Belgium; Department of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium
| | - Pedro J Goncalves
- Machine Learning in Science, Excellence Cluster "Machine Learning," Tübingen University, Tübingen, Germany
| | - Marc Ferrante
- Translational Research Center for Gastrointestinal Disorders (TARGID), Katholieke Universiteit Leuven, Leuven, Belgium; Department of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium
| | - João Sabino
- Translational Research Center for Gastrointestinal Disorders (TARGID), Katholieke Universiteit Leuven, Leuven, Belgium; Department of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium
| | - Jeroen Raes
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium; Center for Microbiology, Vlaams Instituut voor Biotechnologie (VIB), Leuven, Belgium
| | - Sara Vieira-Silva
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium; Institute of Medical Microbiology and Hygiene and Research Center for Immunotherapy (FZI), University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany; Institute of Molecular Biology (IMB), Mainz, Germany
| | - Séverine Vermeire
- Translational Research Center for Gastrointestinal Disorders (TARGID), Katholieke Universiteit Leuven, Leuven, Belgium; Department of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium.
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16
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Puca P, Capobianco I, Coppola G, Di Vincenzo F, Trapani V, Petito V, Laterza L, Pugliese D, Lopetuso LR, Scaldaferri F. Cellular and Molecular Determinants of Biologic Drugs Resistance and Therapeutic Failure in Inflammatory Bowel Disease. Int J Mol Sci 2024; 25:2789. [PMID: 38474034 DOI: 10.3390/ijms25052789] [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: 02/06/2024] [Revised: 02/22/2024] [Accepted: 02/26/2024] [Indexed: 03/14/2024] Open
Abstract
The advent of biologic drugs has revolutionized the treatment of Inflammatory Bowel Disease, increasing rates of response and mucosal healing in comparison to conventional therapies by allowing the treatment of corticosteroid-refractory cases and reducing corticosteroid-related side effects. However, biologic therapies (anti-TNFα inhibitors, anti-α4β7 integrin and anti-IL12/23) are still burdened by rates of response that hover around 40% (in biologic-naïve patients) or lower (for biologic-experienced patients). Moreover, knowledge of the mechanisms underlying drug resistance or loss of response is still scarce. Several cellular and molecular determinants are implied in therapeutic failure; genetic predispositions, in the form of single nucleotide polymorphisms in the sequence of cytokines or Human Leukocyte Antigen, or an altered expression of cytokines and other molecules involved in the inflammation cascade, play the most important role. Accessory mechanisms include gut microbiota dysregulation. In this narrative review of the current and most recent literature, we shed light on the mentioned determinants of therapeutic failure in order to pave the way for a more personalized approach that could help avoid unnecessary treatments and toxicities.
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Affiliation(s)
- Pierluigi Puca
- Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Ivan Capobianco
- Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Gaetano Coppola
- IBD Unit, UOC CEMAD Centro Malattie dell'Apparato Digerente, Dipartimento di Scienze Mediche e Chirurgiche Addominali ed Endocrino Metaboliche, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
| | - Federica Di Vincenzo
- Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Valentina Trapani
- Alleanza Contro il Cancro, Istituto Superiore di Sanità, 00144 Rome, Italy
| | - Valentina Petito
- IBD Unit, UOC CEMAD Centro Malattie dell'Apparato Digerente, Dipartimento di Scienze Mediche e Chirurgiche Addominali ed Endocrino Metaboliche, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
| | - Lucrezia Laterza
- IBD Unit, UOC CEMAD Centro Malattie dell'Apparato Digerente, Dipartimento di Scienze Mediche e Chirurgiche Addominali ed Endocrino Metaboliche, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
| | - Daniela Pugliese
- IBD Unit, UOC CEMAD Centro Malattie dell'Apparato Digerente, Dipartimento di Scienze Mediche e Chirurgiche Addominali ed Endocrino Metaboliche, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
| | - Loris Riccardo Lopetuso
- IBD Unit, UOC CEMAD Centro Malattie dell'Apparato Digerente, Dipartimento di Scienze Mediche e Chirurgiche Addominali ed Endocrino Metaboliche, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
- Department of Medicine and Ageing Sciences, "G. d'Annunzio" University of Chieti-Pescara, 66100 Chieti, Italy
- Center for Advanced Studies and Technology (CAST), "G. d'Annunzio" University of Chieti-Pescara, 66100 Chieti, Italy
| | - Franco Scaldaferri
- Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
- IBD Unit, UOC CEMAD Centro Malattie dell'Apparato Digerente, Dipartimento di Scienze Mediche e Chirurgiche Addominali ed Endocrino Metaboliche, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
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17
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Hu S, Bourgonje AR, Gacesa R, Jansen BH, Björk JR, Bangma A, Hidding IJ, van Dullemen HM, Visschedijk MC, Faber KN, Dijkstra G, Harmsen HJM, Festen EAM, Vich Vila A, Spekhorst LM, Weersma RK. Mucosal host-microbe interactions associate with clinical phenotypes in inflammatory bowel disease. Nat Commun 2024; 15:1470. [PMID: 38368394 PMCID: PMC10874382 DOI: 10.1038/s41467-024-45855-2] [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: 01/12/2023] [Accepted: 02/05/2024] [Indexed: 02/19/2024] Open
Abstract
Disrupted host-microbe interactions at the mucosal level are key to the pathophysiology of IBD. This study aimed to comprehensively examine crosstalk between mucosal gene expression and microbiota in patients with IBD. To study tissue-specific interactions, we perform transcriptomic (RNA-seq) and microbial (16S-rRNA-seq) profiling of 697 intestinal biopsies (645 derived from 335 patients with IBD and 52 from 16 non-IBD controls). Mucosal gene expression patterns in IBD are mainly determined by tissue location and inflammation, whereas the mucosal microbiota composition shows a high degree of individual specificity. Analysis of transcript-bacteria interactions identifies six distinct groups of inflammation-related pathways that are associated with intestinal microbiota (adjusted P < 0.05). An increased abundance of Bifidobacterium is associated with higher expression of genes involved in fatty acid metabolism, while Bacteroides correlates with increased metallothionein signaling. In patients with fibrostenosis, a transcriptional network dominated by immunoregulatory genes is associated with Lachnoclostridium bacteria in non-stenotic tissue (adjusted P < 0.05), while being absent in CD without fibrostenosis. In patients using TNF-α-antagonists, a transcriptional network dominated by fatty acid metabolism genes is linked to Ruminococcaceae (adjusted P < 0.05). Mucosal microbiota composition correlates with enrichment of intestinal epithelial cells, macrophages, and NK-cells. Overall, these data demonstrate the presence of context-specific mucosal host-microbe interactions in IBD, revealing significantly altered inflammation-associated gene-taxa modules, particularly in patients with fibrostenotic CD and patients using TNF-α-antagonists. This study provides compelling insights into host-microbe interactions that may guide microbiota-directed precision medicine and fuels the rationale for microbiota-targeted therapeutics as a strategy to alter disease course in IBD.
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Affiliation(s)
- Shixian Hu
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Institute of Precision Medicine, the First Affiliated Hospital of Sun Yat-Sen University, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Arno R Bourgonje
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Ranko Gacesa
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Bernadien H Jansen
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Johannes R Björk
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Amber Bangma
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Iwan J Hidding
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Hendrik M van Dullemen
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Marijn C Visschedijk
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Klaas Nico Faber
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Gerard Dijkstra
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Hermie J M Harmsen
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Eleonora A M Festen
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Arnau Vich Vila
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Lieke M Spekhorst
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Gastroenterology and Hepatology, Medisch Spectrum Twente, Enschede, the Netherlands
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
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18
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Jiang L, Liu X, Su Y, Chen Y, Yang S, Ke X, Yao K, Guo Z. A metabolomics-driven model for early remission prediction following vedolizumab treatment in patients with moderate-to-severe active ulcerative colitis. Int Immunopharmacol 2024; 128:111527. [PMID: 38215655 DOI: 10.1016/j.intimp.2024.111527] [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: 10/24/2023] [Revised: 01/06/2024] [Accepted: 01/07/2024] [Indexed: 01/14/2024]
Abstract
To predict early remission following anti-integrin therapy (vedolizumab [VDZ]) in patients with moderate-to-severe active ulcerative colitis (UC) using non-invasive biomarkers. The clinical data of a cohort of 33 patients with moderate-to-severe active UC admitted to the Department of Gastroenterology at Suzhou Municipal Hospital between January 2021 and December 2022 were collected. Of these, 9 patients declined VDZ treatment, and 21 received VDZ at doses of 300 mg weeks 0, 2, and 6, each administered within a 30-minute infusion period. The treatment regimen aimed to induce remission of clinical symptoms; hence, the same dose was administered every 8 weeks. At weeks 0 and 14, serum C-reactive protein (CRP) and erythrocyte sedimentation rate were measured using a modified Mayo score. In addition to clinical assessment, stool samples at baseline and weeks 14 were collected and evaluated using 16SrRNA gene sequencing and gas chromatography-mass spectrometry (GC-MS). Clinical remission was determined based on the clinical symptoms and partial Mayo scores. In patients who received VDZ, the strains of bifidobacterium longum (P = 0.022) and bacteroides sartorii (P = 0.039) significantly increased after treatment than before treatment. GC-MS analysis showed that taurine (P = 0.047) and putrescine (P = 0.035) significantly decreased after treatment. Furthermore, while acetamide exhibited a notable increase (P = 0.001), arachidic acid (P < 0.001) and behenic acid (P = 0.005) demonstrated statistically significant elevations. The combined prediction model of acetamide, taurine, and putrescine demonstrated a high predictive value of early remission in patients with moderate-to-severe active UC following VDZ treatment (area under the curve = 0.911, P = 0.014).
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Affiliation(s)
- Leilei Jiang
- Department of Gastroenterology, Suzhou Hospital of Anhui Medical University (Suzhou Municipal Hospital of Anhui Province), No. 616 Bianyangsan Road, Suzhou 234000, Anhui, China
| | - Xiaoming Liu
- Department of Gastroenterology, Huaihe Hospital of Henan University, 115 Ximen Street, Kaifeng 475000, Henan, China
| | - Yue Su
- Department of Gastroenterology, Suzhou Hospital of Anhui Medical University (Suzhou Municipal Hospital of Anhui Province), No. 616 Bianyangsan Road, Suzhou 234000, Anhui, China
| | - Yujie Chen
- Department of Gastroenterology, Suzhou Hospital of Anhui Medical University (Suzhou Municipal Hospital of Anhui Province), No. 616 Bianyangsan Road, Suzhou 234000, Anhui, China
| | - Shaozhi Yang
- Department of Gastroenterology, Suzhou Hospital of Anhui Medical University (Suzhou Municipal Hospital of Anhui Province), No. 616 Bianyangsan Road, Suzhou 234000, Anhui, China
| | - Xiquan Ke
- Department of Gastroenterology, The First Affiliated Hospital of Bengbu Medical College, No. 287 Changhuai Road, Bengbu, Anhui 233004, China.
| | - Kunhou Yao
- Department of General Surgery, Huaihe Hospital of Henan University, 115 Ximen Street, Kaifeng 475000, Henan, China.
| | - Zhiguo Guo
- Department of Gastroenterology, Suzhou Hospital of Anhui Medical University (Suzhou Municipal Hospital of Anhui Province), No. 616 Bianyangsan Road, Suzhou 234000, Anhui, China.
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19
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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.
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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
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20
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Hurych J, Mascellani Bergo A, Lerchova T, Hlinakova L, Kubat M, Malcova H, Cebecauerova D, Schwarz J, Karaskova E, Hecht T, Vyhnanek R, Toukalkova L, Dotlacil V, Greinerova K, Cizkova A, Horvath R, Bronsky J, Havlik J, Hradsky O, Cinek O. Faecal Bacteriome and Metabolome Profiles Associated with Decreased Mucosal Inflammatory Activity Upon Anti-TNF Therapy in Paediatric Crohn's Disease. J Crohns Colitis 2024; 18:106-120. [PMID: 37527838 PMCID: PMC10821711 DOI: 10.1093/ecco-jcc/jjad126] [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: 12/22/2022] [Indexed: 08/03/2023]
Abstract
BACKGROUND AND AIMS Treatment with anti-tumour necrosis factor α antibodies [anti-TNF] changes the dysbiotic faecal bacteriome in Crohn's disease [CD]. However, it is not known whether these changes are due to decreasing mucosal inflammatory activity or whether similar bacteriome reactions might be observed in gut-healthy subjects. Therefore, we explored changes in the faecal bacteriome and metabolome upon anti-TNF administration [and therapeutic response] in children with CD and contrasted those to anti-TNF-treated children with juvenile idiopathic arthritis [JIA]. METHODS Faecal samples collected longitudinally before and during anti-TNF therapy were analysed with regard to the bacteriome by massively parallel sequencing of the 16S rDNA [V4 region] and the faecal metabolome by 1H nuclear magnetic resonance imaging. The response to treatment by mucosal healing was assessed by the MINI index at 3 months after the treatment started. We also tested several representative gut bacterial strains for in vitro growth inhibition by infliximab. RESULTS We analysed 530 stool samples from 121 children [CD 54, JIA 18, healthy 49]. Bacterial community composition changed on anti-TNF in CD: three members of the class Clostridia increased on anti-TNF, whereas the class Bacteroidia decreased. Among faecal metabolites, glucose and glycerol increased, whereas isoleucine and uracil decreased. Some of these changes differed by treatment response [mucosal healing] after anti-TNF. No significant changes in the bacteriome or metabolome were noted upon anti-TNF in JIA. Bacterial growth was not affected by infliximab in a disc diffusion test. CONCLUSIONS Our findings suggest that gut mucosal healing is responsible for the bacteriome and metabolome changes observed in CD, rather than any general effect of anti-TNF.
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Affiliation(s)
- Jakub Hurych
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czechia
- Department of Paediatrics, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czechia
| | - Anna Mascellani Bergo
- Department of Food Science, Faculty of Agrobiology, Food and Natural Resources, Czech Univesity of Life Sciences, Prague, Czechia
| | - Tereza Lerchova
- Department of Paediatrics, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czechia
| | - Lucie Hlinakova
- Department of Paediatrics, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czechia
| | - Michal Kubat
- Department of Paediatrics, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czechia
| | - Hana Malcova
- Department of Pediatric and Adult Rheumatology, Motol University Hospital, Prague, Czechia
| | - Dita Cebecauerova
- Department of Pediatric and Adult Rheumatology, Motol University Hospital, Prague, Czechia
| | - Jan Schwarz
- Department of Paediatrics, Faculty of Medicine in Pilsen, Charles University and University Hospital Pilsen, Czechia
| | - Eva Karaskova
- Department of Paediatrics, Faculty of Medicine, Palacky University Olomouc and University Hospital Olomouc, Czechia
| | - Tomas Hecht
- Department of Paediatrics, 1st Faculty of Medicine, Charles University and Thomayer University Hospital, Prague, Czechia
| | - Radim Vyhnanek
- Department of Paediatrics, 1st Faculty of Medicine, Charles University and Thomayer University Hospital, Prague, Czechia
| | | | - Vojtech Dotlacil
- Department of Paediatric Surgery, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czechia
| | | | | | - Rudolf Horvath
- Department of Pediatric and Adult Rheumatology, Motol University Hospital, Prague, Czechia
| | - Jiri Bronsky
- Department of Paediatrics, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czechia
| | - Jaroslav Havlik
- Department of Food Science, Faculty of Agrobiology, Food and Natural Resources, Czech Univesity of Life Sciences, Prague, Czechia
| | - Ondrej Hradsky
- Department of Paediatrics, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czechia
| | - Ondrej Cinek
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czechia
- Department of Paediatrics, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czechia
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21
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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.
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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
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22
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Zhu J, Yin J, Chen J, Hu M, Lu W, Wang H, Zhang H, Chen W. Integrative analysis with microbial modelling and machine learning uncovers potential alleviators for ulcerative colitis. Gut Microbes 2024; 16:2336877. [PMID: 38563656 PMCID: PMC10989691 DOI: 10.1080/19490976.2024.2336877] [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: 11/07/2023] [Accepted: 03/27/2024] [Indexed: 04/04/2024] Open
Abstract
Ulcerative colitis (UC) is a challenging form of inflammatory bowel disease, and its etiology is intricately linked to disturbances in the gut microbiome. To identify the potential alleviators of UC, we employed an integrative analysis combining microbial community modeling with advanced machine learning techniques. Using metagenomics data sourced from the Integrated Human Microbiome Project, we constructed individualized microbiome community models for each participant. Our analysis highlighted a significant decline in both α and β-diversity of strain-level microbial populations in UC subjects compared to controls. Distinct differences were also observed in the predicted fecal metabolite profiles and strain-to-metabolite contributions between the two groups. Using tree-based machine learning models, we successfully identified specific microbial strains and their associated metabolites as potential alleviators of UC. Notably, our experimental validation using a dextran sulfate sodium-induced UC mouse model demonstrated that the administration of Parabacteroides merdae ATCC 43,184 and N-acetyl-D-mannosamine provided notable relief from colitis symptoms. In summary, our study underscores the potential of an integrative approach to identify novel therapeutic avenues for UC, paving the way for future targeted interventions.
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Affiliation(s)
- Jinlin Zhu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Jialin Yin
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Jing Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Mingyi Hu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Wenwei Lu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
- International Joint Research Laboratory for Pharmabiotics & Antibiotic Resistance, Jiangnan University, Wuxi, China
- (Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou, China
| | - Hongchao Wang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
- (Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, China
- Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch, Wuxi People’s Hospital, Wuxi, China
| | - Wei Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, China
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23
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Troci A, Rausch P, Waschina S, Lieb W, Franke A, Bang C. Long-Term Dietary Effects on Human Gut Microbiota Composition Employing Shotgun Metagenomics Data Analysis. Mol Nutr Food Res 2023; 67:e2101098. [PMID: 35760036 DOI: 10.1002/mnfr.202101098] [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: 12/03/2021] [Revised: 04/21/2022] [Indexed: 11/11/2022]
Abstract
SCOPE The gut microbiome regulates various metabolic pathways in the host and its dysbiosis is involved in the pathogenesis of diverse diseases. One of the major factors triggering gut microbiome establishment is diet. This study aims to unravel interactions and changes between diet and gut microbiome over a period of 3 years. METHODS AND RESULTS This study investigates the relation between diet and the microbiome of 75 individuals over a 3-year time period. Shotgun metagenomic sequencing is performed to profile gut microbial composition and function. This study shows that there are significant changes in gut microbiome taxonomy and functional composition between two time points. Whereas microbial taxonomy is found to be highly individualized, overall microbial functions stay relatively stable. Moreover, in silico metabolic modeling of microbial communities indicates that changes in dietary intake of medium-chain saturated fatty acids is accompanied by an altered utilization of amino acids by the gut microbiome. CONCLUSION The study design allows us to validate functional stability within the gut microbiome of healthy subjects over a 3-year period. However, enduring changes in nutrition such as increased alcohol consumption or decreased intake of vegetables come along with enhanced microbial functions that are associated with disease etiology.
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Affiliation(s)
- Alba Troci
- Institute of Clinical Molecular Biology, Kiel University, 24105, Kiel, Germany
| | - Philipp Rausch
- Institute of Clinical Molecular Biology, Kiel University, 24105, Kiel, Germany
| | - Silvio Waschina
- Institute of Human Nutrition and Food Science, Kiel University, 24118, Kiel, Germany
| | - Wolfgang Lieb
- Institute of Epidemiology, Kiel University, 24105, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, 24105, Kiel, Germany
| | - Corinna Bang
- Institute of Clinical Molecular Biology, Kiel University, 24105, Kiel, Germany
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24
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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.
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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
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25
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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.
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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.
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26
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Rimmer P, Iqbal T. Prognostic modelling in IBD. Best Pract Res Clin Gastroenterol 2023; 67:101877. [PMID: 38103929 DOI: 10.1016/j.bpg.2023.101877] [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: 11/16/2023] [Accepted: 11/24/2023] [Indexed: 12/19/2023]
Abstract
In the ideal world prognostication or predicting disease course in any chronic condition would allow the clinician to anticipate disease behaviour, providing crucial information for the patient and data regarding best use of resources. Prognostication also allows an understanding of likely response to treatment and the risk of adverse effects of a treatment leading to withdrawal in any individual patient. Therefore, the ability to predict outcomes from the onset of disease is the key step to developing precision personalised medicine, which is the design of medical care to optimise efficiency or therapeutic benefit based on careful profiling of patients. An important corollary is to prevent unnecessary healthcare costs. This paper outlines currently available predictors of disease outcome in IBD and looks to the future which will involve the use of artificial intelligence to interrogate big data derived from various important 'omes' to tease out a more holistic approach to IBD.
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Affiliation(s)
- Peter Rimmer
- Queen Elizabeth Hospital Birmingham, B15 2TH, UK; University of Birmingham, College of Medical and Dental Science, UK.
| | - Tariq Iqbal
- Queen Elizabeth Hospital Birmingham, B15 2TH, UK; University of Birmingham, College of Medical and Dental Science, UK.
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27
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Wang D, Wang J, Wu Y, Liu C, Huang Y, Chen Y, Ding Z, Guan Y, Wu Q. Amelioration of Acute Alcoholic Liver Injury via Attenuating Oxidative Damage and Modulating Inflammation by Means of Ursodeoxycholic Acid-Zein Nanoparticles. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:17080-17096. [PMID: 38104279 DOI: 10.1021/acs.jafc.3c04786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Ursodeoxycholic acid (UDCA) has been broadly adopted for the clinical treatment of hepatic and biliary diseases; however, its poor water-solubility becomes an obstacle in wide applications. To overcome these challenges, herein, a two-tier UDCA-embedded system of zein nanoparticles (NPs) along with a polyelectrolyte complex was designed under facile conditions. Both the UDCA-zein NPs and their inclusion microcapsules showed a spherical shape with a uniform size. A typical wall plus capsule/core structure was formed in which UDCA-zein NPs distributed evenly in the interior. The UDCA inclusion microcapsules had an encapsulation rate of 67% and were released in a non-Fickian or anomalous transport manner. The bioavailability and efficacy of UDCA-zein NPs were assessed in vivo through the alcoholic liver disease (ALD) mouse model via intragastric administration. UDCA-zein NPs ameliorated the symptoms of ALD mice remarkably, which were mainly exerted through attenuation of antioxidant stress levels. Meanwhile, it notably upregulated the intestinal tight junction protein expression and improved and maintained the integrity of the mucosal barrier effectively. Collectively, with the improvement of bioavailability, the UDCA-zein NPs prominently alleviated the oxidative damage induced by alcohol, modulating the inflammation so as to restore ALD. It is anticipated that UDCA-zein NPs have great therapeutic potential as sustained-nanovesicles in ALD treatment.
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Affiliation(s)
- Dong Wang
- School of Life Sciences, Key Laboratory of Eco-engineering and Biotechnology of Anhui Province and Anhui Key Laboratory of Modern Biomanufacturing, Anhui University, Hefei 230601, Anhui, PR China
| | - Jing Wang
- School of Life Sciences, Key Laboratory of Eco-engineering and Biotechnology of Anhui Province and Anhui Key Laboratory of Modern Biomanufacturing, Anhui University, Hefei 230601, Anhui, PR China
| | - Yingchao Wu
- School of Life Sciences, Key Laboratory of Eco-engineering and Biotechnology of Anhui Province and Anhui Key Laboratory of Modern Biomanufacturing, Anhui University, Hefei 230601, Anhui, PR China
| | - Caixia Liu
- School of Life Sciences, Key Laboratory of Eco-engineering and Biotechnology of Anhui Province and Anhui Key Laboratory of Modern Biomanufacturing, Anhui University, Hefei 230601, Anhui, PR China
| | - Yuzhe Huang
- School of Life Sciences, Key Laboratory of Eco-engineering and Biotechnology of Anhui Province and Anhui Key Laboratory of Modern Biomanufacturing, Anhui University, Hefei 230601, Anhui, PR China
| | - Yan Chen
- School of Life Sciences, Key Laboratory of Eco-engineering and Biotechnology of Anhui Province and Anhui Key Laboratory of Modern Biomanufacturing, Anhui University, Hefei 230601, Anhui, PR China
| | - Zhifeng Ding
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Yixin Guan
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, China
| | - Qingxi Wu
- School of Life Sciences, Key Laboratory of Eco-engineering and Biotechnology of Anhui Province and Anhui Key Laboratory of Modern Biomanufacturing, Anhui University, Hefei 230601, Anhui, PR China
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28
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Nie D, Li C, Zhang Y. PitNETs and the gut microbiota: potential connections, future directions. Front Endocrinol (Lausanne) 2023; 14:1255911. [PMID: 38027221 PMCID: PMC10657991 DOI: 10.3389/fendo.2023.1255911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 10/20/2023] [Indexed: 12/01/2023] Open
Abstract
The role of the gut microbiome has been widely discussed in numerous works of literature. The biggest concern is the association of the gut microbiome with the central nervous system through the microbiome-brain-gut axis in the past ten years. As more and more research has been done on the relationship between the disease of the central nervous system and gut microbes. This fact is being revealed that gut microbes seem to play an important role from the onset and progression of the disease to clinical symptoms, and new treatments. As a special tumor of the central nervous system, pituitary neuroendocrine tumors (PitNETs)are closely related to metabolism, endocrinology, and immunity. These factors are the vectors through which intestinal microbes interact with the central nervous system. However, little is known about the effects of gut microbes on the PitNET. In this review, the relationship of gut microbiota in PitNETs is introduced, the potential effects of the gut-brain axis in this relationship are analyzed, and future research directions are presented.
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Affiliation(s)
| | | | - Yazhuo Zhang
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
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29
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Cignarella A, Vegeto E, Bolego C, Trabace L, Conti L, Ortona E. Sex-oriented perspectives in immunopharmacology. Pharmacol Res 2023; 197:106956. [PMID: 37820857 DOI: 10.1016/j.phrs.2023.106956] [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: 08/07/2023] [Revised: 09/27/2023] [Accepted: 10/08/2023] [Indexed: 10/13/2023]
Abstract
Several immunopharmacological agents are effective in the treatment of cancer and immune-mediated conditions, with a favorable impact on life expectancy and clinical outcomes for a large number of patients. Nevertheless, response variation and undesirable effects of these drugs represent major issues, and overall efficacy remains unpredictable. Males and females show a distinct difference in immune system responses, with females generally mounting stronger responses to a variety of stimuli. Therefore, exploring sex differences in the efficacy and safety of immunopharmacological agents would strengthen the practice of precision medicine. As a pharmacological target highlight, programmed cell death 1 ligand 1 (PD-L1) is the first functionally characterized ligand of the coinhibitory programmed death receptor 1 (PD-1). The PD-L1/PD-1 crosstalk plays an important role in the immune response and is relevant in cancer, infectious and autoimmune disease. Sex differences in the response to immune checkpoint inhibitors are well documented, with male patients responding better than female patients. Similarly, higher efficacy of and adherence to tumor necrosis factor inhibitors in chronic inflammatory conditions including rheumatoid arthritis and Crohn's disease have been reported in male patients. The pharmacological basis of sex-specific responses to immune system modulating drugs is actively investigated in other settings such as stroke and type 1 diabetes. Advances in therapeutics targeting the endothelium could soon be wielded against autoimmunity and metabolic disorders. Based on the established sexual dimorphism in immune-related pathophysiology and disease presentation, sex-specific immunopharmacological protocols should be integrated into clinical guidelines.
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Affiliation(s)
| | - Elisabetta Vegeto
- Department of Pharmaceutical Sciences, University of Milan, Milan, Italy
| | - Chiara Bolego
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
| | - Luigia Trabace
- Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - Lucia Conti
- Center for Gender-Specific Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Elena Ortona
- Center for Gender-Specific Medicine, Istituto Superiore di Sanità, Rome, Italy
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30
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Li J, Ji Y, Chen N, Dai L, Deng H. Colitis-associated carcinogenesis: crosstalk between tumors, immune cells and gut microbiota. Cell Biosci 2023; 13:194. [PMID: 37875976 PMCID: PMC10594787 DOI: 10.1186/s13578-023-01139-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 09/21/2023] [Indexed: 10/26/2023] Open
Abstract
Colorectal cancer (CRC) is the third most common cancer worldwide. One of the main causes of colorectal cancer is inflammatory bowel disease (IBD), which includes ulcerative colitis (UC) and Crohn's disease (CD). Intestinal epithelial cells (IECs), intestinal mesenchymal cells (IMCs), immune cells, and gut microbiota construct the main body of the colon and maintain colon homeostasis. In the development of colitis and colitis-associated carcinogenesis, the damage, disorder or excessive recruitment of different cells such as IECs, IMCs, immune cells and intestinal microbiota play different roles during these processes. This review aims to discuss the various roles of different cells and the crosstalk of these cells in transforming intestinal inflammation to cancer, which provides new therapeutic methods for chemotherapy, targeted therapy, immunotherapy and microbial therapy.
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Affiliation(s)
- Junshu Li
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Ke Yuan Road 4, No. 1 Gao Peng Street, Chengdu, 610041, China
| | - Yanhong Ji
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Ke Yuan Road 4, No. 1 Gao Peng Street, Chengdu, 610041, China
| | - Na Chen
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Ke Yuan Road 4, No. 1 Gao Peng Street, Chengdu, 610041, China
| | - Lei Dai
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Ke Yuan Road 4, No. 1 Gao Peng Street, Chengdu, 610041, China.
| | - Hongxin Deng
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Ke Yuan Road 4, No. 1 Gao Peng Street, Chengdu, 610041, China.
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31
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Yan D, Ye S, He Y, Wang S, Xiao Y, Xiang X, Deng M, Luo W, Chen X, Wang X. Fatty acids and lipid mediators in inflammatory bowel disease: from mechanism to treatment. Front Immunol 2023; 14:1286667. [PMID: 37868958 PMCID: PMC10585177 DOI: 10.3389/fimmu.2023.1286667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 09/25/2023] [Indexed: 10/24/2023] Open
Abstract
Inflammatory Bowel Disease (IBD) is a chronic, relapsing inflammatory disorder of the gastrointestinal tract. Though the pathogenesis of IBD remains unclear, diet is increasingly recognized as a pivotal factor influencing its onset and progression. Fatty acids, essential components of dietary lipids, play diverse roles in IBD, ranging from anti-inflammatory and immune-regulatory functions to gut-microbiota modulation and barrier maintenance. Short-chain fatty acids (SCFAs), products of indigestible dietary fiber fermentation by gut microbiota, have strong anti-inflammatory properties and are seen as key protective factors against IBD. Among long-chain fatty acids, saturated fatty acids, trans fatty acids, and ω-6 polyunsaturated fatty acids exhibit pro-inflammatory effects, while oleic acid and ω-3 polyunsaturated fatty acids display anti-inflammatory actions. Lipid mediators derived from polyunsaturated fatty acids serve as bioactive molecules, influencing immune cell functions and offering both pro-inflammatory and anti-inflammatory benefits. Recent research has also highlighted the potential of medium- and very long-chain fatty acids in modulating inflammation, mucosal barriers, and gut microbiota in IBD. Given these insights, dietary intervention and supplementation with short-chain fatty acids are emerging as potential therapeutic strategies for IBD. This review elucidates the impact of various fatty acids and lipid mediators on IBD and delves into potential therapeutic avenues stemming from these compounds.
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Affiliation(s)
- Dong Yan
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Shuyu Ye
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Non-Resolving Inflammation and Cancer, Cancer Research Institute, Central South University, Changsha, China
| | - Yue He
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Sidan Wang
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Non-Resolving Inflammation and Cancer, Cancer Research Institute, Central South University, Changsha, China
| | - Yi Xiao
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Non-Resolving Inflammation and Cancer, Cancer Research Institute, Central South University, Changsha, China
| | - Xin Xiang
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Minzi Deng
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Non-Resolving Inflammation and Cancer, Cancer Research Institute, Central South University, Changsha, China
| | - Weiwei Luo
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Non-Resolving Inflammation and Cancer, Cancer Research Institute, Central South University, Changsha, China
| | - Xuejie Chen
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Non-Resolving Inflammation and Cancer, Cancer Research Institute, Central South University, Changsha, China
| | - Xiaoyan Wang
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Non-Resolving Inflammation and Cancer, Cancer Research Institute, Central South University, Changsha, China
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32
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Heinken A, Hulshof TO, Nap B, Martinelli F, Basile A, O'Brolchain A, O’Sullivan NF, Gallagher C, Magee E, McDonagh F, Lalor I, Bergin M, Evans P, Daly R, Farrell R, Delaney RM, Hill S, McAuliffe SR, Kilgannon T, Fleming RM, Thinnes CC, Thiele I. APOLLO: A genome-scale metabolic reconstruction resource of 247,092 diverse human microbes spanning multiple continents, age groups, and body sites. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.02.560573. [PMID: 37873072 PMCID: PMC10592896 DOI: 10.1101/2023.10.02.560573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Computational modelling of microbiome metabolism has proved instrumental to catalyse our understanding of diet-host-microbiome-disease interactions through the interrogation of mechanistic, strain- and molecule-resolved metabolic models. We present APOLLO, a resource of 247,092 human microbial genome-scale metabolic reconstructions spanning 19 phyla and accounting for microbial genomes from 34 countries, all age groups, and five body sites. We explored the metabolic potential of the reconstructed strains and developed a machine learning classifier able to predict with high accuracy the taxonomic strain assignments. We also built 14,451 sample-specific microbial community models, which could be stratified by body site, age, and disease states. Finally, we predicted faecal metabolites enriched or depleted in gut microbiomes of people with Crohn's disease, Parkinson disease, and undernourished children. APOLLO is compatible with the human whole-body models, and thus, provide unprecedented opportunities for systems-level modelling of personalised host-microbiome co-metabolism. APOLLO will be freely available under https://www.vmh.life/.
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Affiliation(s)
- Almut Heinken
- School of Medicine, University of Galway, Galway, Ireland
- Ryan Institute, University of Galway, Galway, Ireland
- Inserm UMRS 1256 NGERE, University of Lorraine, Nancy, France
| | - Timothy Otto Hulshof
- School of Medicine, University of Galway, Galway, Ireland
- Ryan Institute, University of Galway, Galway, Ireland
| | - Bram Nap
- School of Medicine, University of Galway, Galway, Ireland
- Ryan Institute, University of Galway, Galway, Ireland
| | - Filippo Martinelli
- School of Medicine, University of Galway, Galway, Ireland
- Ryan Institute, University of Galway, Galway, Ireland
| | - Arianna Basile
- School of Medicine, University of Galway, Galway, Ireland
- Department of Biology, University of Padova, Padova, Italy
| | | | | | | | | | | | - Ian Lalor
- University of Galway, Galway, Ireland
| | | | | | | | | | | | | | | | | | | | - Cyrille C. Thinnes
- School of Medicine, University of Galway, Galway, Ireland
- Ryan Institute, University of Galway, Galway, Ireland
| | - Ines Thiele
- School of Medicine, University of Galway, Galway, Ireland
- Ryan Institute, University of Galway, Galway, Ireland
- Division of Microbiology, University of Galway, Galway, Ireland
- APC Microbiome Ireland, Cork, Ireland
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33
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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.
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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
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34
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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.
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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
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35
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Effenberger M, Waschina S, Bronowski C, Sturm G, Tassiello O, Sommer F, Zollner A, Watschinger C, Grabherr F, Gstir R, Grander C, Enrich B, Bale R, Putzer D, Djanani A, Moschen AR, Zoller H, Rupp J, Schreiber S, Burcelin R, Lass-Flörl C, Trajanoski Z, Oberhuber G, Rosenstiel P, Adolph TE, Aden K, Tilg H. A gut bacterial signature in blood and liver tissue characterizes cirrhosis and hepatocellular carcinoma. Hepatol Commun 2023; 7:e00182. [PMID: 37314752 DOI: 10.1097/hc9.0000000000000182] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 04/18/2023] [Indexed: 06/15/2023] Open
Abstract
BACKGROUND HCC is the leading cause of cancer in chronic liver disease. A growing body of experimental mouse models supports the notion that gut-resident and liver-resident microbes control hepatic immune responses and, thereby, crucially contribute to liver tumorigenesis. However, a comprehensive characterization of the intestinal microbiome in fueling the transition from chronic liver disease to HCC in humans is currently missing. METHODS Here, we profiled the fecal, blood, and liver tissue microbiome of patients with HCC by 16S rRNA sequencing and compared profiles to nonmalignant cirrhotic and noncirrhotic NAFLD patients. RESULTS We report a distinct bacterial profile, defined from 16S rRNA gene sequences, with reduced α-and β-diversity in the feces of patients with HCC and cirrhosis compared to NAFLD. Patients with HCC and cirrhosis exhibited an increased proportion of fecal bacterial gene signatures in the blood and liver compared to NAFLD. Differential analysis of the relative abundance of bacterial genera identified an increased abundance of Ruminococcaceae and Bacteroidaceae in blood and liver tissue from both HCC and cirrhosis patients compared to NAFLD. Fecal samples from cirrhosis and HCC patients both showed a reduced abundance for several taxa, including short-chain fatty acid-producing genera, such as Blautia and Agathobacter. Using paired 16S rRNA and transcriptome sequencing, we identified a direct association between gut bacterial genus abundance and host transcriptome response within the liver tissue. CONCLUSIONS Our study indicates perturbations of the intestinal and liver-resident microbiome as a critical determinant of patients with cirrhosis and HCC.
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Affiliation(s)
- Maria Effenberger
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology & Metabolism, Medical University of Innsbruck, Innsbruck, Austria
| | - Silvio Waschina
- Institute for Human Nutrition and Food Science, Division of Nutriinformatics, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Christina Bronowski
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Gregor Sturm
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Oronzo Tassiello
- Institute for Human Nutrition and Food Science, Division of Nutriinformatics, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Felix Sommer
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Andreas Zollner
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology & Metabolism, Medical University of Innsbruck, Innsbruck, Austria
| | - Christina Watschinger
- Department of Internal Medicine I, Gastroenterology, Nephrology, Metabolism & Endocrinology, Johannes Kepler University, Linz, Austria
| | - Felix Grabherr
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology & Metabolism, Medical University of Innsbruck, Innsbruck, Austria
| | - Ronald Gstir
- Institute of Hygiene and Medical Microbiology, ECMM, Medical University of Innsbruck, Innsbruck, Austria
| | - Christoph Grander
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology & Metabolism, Medical University of Innsbruck, Innsbruck, Austria
| | - Barbara Enrich
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology & Metabolism, Medical University of Innsbruck, Innsbruck, Austria
| | - Reto Bale
- Department of Radiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Daniel Putzer
- Department of Radiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Angela Djanani
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology & Metabolism, Medical University of Innsbruck, Innsbruck, Austria
| | - Alexander R Moschen
- Department of Internal Medicine I, Gastroenterology, Nephrology, Metabolism & Endocrinology, Johannes Kepler University, Linz, Austria
- Christian Doppler Laboratory for Mucosal Immunology, Johannes Kepler University, Linz, Austria
| | - Heinz Zoller
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology & Metabolism, Medical University of Innsbruck, Innsbruck, Austria
| | - Jan Rupp
- Department of Infectious Diseases and Microbiology, University Hospital Schleswig-Holstein, Luebeck, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
- Department of Internal Medicine I, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Remy Burcelin
- INSERM 1297 and University Paul Sabatier: Institut des Maladies Métaboliques et Cardiovasculaires, France and Université Paul Sabatier, Toulouse, France
| | - Cornelia Lass-Flörl
- Institute of Hygiene and Medical Microbiology, ECMM, Medical University of Innsbruck, Innsbruck, Austria
| | - Zlatko Trajanoski
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Georg Oberhuber
- INNPATH, Institute of Pathology, University Hospital of Innsbruck, Innsbruck, Austria
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Timon E Adolph
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology & Metabolism, Medical University of Innsbruck, Innsbruck, Austria
| | - Konrad Aden
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
- Department of Internal Medicine I, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Herbert Tilg
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology & Metabolism, Medical University of Innsbruck, Innsbruck, Austria
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Liu J, Fang H, Hong N, Lv C, Zhu Q, Feng Y, Wang B, Tian J, Yu Y. Gut Microbiome and Metabonomic Profile Predict Early Remission to Anti-Integrin Therapy in Patients with Moderate to Severe Ulcerative Colitis. Microbiol Spectr 2023; 11:e0145723. [PMID: 37199618 PMCID: PMC10269848 DOI: 10.1128/spectrum.01457-23] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 05/09/2023] [Indexed: 05/19/2023] Open
Abstract
Patients with ulcerative colitis (UC) have low response rates to anti-integrin medications, necessitating the identification of noninvasive biomarkers for predicting remission to anti-integrin therapy. In this study, patients with moderate to severe UC commencing anti-integrin therapy (n = 29), inactive to mild UC patients (n = 13), and healthy controls (n = 11) were selected. Besides clinical evaluation, fecal samples were collected at baseline and week 14 from moderate to severe UC patients. The clinical remission was defined based on the Mayo score. Fecal samples were assessed with 16S rRNA gene sequencing, liquid chromatography-tandem mass spectrometry, and gas chromatography-mass spectrometry (GC-MS). We identified that Verrucomicrobiota was significantly more abundant in the remission group (P < 0.001) than that of nonremission group at phylum level for patients commencing vedolizumab. GC-MS analysis revealed that the concentrations of butyric acid (P = 0.024) and isobutyric acid (P = 0.042) were significantly higher in the remission group compared to the nonremission group at baseline. Finally, the combination of Verrucomicrobiota, butyric acid, and isobutyric acid improved the diagnosis of early remission to anti-integrin therapy (area under the concentration-time curve = 0.961). We identified significantly higher phylum level diversity of Verrucomicrobiota in remission than the nonremission groups at baseline. Notably, the combination of gut microbiome and metabonomic profiles improved the diagnosis of early remission to anti-integrin therapy. IMPORTANCE It is reported that patients with ulcerative colitis (UC) have low response rates to anti-integrin medications in the latest VARSITY study. Therefore, our primary goals were to discover differences in the gut microbiome and metabonomics patterns between early remission and nonremission patients and to explore the diagnostic value in predicting clinical remission to anti-integrin therapy accurately. In this study, we found that Verrucomicrobiota was significantly more abundant in the remission group (P < 0.001) than that of nonremission group at phylum level for patients commencing vedolizumab. Gas chromatography-mass spectrometry analysis revealed that the concentrations of butyric acid (P = 0.024) and isobutyric acid (P = 0.042) were significantly higher in the remission group compared with the nonremission group at baseline. Notably, the combination of Verrucomicrobiota, butyric acid, and isobutyric acid improved the diagnosis of early remission to anti-integrin therapy (area under the concentration-time curve = 0.961).
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Affiliation(s)
- Jie Liu
- Department of Gastroenterology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
| | - Huaying Fang
- Department of Gastroenterology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
- Endoscopy Center Department, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
| | - Na Hong
- Department of Gastroenterology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
- Endoscopy Center Department, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
| | - Chaolan Lv
- Department of Gastroenterology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
- Endoscopy Center Department, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
| | - Qihua Zhu
- Department of Gastroenterology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
- Department of Nursing, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
| | - Yinping Feng
- Department of Gastroenterology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
- Department of Nursing, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
| | - Bo Wang
- Department of Gastroenterology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
| | - Jiashuang Tian
- Department of Gastroenterology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
| | - Yue Yu
- Department of Gastroenterology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
- Endoscopy Center Department, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
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Lyu Z, Hu Y, Guo Y, Liu D. Modulation of bone remodeling by the gut microbiota: a new therapy for osteoporosis. Bone Res 2023; 11:31. [PMID: 37296111 PMCID: PMC10256815 DOI: 10.1038/s41413-023-00264-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 04/01/2023] [Accepted: 04/18/2023] [Indexed: 06/12/2023] Open
Abstract
The gut microbiota (GM) plays a crucial role in maintaining the overall health and well-being of the host. Recent studies have demonstrated that the GM may significantly influence bone metabolism and degenerative skeletal diseases, such as osteoporosis (OP). Interventions targeting GM modification, including probiotics or antibiotics, have been found to affect bone remodeling. This review provides a comprehensive summary of recent research on the role of GM in regulating bone remodeling and seeks to elucidate the regulatory mechanism from various perspectives, such as the interaction with the immune system, interplay with estrogen or parathyroid hormone (PTH), the impact of GM metabolites, and the effect of extracellular vesicles (EVs). Moreover, this review explores the potential of probiotics as a therapeutic approach for OP. The insights presented may contribute to the development of innovative GM-targeted therapies for OP.
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Affiliation(s)
- Zhengtian Lyu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Yongfei Hu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Yuming Guo
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Dan Liu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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Hasselblatt P, Reindl W, Gauss A, Neeff H, Fusco S, Klaus J. Questions to consider when caring for patients with ulcerative colitis. ZEITSCHRIFT FUR GASTROENTEROLOGIE 2023; 61:690-700. [PMID: 36257329 DOI: 10.1055/a-1890-6015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Although the management of patients with ulcerative colitis (UC) is well defined by national and international guidelines, there are many debates and open questions related to daily care of UC patients. Here, we aimed to review topics with high clinical relevance including therapy algorithms, potential biomarkers for disease prognosis and response to therapy, the role of interventions targeting the gut microbiota, insights from head-to-head trials, novel UC medications, exit strategies, the impact of COVID19 on UC, care of patients with acute severe disease, cancer screening, and the role of surgery.
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Affiliation(s)
- Peter Hasselblatt
- Department of Medicine II, University Hospital Freiburg, Freiburg, Germany
| | - Wolfgang Reindl
- Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Annika Gauss
- University Hospital Heidelberg, Heidelberg, Germany
| | - Hannes Neeff
- Dept. of General and Visceral Surgery, Medical Center - University of Freiburg, Freiburg, Germany
| | - Stefano Fusco
- Department of Gastroenterology, Eberhard-Karls-Universität Tübingen Medizinische Fakultät, Tübingen, Germany
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Kim SY, Shin SY, Park SJ, Im JP, Kim HJ, Lee KM, Kim JW, Jung SA, Lee J, Kang SB, Shin SJ, Kim ES, Kim YS, Kim TO, Kim HS, Park DI, Kim HK, Kim ES, Kim YH, Teng D, Kim JH, Kim W, Saeed M, Moon JM, Kim K, Choi CH, Choi HK. Changes in fecal metabolic and lipidomic features by anti-TNF treatment and prediction of clinical remission in patients with ulcerative colitis. Therap Adv Gastroenterol 2023; 16:17562848231168199. [PMID: 37153496 PMCID: PMC10161336 DOI: 10.1177/17562848231168199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 03/21/2023] [Indexed: 05/09/2023] Open
Abstract
Background Therapeutic targets for ulcerative colitis (UC) and prediction models of antitumor necrosis factor (TNF) therapy outcomes have not been fully reported. Objective Investigate the characteristic metabolite and lipid profiles of fecal samples of UC patients before and after adalimumab treatment and develop a prediction model of clinical remission following adalimumab treatment. Design Prospective, observational, multicenter study was conducted on moderate-to-severe UC patients (n = 116). Methods Fecal samples were collected from UC patients at 8 and 56 weeks of adalimumab treatment and from healthy controls (HC, n = 37). Clinical remission was assessed using the Mayo score. Metabolomic and lipidomic analyses were performed using gas chromatography mass spectrometry and nano electrospray ionization mass spectrometry, respectively. Orthogonal partial least squares discriminant analysis was performed to establish a remission prediction model. Results Fecal metabolites in UC patients markedly differed from those in HC at baseline and were changed similarly to those in HC during treatment; however, lipid profiles did not show these patterns. After treatment, the fecal characteristics of remitters (RM) were closer to those of HC than to those of non-remitters (NRM). At 8 and 56 weeks, amino acid levels in RM were lower than those in NRM and similar to those in HC. After 56 weeks, levels of 3-hydroxybutyrate, lysine, and phenethylamine decreased, and dodecanoate level increased in RM similarly to those in HC. The prediction model of long-term remission in male patients based on lipid biomarkers showed a higher performance than clinical markers. Conclusion Fecal metabolites in UC patients markedly differ from those in HC, and the levels in RM are changed similarly to those in HC after anti-TNF therapy. Moreover, 3-hydroxybutyrate, lysine, phenethylamine, and dodecanoate are suggested as potential therapeutic targets for UC. A prediction model of long-term remission based on lipid biomarkers may help implement personalized treatment.
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Affiliation(s)
- Seok-Young Kim
- College of Pharmacy, Chung-Ang University, Seoul, Republic of Korea
| | - Seung Yong Shin
- Department of Internal Medicine, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Soo Jung Park
- Department of Internal Medicine and Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, South Korea
| | - Jong Pil Im
- Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, Seoul, South Korea
| | - Hyo Jong Kim
- Department of Gastroenterology, Kyung Hee University Hospital, Seoul, South Korea
| | - Kang-Moon Lee
- Department of Gastroenterology, The Catholic University of Korea St. Vincent’s Hospital, Suwon, South Korea
| | - Ji Won Kim
- Department of Gastroenterology, SMG-SNU Boramae Medical Center, Seoul, South Korea
| | - Sung-Ae Jung
- Department of Gastroenterology, Ewha Woman’s University College of Medicine, Seoul, South Korea
| | - Jun Lee
- Department of Internal Medicine, College of Medicine, Chosun University, Gwangju, South Korea
| | - Sang-Bum Kang
- Department of Gastroenterology, The Catholic University of Korea Daejeon St. Mary’s Hospital, Daejeon, South Korea
| | - Sung Jae Shin
- Department of Gastroenterology, Ajou University School of Medicine, Suwon, South Korea
| | - Eun Sun Kim
- Department of Gastroenterology, Korea University Anam Hospital, Seoul, South Korea
| | - You Sun Kim
- Department of Gastroenterology, Inje University Seoul Paik Hospital, Seoul, South Korea
| | - Tae Oh Kim
- Department of Gastroenterology, Inje University Haeundae Paik Hospital, Busan, South Korea
| | - Hyun-Soo Kim
- Department of Gastroenterology, Chonnam National University Hospital, Gwangju, South Korea
| | - Dong Il Park
- Department of Internal Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University, Seoul, South Korea
| | - Hyung Kil Kim
- Department of Gastroenterology, Inha University Hospital, Incheon, South Korea
| | - Eun Soo Kim
- Department of Internal Medicine, Kyungpook National University, School of Medicine, Daegu, South Korea
| | - Young-Ho Kim
- Department of Internal Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | | | - Jong-Hwa Kim
- Department of Microbiology, Chung-Ang University, College of Medicine, Seoul, South Korea
| | - Wonyong Kim
- Department of Microbiology, Chung-Ang University, College of Medicine, Seoul, South Korea
| | - Maham Saeed
- College of Pharmacy, Chung-Ang University, Seoul, Republic of Korea
| | - Jung Min Moon
- Department of Internal Medicine, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Kisung Kim
- Department of Internal Medicine, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Chang Hwan Choi
- Professor of Medicine, Internal Medicine, Chung-Ang University College of Medicine, 102 Heukseok-ro, Dongjak-gu, Seoul 06973, Republic of Korea
| | - Hyung-Kyoon Choi
- Professor of College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
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Inflammation and malnutrition in inflammatory bowel disease. Lancet Gastroenterol Hepatol 2023; 8:579-590. [PMID: 36933563 DOI: 10.1016/s2468-1253(23)00011-0] [Citation(s) in RCA: 70] [Impact Index Per Article: 70.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 03/17/2023]
Abstract
Inflammatory bowel disease (IBD), which includes Crohn's disease and ulcerative colitis, has become increasingly prevalent worldwide in the past decade. The nutritional status of patients with IBD is often impaired, with malnutrition presenting as imbalanced energy or nutrient intake, including protein-energy malnutrition, disease-related malnutrition, sarcopenia, and micronutrient deficiency. Additionally, malnutrition can manifest as overweight, obesity, and sarcopenic obesity. Malnutrition can lead to disturbances in gut microbiome composition that might alter homoeostasis and cause a dysbiotic state, potentially triggering inflammatory responses. Despite the clear link between IBD and malnutrition, little is known about the pathophysiological mechanisms beyond protein-energy malnutrition and micronutrient deficiencies that could promote inflammation through malnutrition, and vice versa. This Review focuses on potential mechanisms that trigger a vicious cycle between malnutrition and inflammation, and their clinical and therapeutic implications.
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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.
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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
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Zhang B, Yang L, Ning H, Cao M, Chen Z, Chen Q, Lian G, Tang H, Wang Q, Wang J, Lin Z, Wen J, Liu Y, Xuan J, Li X, Lin A, He J, Zhang L, Hou X, Zeng Q, Xiao C. A Matching Strategy To Guide Donor Selection for Ulcerative Colitis in Fecal Microbiota Transplantation: Meta-Analysis and Analytic Hierarchy Process. Microbiol Spectr 2023; 11:e0215921. [PMID: 36472435 PMCID: PMC9927247 DOI: 10.1128/spectrum.02159-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Fecal microbiota transplantation (FMT) targeting gut microbiota has recently been applied to the treatment of ulcerative colitis (UC). However, preliminary trials showed that only a subset of patients responded to FMT, and the heterogeneity in donor gut microbiota probably played important roles in patients' responses, implying the significance of matching an appropriate donor to a specified patient. We developed a strategy to build a donor-recipient matching model to guide rational donor selection for UC in FMT. We collected and uniformly reanalyzed 656 fecal 16S rRNA gene sequencing samples (350 from UC patients and 306 from healthy subjects) from 9 studies. Significantly lower α-diversity indexes were observed in UC patients by random effects model. Thirty-four bacterial genera and 34 predicted pathways were identified with significant odds ratios and classification potentials for UC patients. Based on six bacterial indicators, including richness, overall distance, genera, and pathways (beneficial and harmful), the analytic hierarchy process-based donor-recipient matching model was set to rank and select appropriate donors for patients with UC. Finally, the model showed favorable classification powers (>70%) for FMT effectiveness in two previous clinical trials. This study revealed the dysbiosis of fecal bacterial diversity, composition, and predicted pathways of patients with UC by meta-analysis and hereby developed a donor-recipient matching strategy to guide donor selection for UC in FMT. This strategy can also be applied to other diseases associated with gut microbiota. IMPORTANCE Modulation of gut microbiota by FMT from donors has been applied to the treatment of UC and yielded variable effectiveness in clinical trials. One possibility is that this variable effectiveness was related to donor selection, as a patient's response to FMT may rely on the capability of the used donor's microbiota to restore the specific gut disturbances of the patient. However, the biggest issues on the practical level are what should be considered in the selection process and how to set up such a donor-recipient matching model. In this study, we presented a bacterial profile-based donor-recipient matching strategy to guide donor selection for UC in FMT by first meta-analysis of 656 fecal 16S rRNA gene sequencing samples from 9 studies to identify significant indicators and then setting up the model by an analytic hierarchy process. The applicability and accuracy of this model were verified in the data sets from two previous FMT clinical studies. Our data indicate that the donor-recipient matching model built in this study enables researchers to rationally select donors for UC patients in FMT clinical practice, although it needs more samples and prospective trials for validation. The strategy adopted in this study to leverage existing data sets to build donor-recipient matching models for precision FMT is feasible for other diseases associated with gut microbiota.
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Affiliation(s)
- Bangzhou Zhang
- School of Life Sciences, Xiamen Universitygrid.12955.3a, Xiamen, China
- School of Medicine, Xiamen Universitygrid.12955.3a, Xiamen, China
| | - Luxi Yang
- School of Life Sciences, Xiamen Universitygrid.12955.3a, Xiamen, China
| | - Hanbing Ning
- Department of Digestive Diseases, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Man Cao
- Xiamen Treatgut Biotechnology Co., Ltd., Xiamen, China
| | - Zhangran Chen
- School of Medicine, Xiamen Universitygrid.12955.3a, Xiamen, China
| | - Qiongyun Chen
- School of Medicine, Xiamen Universitygrid.12955.3a, Xiamen, China
| | - Guanghui Lian
- Department of Gastroenterology, Xiangya Hospital, Changsha, China
| | - Hailing Tang
- Department of Gastroenterology, Xi'an Central Hospital, Xi’an, China
| | - Qizhi Wang
- Department of Gastroenterology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Junping Wang
- Department of Gastroenterology, The Affiliated People's Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Zhihui Lin
- Department of Gastroenterology, Fujian Provincial Hospital, Fuzhou, China
| | - Jianbo Wen
- Department of Gastroenterology, Pingxiang People’s Hospital, Pingxiang, China
| | - Yuedong Liu
- Department of Gastroenterology, The Third Affiliated Hospital of Liaoning University of Traditional Chinese Medicine, Shenyang, China
| | - Ji Xuan
- Department of Gastroenterology, Jinling Hospital, Nanjing, China
| | - Xuejun Li
- Department of Gastroenterology, The Second Affiliated Hospital of Anhui University of Traditional Chinese Medicine, Hefei, China
| | - Aiqiang Lin
- Xiamen Treatgut Biotechnology Co., Ltd., Xiamen, China
| | - Jianquan He
- School of Medicine, Xiamen Universitygrid.12955.3a, Xiamen, China
| | - Lei Zhang
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Technology and Science, Wuhan, China
| | - Xiaohua Hou
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Technology and Science, Wuhan, China
| | - Qiang Zeng
- Health Management Institute, The Second Medical Center & National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, China
| | - Chuanxing Xiao
- Xiamen Treatgut Biotechnology Co., Ltd., Xiamen, China
- School of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, China
- Department of Gastroenterology, The Second Affiliated Hospital of Fujian University of Traditional Chinese Medicine, Fuzhou, China
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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.
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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
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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.
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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.
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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
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Vieujean S, Louis E. Precision medicine and drug optimization in adult inflammatory bowel disease patients. Therap Adv Gastroenterol 2023; 16:17562848231173331. [PMID: 37197397 PMCID: PMC10184262 DOI: 10.1177/17562848231173331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 04/16/2023] [Indexed: 05/19/2023] Open
Abstract
Inflammatory bowel diseases (IBD) encompass two main entities including ulcerative colitis and Crohn's disease. Although having a common global pathophysiological mechanism, IBD patients are characterized by a significant interindividual heterogeneity and may differ by their disease type, disease locations, disease behaviours, disease manifestations, disease course as well as treatment needs. Indeed, although the therapeutic armamentarium for these diseases has expanded rapidly in recent years, a proportion of patients remains with a suboptimal response to medical treatment due to primary non-response, secondary loss of response or intolerance to currently available drugs. Identifying, prior to treatment initiation, which patients are likely to respond to a specific drug would improve the disease management, avoid unnecessary side effects and reduce the healthcare expenses. Precision medicine classifies individuals into subpopulations according to clinical and molecular characteristics with the objective to tailor preventative and therapeutic interventions to the characteristics of each patient. Interventions would thus be performed only on those who will benefit, sparing side effects and expense for those who will not. This review aims to summarize clinical factors, biomarkers (genetic, transcriptomic, proteomic, metabolic, radiomic or from the microbiota) and tools that could predict disease progression to guide towards a step-up or top-down strategy. Predictive factors of response or non-response to treatment will then be reviewed, followed by a discussion about the optimal dose of drug required for patients. The time at which these treatments should be administered (or rather can be stopped in case of a deep remission or in the aftermath of a surgery) will also be addressed. IBD remain biologically complex, with multifactorial etiopathology, clinical heterogeneity as well as temporal and therapeutic variabilities, which makes precision medicine especially challenging in this area. Although applied for many years in oncology, it remains an unmet medical need in IBD.
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Affiliation(s)
- Sophie Vieujean
- Hepato-Gastroenterology and Digestive Oncology, University Hospital CHU of Liège, Liège, Belgium
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Treatment with butyrate alleviates dextran sulfate sodium and Clostridium difficile-induced colitis by preventing activity of Th17 cells via regulation of SIRT1/mTOR in mice. J Nutr Biochem 2023; 111:109155. [PMID: 36162566 DOI: 10.1016/j.jnutbio.2022.109155] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 04/23/2022] [Accepted: 08/09/2022] [Indexed: 11/20/2022]
Abstract
Inflammatory bowel disease (IBD) patients are particularly vulnerable to infection with Clostridium difficile infection (CDI).Available treatments of IBD with CDI have not effective. Butyrate, the metabolites of microbiota, plays a vital role in maintaining immune homeostasis and potential drugs for treatment of IBD with CDI. The aim of this study was to investigate the effect of butyrate on IBD with CDI. Mice were given dextran sulfate sodium (DSS) and were infected with C. difficile (CD). Butyrate was treated during the study period. Butyrate protected from DSS+CD induced colitis by improving weight loss, survival, colon shorten, activity index score, and suppressing the expression of proinflammatory cytokines including IL-6, IL-17, TNF-α, IL-1β as well as regulating Th17/Treg balance through activation of SIRT1/mTOR. Besides, SR1001, an inhitor of the orphan nuclear receptors retinoic acid-related receptor γt, which is a transcription factor specific to the formation of Th17 cells can suppress the Th17 development and alleviate the DSS+CD induced colitis in mice. Notably, the therapeutic effect of butyrate was revered when disease mice treated with butyrate and Ex-527, a SIRT1 inhibitor. Taken together, we demonstrate that butyrate alleviates dextran sulfate sodium and clostridium difficile induced colitis by preventing Th17 through activation of SIRT1/mTOR.
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Xu YH, Zhu WM, Guo Z. Current status of novel biologics and small molecule drugs in the individualized treatment of inflammatory bowel disease. World J Gastroenterol 2022; 28:6888-6899. [PMID: 36632311 PMCID: PMC9827580 DOI: 10.3748/wjg.v28.i48.6888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/11/2022] [Accepted: 12/01/2022] [Indexed: 12/26/2022] Open
Abstract
Treatment strategies for inflammatory bowel disease (IBD) are rapidly evolving with the development of biologics and small molecule drugs (SMDs). However, these drugs are not guaranteed to be effective in all patients, and a “ceiling effect” of biologic monotherapy may occur. This issue highlights an unmet need for optimizing the use of biologics and predicting therapeutic responses. Thus, the development of new drugs with novel mechanisms of action is urgently needed for patients with primary nonresponse and secondary loss of response to conventional biologics and SMDs. In addition, combining different biologics or SMDs has been proposed as a novel strategy to enhance treatment efficacy in IBD, which theoretically has multidimensional anti-inflammatory potential. Based on the current evidence available for IBD, dual targeted therapy may be a promising strategy for refractory IBD patients who have failed in multiple biologic trea-tments or who have extraintestinal manifestation. Additionally, identifying the subgroup of IBD patients who are responding to biological combination therapies is also equally important in stable disease remission. In this review, we sum-marize the newly developed biologics and SMDs and the current status of bio-logics/SMDs to highlight the development of individualized treatment in IBD.
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Affiliation(s)
- Yi-Han Xu
- Department of General Surgery, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing 210002, Jiangsu Province, China
| | - Wei-Ming Zhu
- Department of General Surgery, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing 210002, Jiangsu Province, China
| | - Zhen Guo
- Department of General Surgery, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing 210002, Jiangsu Province, China
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Zacharias HU, Kaleta C, Cossais F, Schaeffer E, Berndt H, Best L, Dost T, Glüsing S, Groussin M, Poyet M, Heinzel S, Bang C, Siebert L, Demetrowitsch T, Leypoldt F, Adelung R, Bartsch T, Bosy-Westphal A, Schwarz K, Berg D. Microbiome and Metabolome Insights into the Role of the Gastrointestinal-Brain Axis in Parkinson's and Alzheimer's Disease: Unveiling Potential Therapeutic Targets. Metabolites 2022; 12:metabo12121222. [PMID: 36557259 PMCID: PMC9786685 DOI: 10.3390/metabo12121222] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/25/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022] Open
Abstract
Neurodegenerative diseases such as Parkinson's (PD) and Alzheimer's disease (AD), the prevalence of which is rapidly rising due to an aging world population and westernization of lifestyles, are expected to put a strong socioeconomic burden on health systems worldwide. Clinical trials of therapies against PD and AD have only shown limited success so far. Therefore, research has extended its scope to a systems medicine point of view, with a particular focus on the gastrointestinal-brain axis as a potential main actor in disease development and progression. Microbiome and metabolome studies have already revealed important insights into disease mechanisms. Both the microbiome and metabolome can be easily manipulated by dietary and lifestyle interventions, and might thus offer novel, readily available therapeutic options to prevent the onset as well as the progression of PD and AD. This review summarizes our current knowledge on the interplay between microbiota, metabolites, and neurodegeneration along the gastrointestinal-brain axis. We further illustrate state-of-the art methods of microbiome and metabolome research as well as metabolic modeling that facilitate the identification of disease pathomechanisms. We conclude with therapeutic options to modulate microbiome composition to prevent or delay neurodegeneration and illustrate potential future research directions to fight PD and AD.
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Affiliation(s)
- Helena U. Zacharias
- Peter L. Reichertz Institute for Medical Informatics of TU Braunschweig and Hannover Medical School, 30625 Hannover, Germany
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
- Correspondence: (H.U.Z.); (C.K.)
| | - Christoph Kaleta
- Research Group Medical Systems Biology, Institute for Experimental Medicine, Kiel University, 24105 Kiel, Germany
- Kiel Nano, Surface and Interface Science—KiNSIS, Kiel University, 24118 Kiel, Germany
- Correspondence: (H.U.Z.); (C.K.)
| | | | - Eva Schaeffer
- Department of Neurology, Kiel University and University Medical Center Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Henry Berndt
- Research Group Comparative Immunobiology, Zoological Institute, Kiel University, 24118 Kiel, Germany
| | - Lena Best
- Research Group Medical Systems Biology, Institute for Experimental Medicine, Kiel University, 24105 Kiel, Germany
| | - Thomas Dost
- Research Group Medical Systems Biology, Institute for Experimental Medicine, Kiel University, 24105 Kiel, Germany
| | - Svea Glüsing
- Institute of Human Nutrition and Food Science, Food Technology, Kiel University, 24118 Kiel, Germany
| | - Mathieu Groussin
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Mathilde Poyet
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sebastian Heinzel
- Department of Neurology, Kiel University and University Medical Center Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
- Institute of Medical Informatics and Statistics, Kiel University and University Medical Center Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Corinna Bang
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Leonard Siebert
- Kiel Nano, Surface and Interface Science—KiNSIS, Kiel University, 24118 Kiel, Germany
- Functional Nanomaterials, Department of Materials Science, Kiel University, 24143 Kiel, Germany
| | - Tobias Demetrowitsch
- Institute of Human Nutrition and Food Science, Food Technology, Kiel University, 24118 Kiel, Germany
- Kiel Network of Analytical Spectroscopy and Mass Spectrometry, Kiel University, 24118 Kiel, Germany
| | - Frank Leypoldt
- Department of Neurology, Kiel University and University Medical Center Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
- Neuroimmunology, Institute of Clinical Chemistry, University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Rainer Adelung
- Kiel Nano, Surface and Interface Science—KiNSIS, Kiel University, 24118 Kiel, Germany
- Functional Nanomaterials, Department of Materials Science, Kiel University, 24143 Kiel, Germany
| | - Thorsten Bartsch
- Kiel Nano, Surface and Interface Science—KiNSIS, Kiel University, 24118 Kiel, Germany
- Department of Neurology, Kiel University and University Medical Center Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Anja Bosy-Westphal
- Institute of Human Nutrition and Food Science, Kiel University, 24107 Kiel, Germany
| | - Karin Schwarz
- Kiel Nano, Surface and Interface Science—KiNSIS, Kiel University, 24118 Kiel, Germany
- Institute of Human Nutrition and Food Science, Food Technology, Kiel University, 24118 Kiel, Germany
- Kiel Network of Analytical Spectroscopy and Mass Spectrometry, Kiel University, 24118 Kiel, Germany
| | - Daniela Berg
- Kiel Nano, Surface and Interface Science—KiNSIS, Kiel University, 24118 Kiel, Germany
- Department of Neurology, Kiel University and University Medical Center Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
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Hou X, Zhu F, Zheng W, Jacques ML, Huang J, Guan F, Lei J. Protective effect of Schistosoma japonicum eggs on TNBS-induced colitis is associated with regulating Treg/Th17 balance and reprogramming glycolipid metabolism in mice. Front Cell Infect Microbiol 2022; 12:1028899. [PMID: 36304936 PMCID: PMC9592807 DOI: 10.3389/fcimb.2022.1028899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 09/28/2022] [Indexed: 11/28/2022] Open
Abstract
Inflammatory bowel diseases (IBDs) have been classified as modern refractory diseases. However, safe, well-tolerated, and effective treatments for IBDs are still lacking. Therefore, there is an urgent need to develop novel therapeutic targets with fewer undesirable adverse reactions. A growing body of research has shown that infection with live helminths or exposure to defined helminth-derived components can downregulate pathogenic inflammation due to their immunoregulatory ability. Here we were to explore the protective role of Schistosoma japonicum eggs on murine experimental colitis caused by trinitrobenzene sulfonic acid (TNBS) and the underlying mechanism. Frequencies of splenic Treg and Th17 cells were detected by flow cytometry. Protein and mRNA expressions of Foxp3 and RORγt were investigated by Western Blot and quantitative real-time polymerase chain reaction (qPCR), respectively. Concentrations of transforming growth factor-beta1 (TGF-β1), interleukin-10 (IL-10) and IL-17A were assessed with ELISA. Expression levels of genes related to glycolipid metabolism were measured with qPCR. The results showed that pre-exposure to S. japonicum eggs contributed to the relief of colitis in the TNBS model, evidenced by improved body weight loss, reversing spleen enlargement and colon shortening, and decreased histology scores. Compared with the TNBS group, the TNBS+Egg group had increased Treg immune response, accompanied by decreased Th17 immune response, leading to the reconstruction of Treg/Th17 balance. In addition, a ratio of Treg/Th17 was correlated negatively with the histological scores in the experiment groups. Furthermore, the regulation of Treg/Th17 balance by S. japonicum eggs was associated with inhibiting the glycolysis pathway and lipogenesis, along with promoting fatty acid oxidation in the TNBS+Egg group. These data indicate that S. japonicum eggs have a protective effect against TNBS-induced colitis, which is related to restoring Treg/Th17 balance and regulating glucose and lipid metabolism.
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Affiliation(s)
- Xiao Hou
- Department of Clinical Laboratory, The General Hospital of Central Theater Command, The People's Liberation Army, Wuhan, China
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Feifan Zhu
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wenwen Zheng
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Muziazia Lupemba Jacques
- Department of Parasitology, Kinshasa Institute of Medical, Kinshasa, Democratic Republic of the Congo
| | - Jin Huang
- Department of Clinical Laboratory, Wuhan Pu’ai Hospital, Wuhan, China
| | - Fei Guan
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiahui Lei
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- *Correspondence: Jiahui Lei,
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