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Chang CC, Liu TC, Lu CJ, Chiu HC, Lin WN. Explainable machine learning model for identifying key gut microbes and metabolites biomarkers associated with myasthenia gravis. Comput Struct Biotechnol J 2024; 23:1572-1583. [PMID: 38650589 PMCID: PMC11035017 DOI: 10.1016/j.csbj.2024.04.025] [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: 11/19/2023] [Revised: 03/14/2024] [Accepted: 04/07/2024] [Indexed: 04/25/2024] Open
Abstract
Diagnostic markers for myasthenia gravis (MG) are limited; thus, innovative approaches are required for supportive diagnosis and personalized care. Gut microbes are associated with MG pathogenesis; however, few studies have adopted machine learning (ML) to identify the associations among MG, gut microbiota, and metabolites. In this study, we developed an explainable ML model to predict biomarkers for MG diagnosis. We enrolled 19 MG patients and 10 non-MG individuals. Stool samples were collected and microbiome assessment was performed using 16S rRNA sequencing. Untargeted metabolic profiling was conducted to identify fecal amplicon significant variants (ASVs) and metabolites. We developed an explainable ML model in which the top ASVs and metabolites are combined to identify the best predictive performance. This model uses the SHapley Additive exPlanations method to generate both global and personalized explanations. Fecal microbe-metabolite composition differed significantly between groups. The key bacterial families were Lachnospiraceae and Ruminococcaceae, and the top three features were Lachnospiraceae, inosine, and methylhistidine. An ML model trained with the top 1 % ASVs and top 15 % metabolites combined outperformed all other models. Personalized explanations revealed different patterns of microbe-metabolite contributions in patients with MG. The integration of the microbiota-metabolite features and the development of an explainable ML framework can accurately identify MG and provide personalized explanations, revealing the associations between gut microbiota, metabolites, and MG. An online calculator employing this algorithm was developed that provides a streamlined interface for MG diagnosis screening and conducting personalized evaluations.
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Affiliation(s)
- Che-Cheng Chang
- PhD Program in Nutrition and Food Science, Fu Jen Catholic University, New Taipei City, Taiwan
- Department of Neurology, Fu Jen Catholic University Hospital, Fu Jen Catholic University, New Taipei City, Taiwan
- Graduate Institute of Biomedical and Pharmaceutical Science, Fu Jen Catholic University, New Taipei City, Taiwan
| | - Tzu-Chi Liu
- Graduate Institute of Business Administration, Fu Jen Catholic University, New Taipei City, Taiwan
| | - Chi-Jie Lu
- Graduate Institute of Business Administration, Fu Jen Catholic University, New Taipei City, Taiwan
- Artificial Intelligence Development Center, Fu Jen Catholic University, New Taipei City, Taiwan
- Department of Information Management, Fu Jen Catholic University, New Taipei City, Taiwan
| | - Hou-Chang Chiu
- School of Medicine, Fu Jen Catholic University, New Taipei City, Taiwan
- Department of Neurology, Taipei Medical University, Shuang-Ho Hospital, New Taipei City, Taiwan
| | - Wei-Ning Lin
- PhD Program in Nutrition and Food Science, Fu Jen Catholic University, New Taipei City, Taiwan
- Graduate Institute of Biomedical and Pharmaceutical Science, Fu Jen Catholic University, New Taipei City, Taiwan
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Xia P, Li R, Chen M, Zeng F, Zhou W, Hou T. Proanthocyanidins and β-Glucan Synergistically Regulate Intestinal Inflammation in Dextran Sulfate Sodium-Induced Colitis Mice. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:19366-19377. [PMID: 39178327 DOI: 10.1021/acs.jafc.4c03544] [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: 08/25/2024]
Abstract
Proanthocyanidins (PA) have been proven to have an anti-inflammation effect in multiple models by regulating oxidative stress. β-glucan (BG) could alleviate colitis from the perspectives of intestinal permeability and gut microbiota. In the present study, the synergistic anti-inflammatory function of PA and BG was explored from multiple aspects including immune response, intestinal barrier, gut microbiota, and differential metabolites. The results showed that the supplementation of PA and BG improved the colitis symptoms including atrophy of the colon, body weight loss, and organ index increase. Additionally, inflammatory cytokine levels and oxidative stress status were significantly regulated with the intake of PA and BG. Moreover, PA and BG intervention improved intestinal permeability and promoted the expression of barrier proteins. The microbiome and metabolic profile of cecal contents showed that PA and BG supplementation increased the abundance of anti-inflammatory bacteria and decreased the abundance of pro-inflammatory bacteria. Furthermore, some beneficial metabolites involved in amino acid metabolism, carbohydrate metabolism, and biosynthesis of other secondary metabolite pathways were increased. Overall, these findings have demonstrated the regulation of the inflammatory response and remodel of metabolite profiles by PA and BG complexes, indicating that it may serve as a new strategy for inflammatory bowel disease treatment in the future.
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Affiliation(s)
- Pengkui Xia
- Key Laboratory of Tropical Crop Products Processing of Ministry of Agriculture and Rural Affairs, Agricultural Products Processing Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, Guangdong 524001, China
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ruyi Li
- Key Laboratory of Tropical Crop Products Processing of Ministry of Agriculture and Rural Affairs, Agricultural Products Processing Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, Guangdong 524001, China
| | - Mianhong Chen
- Key Laboratory of Tropical Crop Products Processing of Ministry of Agriculture and Rural Affairs, Agricultural Products Processing Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, Guangdong 524001, China
| | - Fanke Zeng
- Key Laboratory of Tropical Crop Products Processing of Ministry of Agriculture and Rural Affairs, Agricultural Products Processing Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, Guangdong 524001, China
| | - Wei Zhou
- Key Laboratory of Tropical Crop Products Processing of Ministry of Agriculture and Rural Affairs, Agricultural Products Processing Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, Guangdong 524001, China
| | - Tao Hou
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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Lu X, Fan M, Ma Y, Feng Y, Pan L. Redox-sensitive hydrogel based on hyaluronic acid with selenocystamine cross-linking for the delivery of Limosilactobacillus reuteri in a DSS-induced colitis mouse model. Int J Biol Macromol 2024; 276:133855. [PMID: 39032895 DOI: 10.1016/j.ijbiomac.2024.133855] [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: 01/03/2024] [Revised: 06/30/2024] [Accepted: 07/11/2024] [Indexed: 07/23/2024]
Abstract
Disrupted gut microbiota homeostasis is an important cause of inflammatory colitis. Studies have shown that effective supplementation with probiotics can maintain microbial homeostasis and alleviate colitis. Here, to increase the viability of probiotics in the harsh gastrointestinal environments and enable targeted delivery, a redox-sensitive selenium hyaluronic acid (HA-Se) hydrogel encapsulating probiotics was developed. HA was modified with selenocystamine dihydrochloride and crosslinked by an amide reaction to generate a redox-sensitive hydrogel with stable mechanical properties, a low hemolysis rate and satisfactory biocompatibility. The HA-Se hydrogel exhibited suitable sensitivity to 10 mM GSH or 100 μM H2O2. The encapsulation of Limosilactobacillus reuteri (LR) in the HA-Se hydrogel (HA-Se-LR) significantly increased the survival rate of the probiotics in simulated gastric and intestinal fluid. HA-Se-LR administration increased the survival rate of mice with dextran sulfate sodium (DSS)-induced colitis, significantly alleviated oxidative stress and inflammation, and increased the effect of LR on microbiota α diversity. These results indicate that the HA-Se hydrogel constructed in this study can be used as a delivery platform to treat colitis, expanding the targeted applications of the natural polymer HA in disease treatment and the administration of probiotics as drugs to alleviate disease symptoms.
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Affiliation(s)
- Xi Lu
- College of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710000, China.
| | - Mingming Fan
- College of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710000, China
| | - Yuzhe Ma
- College of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710000, China
| | - Yimeng Feng
- Mathematics Teaching and Research Group, Dajindian Town Junior High School, Zhengzhou 450000, China
| | - Lei Pan
- Tangdu Hospital, Air Force Military Medical University, Xi'an 710000, China
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Cheng WW, Liu BH, Hou XT, Meng H, Wang D, Zhang CH, Yuan S, Zhang QG. Natural Products on Inflammatory Bowel Disease: Role of Gut Microbes. THE AMERICAN JOURNAL OF CHINESE MEDICINE 2024:1-27. [PMID: 39192679 DOI: 10.1142/s0192415x24500514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/29/2024]
Abstract
Inflammatory bowel disease (IBD) refers to long-term medical conditions that involve inflammation of the digestive tract, and the global incidence and prevalence of IBD are on the rise. Gut microbes play an important role in maintaining the intestinal health of the host, and the occurrence, development, and therapeutic effects of IBD are closely related to the structural and functional changes of gut microbes. Published studies have shown that the natural products from traditional Chinese medicine have direct or indirect regulatory impacts on the composition and metabolism of the gut microbes. In this review, we summarize the research progress of several groups of natural products, i.e., flavonoids, alkaloids, saponins, polysaccharides, polyphenols, and terpenoids, for the therapeutic activities in relieving IBD symptoms. The role of gut microbes and their intestinal metabolites in managing the IBD is presented, with focusing on the mechanism of action of those natural products. Traditional Chinese medicine alleviated IBD symptoms by regulating gut microbes, providing important theoretical and practical basis for the treatment of variable inflammatory intestinal diseases.
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Affiliation(s)
- Wen-Wen Cheng
- Chronic Diseases Research Center, Dalian University College of Medicine, Dalian, Liaoning 116622, P. R. China
| | - Bao-Hong Liu
- Chronic Diseases Research Center, Dalian University College of Medicine, Dalian, Liaoning 116622, P. R. China
| | - Xiao-Ting Hou
- Chronic Diseases Research Center, Dalian University College of Medicine, Dalian, Liaoning 116622, P. R. China
| | - Huan Meng
- Chronic Diseases Research Center, Dalian University College of Medicine, Dalian, Liaoning 116622, P. R. China
| | - Dan Wang
- Chronic Diseases Research Center, Dalian University College of Medicine, Dalian, Liaoning 116622, P. R. China
| | - Cheng-Hao Zhang
- Department of Oral Teaching and Research, Yanbian University College of Medicine, Yanji, Jilin Province 133002, P. R. China
| | - Shuo Yuan
- Chronic Diseases Research Center, Dalian University College of Medicine, Dalian, Liaoning 116622, P. R. China
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, College of Pharmacy, Yanbian University, Yanji, Jilin Province 133002, P. R. China
| | - Qing-Gao Zhang
- Chronic Diseases Research Center, Dalian University College of Medicine, Dalian, Liaoning 116622, P. R. China
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Wang X, Peng J, Cai P, Xia Y, Yi C, Shang A, Akanyibah FA, Mao F. The emerging role of the gut microbiota and its application in inflammatory bowel disease. Biomed Pharmacother 2024; 179:117302. [PMID: 39163678 DOI: 10.1016/j.biopha.2024.117302] [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: 06/19/2024] [Revised: 08/08/2024] [Accepted: 08/13/2024] [Indexed: 08/22/2024] Open
Abstract
Inflammatory bowel disease (IBD), including Crohn's disease and ulcerative colitis, is a complex disorder with an unknown cause. However, the dysbiosis of the gut microbiome has been found to play a role in IBD etiology, including exacerbated immune responses and defective intestinal barrier integrity. The gut microbiome can also be a potential biomarker for several diseases, including IBD. Currently, conventional treatments targeting pro-inflammatory cytokines and pathways in IBD-associated dysbiosis do not yield effective results. Other therapies that directly target the dysbiotic microbiome for effective outcomes are emerging. We review the role of the gut microbiome in health and IBD and its potential as a diagnostic, prognostic, and therapeutic target for IBD. This review also explores emerging therapeutic advancements that target gut microbiome-associated alterations in IBD, such as nanoparticle or encapsulation delivery, fecal microbiota transplantation, nutritional therapies, microbiome/probiotic engineering, phage therapy, mesenchymal stem cells (MSCs), gut proteins, and herbal formulas.
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Affiliation(s)
- Xiu Wang
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China; Department of Laboratory Medicine, Lianyungang Clinical College, Jiangsu University, Lianyungang, Jiangsu 222006, China
| | - Jianhua Peng
- The People's Hospital of Danyang, Affiliated Danyang Hospital of Nantong University, Zhenjiang, Jiangsu 212300, China
| | - Peipei Cai
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Yuxuan Xia
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Chengxue Yi
- School of Medical Technology, Zhenjiang College, Zhenjiang 212028, China
| | - Anquan Shang
- Department of Laboratory Medicine, Lianyungang Clinical College, Jiangsu University, Lianyungang, Jiangsu 222006, China
| | - Francis Atim Akanyibah
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China.
| | - Fei Mao
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China; Department of Laboratory Medicine, Lianyungang Clinical College, Jiangsu University, Lianyungang, Jiangsu 222006, China.
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Qiu Y, Hu S, Chao K, Huang L, Huang Z, Mao R, Su F, Zhang C, Lin X, Cao Q, Gao X, Chen M. Developing a Machine-Learning Prediction Model for Infliximab Response in Crohn's Disease: Integrating Clinical Characteristics and Longitudinal Laboratory Trends. Inflamm Bowel Dis 2024:izae176. [PMID: 39126463 DOI: 10.1093/ibd/izae176] [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: 03/11/2024] [Indexed: 08/12/2024]
Abstract
BACKGROUND Achieving long-term clinical remission in Crohn's disease (CD) with antitumor necrosis factor α (anti-TNF-α) agents remains challenging. AIMS This study aims to establish a prediction model based on patients' clinical characteristics using a machine-learning approach to predict the long-term efficacy of infliximab (IFX). METHODS Three cohorts comprising 746 patients with CD were included from 3 inflammatory bowel disease (IBD) centers between June 2013 and January 2022. Clinical records were collected from baseline, 14-, 30-, and 52-week post-IFX treatment. Three machine-learning approaches were employed to develop predictive models based on 23 baseline predictors. The SHapley Additive exPlanations (SHAP) algorithm was used to dissect underlying predictors, and latent class mixed model (LCMM) was applied for trajectory analysis of the longitudinal change of blood routine tests along with long-term IFX therapy. RESULTS The XGBoost model exhibited the best discrimination between long-term responders and nonresponders. In the internal training and testing set, the model achieved an AUC of 0.91 (95% CI, 0.86-0.95) and 0.71 (95% CI, 0.66-0.87), respectively. Moreover, it achieved a moderate predictive performance in the independent external cohort, with an AUC of 0.68 (95% CI, 0.59-0.77). The SHAP algorithm revealed disease-relevant laboratory measurements, notably hemoglobin (HB), white blood cells (WBC), erythrocyte sedimentation rate (ESR), albumin (ALB), and platelets (PLT), alongside age at diagnosis and the Montreal classification, as the most influential predictors. Furthermore, 2 distinct patient clusters based on dynamic laboratory tests were identified for monitoring the long-term remission. CONCLUSIONS The established prediction model demonstrated remarkable discriminatory power in distinguishing long-term responders from nonresponders to IFX therapy. The identification of distinct patient clusters further emphasizes the need for tailored therapeutic approaches in CD management.
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Affiliation(s)
- Yun Qiu
- Department of Gastroenterology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Shixian Hu
- The Translational Medicine Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Kang Chao
- Department of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Lingjie Huang
- Department of Gastroenterology, Sir Run Run Shaw Hospital of Zhejiang University, Hangzhou, China
| | - Zicheng Huang
- Department of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Ren Mao
- Department of Gastroenterology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Fengyuan Su
- The Translational Medicine Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Chuhan Zhang
- Department of Gastroenterology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xiaoqing Lin
- Department of Gastroenterology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Qian Cao
- Department of Gastroenterology, Sir Run Run Shaw Hospital of Zhejiang University, Hangzhou, China
| | - Xiang Gao
- Department of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Minhu Chen
- Department of Gastroenterology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
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Hong SM, Baek DH. Diagnostic Procedures for Inflammatory Bowel Disease: Laboratory, Endoscopy, Pathology, Imaging, and Beyond. Diagnostics (Basel) 2024; 14:1384. [PMID: 39001273 PMCID: PMC11241288 DOI: 10.3390/diagnostics14131384] [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: 05/17/2024] [Revised: 06/26/2024] [Accepted: 06/27/2024] [Indexed: 07/16/2024] Open
Abstract
Diagnosing inflammatory bowel disease (IBD) can often be challenging, and differentiating between Crohn's disease and ulcerative colitis can be particularly difficult. Diagnostic procedures for IBD include laboratory tests, endoscopy, pathological tests, and imaging tests. Serological and stool tests can be easily performed in an outpatient setting and provide critical diagnostic clues. Although endoscopy is an invasive procedure, it offers essential diagnostic information and allows for tissue biopsy and therapeutic procedures. Video capsule endoscopy and device-assisted enteroscopy are endoscopic procedures used to evaluate the small bowel. In addition to endoscopy, magnetic resonance imaging, computed tomography, and ultrasound (US) are valuable tools for small bowel assessment. Among these, US is noninvasive and easily utilized, making its use highly practical in daily clinical practice. Endoscopic biopsy aids in the diagnosis of IBD and is crucial for assessing the histological activity of the disease, facilitating a thorough evaluation of disease remission, and aiding in the development of treatment strategies. Recent advances in artificial intelligence hold promise for enhancing various aspects of IBD management, including diagnosis, monitoring, and precision medicine. This review compiles current procedures and promising future tools for the diagnosis of IBD, providing comprehensive insights.
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Affiliation(s)
- Seung Min Hong
- Department of Internal Medicine, Pusan National University School of Medicine and Biomedical Research Institute, Pusan National University Hospital, Busan 49241, Republic of Korea
| | - Dong Hoon Baek
- Department of Internal Medicine, Pusan National University School of Medicine and Biomedical Research Institute, Pusan National University Hospital, Busan 49241, Republic of Korea
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Diez-Martin E, Hernandez-Suarez L, Muñoz-Villafranca C, Martin-Souto L, Astigarraga E, Ramirez-Garcia A, Barreda-Gómez G. Inflammatory Bowel Disease: A Comprehensive Analysis of Molecular Bases, Predictive Biomarkers, Diagnostic Methods, and Therapeutic Options. Int J Mol Sci 2024; 25:7062. [PMID: 39000169 PMCID: PMC11241012 DOI: 10.3390/ijms25137062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 06/15/2024] [Accepted: 06/25/2024] [Indexed: 07/16/2024] Open
Abstract
In inflammatory bowel diseases (IBDs), such as Crohn's disease (CD) and ulcerative colitis (UC), the immune system relentlessly attacks intestinal cells, causing recurrent tissue damage over the lifetime of patients. The etiology of IBD is complex and multifactorial, involving environmental, microbiota, genetic, and immunological factors that alter the molecular basis of the organism. Among these, the microbiota and immune cells play pivotal roles; the microbiota generates antigens recognized by immune cells and antibodies, while autoantibodies target and attack the intestinal membrane, exacerbating inflammation and tissue damage. Given the altered molecular framework, the analysis of multiple molecular biomarkers in patients proves exceedingly valuable for diagnosing and prognosing IBD, including markers like C reactive protein and fecal calprotectin. Upon detection and classification of patients, specific treatments are administered, ranging from conventional drugs to new biological therapies, such as antibodies to neutralize inflammatory molecules like tumor necrosis factor (TNF) and integrin. This review delves into the molecular basis and targets, biomarkers, treatment options, monitoring techniques, and, ultimately, current challenges in IBD management.
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Affiliation(s)
- Eguzkiñe Diez-Martin
- Research and Development Department, IMG Pharma Biotech S.L., 48170 Zamudio, Spain
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain
| | - Leidi Hernandez-Suarez
- Research and Development Department, IMG Pharma Biotech S.L., 48170 Zamudio, Spain
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain
| | - Carmen Muñoz-Villafranca
- Department of Gastroenterology, University Hospital of Basurto, Avda Montevideo 18, 48013 Bilbao, Spain
| | - Leire Martin-Souto
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain
| | - Egoitz Astigarraga
- Research and Development Department, IMG Pharma Biotech S.L., 48170 Zamudio, Spain
| | - Andoni Ramirez-Garcia
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain
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Yan J, Zhou G, Ren R, Zhang X, Zhang N, Wang Z, Peng L, Yang Y. Siderophore-harboring gut bacteria and fecal siderophore genes for predicting the responsiveness of fecal microbiota transplantation for active ulcerative colitis. J Transl Med 2024; 22:589. [PMID: 38915068 PMCID: PMC11194913 DOI: 10.1186/s12967-024-05419-w] [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: 03/22/2024] [Accepted: 06/18/2024] [Indexed: 06/26/2024] Open
Abstract
BACKGROUND Predictive markers for fecal microbiota transplantation (FMT) outcomes in patients with active ulcerative colitis (UC) are poorly defined. We aimed to investigate changes in gut microbiota pre- and post-FMT and to assess the potential value in determining the total copy number of fecal bacterial siderophore genes in predicting FMT responsiveness. METHODS Patients with active UC (Mayo score ≥ 3) who had undergone two FMT procedures were enrolled. Fecal samples were collected before and 8 weeks after each FMT session. Patients were classified into clinical response and non-response groups, based on their Mayo scores. The fecal microbiota profile was accessed using metagenomic sequencing, and the total siderophore genes copy number via quantitative real-time polymerase chain reaction. Additionally, we examined the association between the total siderophore genes copy number and FMT efficacy. RESULTS Seventy patients with UC had undergone FMT. The clinical response and remission rates were 50% and 10% after the first FMT procedure, increasing to 72.41% and 27.59% after the second FMT. The cumulative clinical response and clinical remission rates were 72.86% and 25.71%. Compared with baseline, the response group showed a significant increase in Faecalibacterium, and decrease in Enterobacteriaceae, consisted with the changes of the total bacterial siderophore genes copy number after the second FMT (1889.14 vs. 98.73 copies/ng, P < 0.01). Virulence factor analysis showed an enriched iron uptake system, especially bacterial siderophores, in the pre-FMT response group, with a greater contribution from Escherichia coli. The total baseline copy number was significantly higher in the response group than non-response group (1889.14 vs. 94.86 copies/ng, P < 0.01). A total baseline copy number cutoff value of 755.88 copies/ng showed 94.7% specificity and 72.5% sensitivity in predicting FMT responsiveness. CONCLUSIONS A significant increase in Faecalibacterium, and decrease in Enterobacteriaceae and the total fecal siderophore genes copy number were observed in responders after FMT. The siderophore genes and its encoding bacteria may be of predictive value for the clinical responsiveness of FMT to active ulcerative colitis.
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Affiliation(s)
- Jingshuang Yan
- School of Medicine, Nankai University, Tianjin, 300071, China
- Microbiota Laboratory and Microbiota Division, Department of Gastroenterology and Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Guanzhou Zhou
- School of Medicine, Nankai University, Tianjin, 300071, China
- Microbiota Laboratory and Microbiota Division, Department of Gastroenterology and Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Rongrong Ren
- Microbiota Laboratory and Microbiota Division, Department of Gastroenterology and Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Xiaohan Zhang
- School of Medicine, Nankai University, Tianjin, 300071, China
- Microbiota Laboratory and Microbiota Division, Department of Gastroenterology and Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Nana Zhang
- Microbiota Laboratory and Microbiota Division, Department of Gastroenterology and Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Zikai Wang
- Microbiota Laboratory and Microbiota Division, Department of Gastroenterology and Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Lihua Peng
- Microbiota Laboratory and Microbiota Division, Department of Gastroenterology and Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Yunsheng Yang
- School of Medicine, Nankai University, Tianjin, 300071, China.
- Microbiota Laboratory and Microbiota Division, Department of Gastroenterology and Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China.
- National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, 100853, China.
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10
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Palmieri O, Bossa F, Castellana S, Latiano T, Carparelli S, Martino G, Mangoni M, Corritore G, Nardella M, Guerra M, Biscaglia G, Perri F, Mazza T, Latiano A. Deciphering Microbial Composition in Patients with Inflammatory Bowel Disease: Implications for Therapeutic Response to Biologic Agents. Microorganisms 2024; 12:1260. [PMID: 39065032 PMCID: PMC11278628 DOI: 10.3390/microorganisms12071260] [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: 06/05/2024] [Accepted: 06/19/2024] [Indexed: 07/28/2024] Open
Abstract
Growing evidence suggests that alterations in the gut microbiome impact the development of inflammatory bowel diseases (IBDs), including Crohn's disease (CD) and ulcerative colitis (UC). Although IBD often requires the use of immunosuppressant drugs and biologic therapies to facilitate clinical remission and mucosal healing, some patients do not benefit from these drugs, and the reasons for this remain poorly understood. Despite advancements, there is still a need to develop biomarkers to help predict prognosis and guide treatment decisions. The aim of this study was to investigate the gut microbiome of IBD patients using biologics to identify microbial signatures associated with responses, following standard accepted criteria. Microbiomes in 66 stool samples from 39 IBD patients, comprising 20 CD and 19 UC patients starting biologic therapies, and 29 samples from healthy controls (HCs) were prospectively analyzed via NGS and an ensemble of metagenomics analysis tools. At baseline, differences were observed in alpha and beta metrics among patients with CD, UC and HC, as well as between the CD and UC groups. The degree of dysbiosis was more pronounced in CD patients, and those with dysbiosis exhibited a limited response to biological drugs. Pairwise differential abundance analyses revealed an increasing trend in the abundance of an unannotated genus from the Clostridiales order, Gemmiger genus and an unannotated genus from the Rikenellaceae family, which were consistently identified in greater abundance in HC. The Clostridium genus was more abundant in CD patients. At baseline, a greater abundance of the Odoribacter and Ruminococcus genera was found in IBD patients who responded to biologics at 14 weeks, whereas a genus identified as SMB53 was more enriched at 52 weeks. The Collinsella genus showed a higher prevalence among non-responder IBD patients. Additionally, a greater abundance of an unclassified genus from the Barnesiellaceae family and one from Lachnospiraceae was observed in IBD patients responding to Vedolizumab at 14 weeks. Our analyses showed global microbial diversity, mainly in CD. This indicated the absence or depletion of key taxa responsible for producing short-chain fatty acids (SCFAs). We also identified an abundance of pathobiont microbes in IBD patients at baseline, particularly in non-responders to biologic therapies. Furthermore, specific bacteria-producing SCFAs were abundant in patients responding to biologics and in those responding to Vedolizumab.
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Affiliation(s)
- Orazio Palmieri
- Division of Gastroenterology and Endoscopy, Fondazione IRCCS “Casa Sollievo della Sofferenza”, 71013 San Giovanni Rotondo, Italy; (F.B.); (T.L.); (S.C.); (G.M.); (G.C.); (M.G.); (G.B.); (F.P.); (A.L.)
| | - Fabrizio Bossa
- Division of Gastroenterology and Endoscopy, Fondazione IRCCS “Casa Sollievo della Sofferenza”, 71013 San Giovanni Rotondo, Italy; (F.B.); (T.L.); (S.C.); (G.M.); (G.C.); (M.G.); (G.B.); (F.P.); (A.L.)
| | - Stefano Castellana
- Unit of Bioinformatics, Fondazione IRCCS “Casa Sollievo della Sofferenza”, 71013 San Giovanni Rotondo, Italy (M.M.); (T.M.)
| | - Tiziana Latiano
- Division of Gastroenterology and Endoscopy, Fondazione IRCCS “Casa Sollievo della Sofferenza”, 71013 San Giovanni Rotondo, Italy; (F.B.); (T.L.); (S.C.); (G.M.); (G.C.); (M.G.); (G.B.); (F.P.); (A.L.)
| | - Sonia Carparelli
- Division of Gastroenterology and Endoscopy, Fondazione IRCCS “Casa Sollievo della Sofferenza”, 71013 San Giovanni Rotondo, Italy; (F.B.); (T.L.); (S.C.); (G.M.); (G.C.); (M.G.); (G.B.); (F.P.); (A.L.)
| | - Giuseppina Martino
- Division of Gastroenterology and Endoscopy, Fondazione IRCCS “Casa Sollievo della Sofferenza”, 71013 San Giovanni Rotondo, Italy; (F.B.); (T.L.); (S.C.); (G.M.); (G.C.); (M.G.); (G.B.); (F.P.); (A.L.)
| | - Manuel Mangoni
- Unit of Bioinformatics, Fondazione IRCCS “Casa Sollievo della Sofferenza”, 71013 San Giovanni Rotondo, Italy (M.M.); (T.M.)
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy
| | - Giuseppe Corritore
- Division of Gastroenterology and Endoscopy, Fondazione IRCCS “Casa Sollievo della Sofferenza”, 71013 San Giovanni Rotondo, Italy; (F.B.); (T.L.); (S.C.); (G.M.); (G.C.); (M.G.); (G.B.); (F.P.); (A.L.)
| | - Marianna Nardella
- Division of Gastroenterology and Endoscopy, Fondazione IRCCS “Casa Sollievo della Sofferenza”, 71013 San Giovanni Rotondo, Italy; (F.B.); (T.L.); (S.C.); (G.M.); (G.C.); (M.G.); (G.B.); (F.P.); (A.L.)
| | - Maria Guerra
- Division of Gastroenterology and Endoscopy, Fondazione IRCCS “Casa Sollievo della Sofferenza”, 71013 San Giovanni Rotondo, Italy; (F.B.); (T.L.); (S.C.); (G.M.); (G.C.); (M.G.); (G.B.); (F.P.); (A.L.)
| | - Giuseppe Biscaglia
- Division of Gastroenterology and Endoscopy, Fondazione IRCCS “Casa Sollievo della Sofferenza”, 71013 San Giovanni Rotondo, Italy; (F.B.); (T.L.); (S.C.); (G.M.); (G.C.); (M.G.); (G.B.); (F.P.); (A.L.)
| | - Francesco Perri
- Division of Gastroenterology and Endoscopy, Fondazione IRCCS “Casa Sollievo della Sofferenza”, 71013 San Giovanni Rotondo, Italy; (F.B.); (T.L.); (S.C.); (G.M.); (G.C.); (M.G.); (G.B.); (F.P.); (A.L.)
| | - Tommaso Mazza
- Unit of Bioinformatics, Fondazione IRCCS “Casa Sollievo della Sofferenza”, 71013 San Giovanni Rotondo, Italy (M.M.); (T.M.)
| | - Anna Latiano
- Division of Gastroenterology and Endoscopy, Fondazione IRCCS “Casa Sollievo della Sofferenza”, 71013 San Giovanni Rotondo, Italy; (F.B.); (T.L.); (S.C.); (G.M.); (G.C.); (M.G.); (G.B.); (F.P.); (A.L.)
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11
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Chen Y, Ye S, Shi J, Wang H, Deng G, Wang G, Wang S, Yuan Q, Yang L, Mou T. Functional evaluation of pure natural edible Ferment: protective function on ulcerative colitis. Front Microbiol 2024; 15:1367630. [PMID: 38952444 PMCID: PMC11215050 DOI: 10.3389/fmicb.2024.1367630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 05/31/2024] [Indexed: 07/03/2024] Open
Abstract
Purpose To investigate the therapeutic efficiency of a novel drink termed "Ferment" in cases of ulcerative colitis (UC) and its influence on the gut microbiota. Method In this study, we developed a complex of mixed fruit juice and lactic acid bacteria referred to as Ferment. Ferment was fed to mice for 35 days, before inducing UC with Dextran Sulfate Sodium Salt. We subsequently investigated the gut microbiome composition using 16S rRNA sequencing. Result After Ferment treatment, mouse body weight increased, and animals displayed less diarrhea, reduced frequency of bloody stools, and reduced inflammation in the colon. Beneficial bacteria belonging to Ileibacterium, Akkermansia, and Prevotellacea were enriched in the gut after Ferment treatment, while detrimental organisms including Erysipelatoclostridium, Dubosiella, and Alistipes were reduced. Conclusion These data place Ferment as a promising dietary candidate for enhancing immunity and protecting against UC.
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Affiliation(s)
- Yanjun Chen
- Department of General Surgery & Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Cancer, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Shengzhi Ye
- Department of General Surgery & Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Cancer, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jiaolong Shi
- Department of General Surgery & Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Cancer, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Hao Wang
- First Department of Gastrointestinal Surgery, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, China
| | - Guangxu Deng
- Department of Gastrointestinal and Anorectal, The First People’s Hospital of Zhaoqing, Zhaoqing, China
| | | | - Shijie Wang
- College of Foods Science and Biology, Hebei University of Science and Technology, Shijiazhuang, China
- Junlebao Dairy Group Co., Ltd., Shijiazhuang, China
| | - Qingbin Yuan
- Junlebao Dairy Group Co., Ltd., Shijiazhuang, China
| | - Lunan Yang
- Department of Plastic and Aesthetic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Tingyu Mou
- Department of General Surgery & Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Cancer, Nanfang Hospital, Southern Medical University, Guangzhou, China
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12
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Fejrskov A, Füchtbauer JD, Davíðsdóttir LG, Halfvarson J, Høivik ML, Jensen MD, Mortensen JH, Nielsen LN, Rejler M, Repsilber D, Söderholm JD, Aalykke C, Andersen V, Christensen R, Kjeldsen J. Novel biomarker profiles to improve individual diagnosis and prognosis in patients with suspected inflammatory bowel disease: protocol for the Nordic inception cohort study (NORDTREAT). BMJ Open 2024; 14:e083144. [PMID: 38754881 PMCID: PMC11097809 DOI: 10.1136/bmjopen-2023-083144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 04/25/2024] [Indexed: 05/18/2024] Open
Abstract
INTRODUCTION Inflammatory bowel disease (IBD), including ulcerative colitis and Crohn's disease, can be challenging to diagnose, and treatment outcomes are difficult to predict. In the NORDTREAT cohort study, a Nordic prospective multicentre study, we aim to identify novel molecular biomarkers of diagnostic value by assessing the diagnostic test accuracy (cross-sectionally), as well as the prognostic utility when used as prognostic markers in the long-term (cohort study). In the diagnostic test accuracy study, the primary outcome is a successful diagnosis using one or more novel index tests at baseline compared with the ECCO criteria as the reference standard. The composite outcome of the prognostic utility study is 'severe IBD' within 52 weeks from inclusion, defined as one or more of the following three events: IBD-related surgery, IBD-related hospitalisation or IBD-related death. METHODS AND ANALYSIS We aim to recruit 800 patients referred on suspicion of IBD to this longitudinal observational study, a collaboration between 11 inclusion sites in Denmark, Iceland, Norway and Sweden. Inclusion will occur from February 2022 until December 2023 with screening and baseline visits for all participants and three outcome visits at weeks 12, 26 and 52 after baseline for IBD-diagnosed patients. Biological material (blood, faeces, biopsies, urine and hair), clinical data and lifestyle information will be collected during these scheduled visits. ETHICS AND DISSEMINATION This study will explore novel biomarkers to improve diagnostic accuracy and prediction of disease progression, thereby improving medical therapy and the quality of life for patients with IBD.The study is approved by the Ethics Committee (DK: S-20200051, v1.4, 16.10.2021; IS: VSNb2021070006/03.01, NO: 193064; SE: DNR 2021-05090) and the Danish Data Protecting Agency (20/54594). Results will be disseminated through peer-reviewed journals, patient associations and presentations at international conferences. CLINICAL TRIAL REGISTRATION NUMBER NCT05414578; Pre-results.
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Affiliation(s)
- Anja Fejrskov
- Department of Medical Gastroenterology, Odense University Hospital, Odense, Denmark
- Department of Internal Medicine, Molecular Diagnostics and Clinical Research Unit, Institute of Regional Health Research, University Hospital of Southern Denmark, Aabenraa, Denmark
- Section for Biostatistics and Evidence-Based Research, Parker Institute, Frederiksberg, Denmark
| | - Johannes David Füchtbauer
- Department of Medical Gastroenterology, Odense University Hospital, Odense, Denmark
- Research Unit of Medical Gastroenterology, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
- Internal Medicine and Emergency Department, Odense University Hospital, Svendborg, Denmark
| | - Lóa G Davíðsdóttir
- Department of Gastroenterology, Landspitali National University Hospital of Iceland, Reykjavik, Iceland
| | - Jonas Halfvarson
- Department of Internal Medicine, Örebro University Hospital, Örebro, Region Örebro län, Sweden
| | - Marte Lie Høivik
- Department of Gastroenterology, Oslo University Hospital, Oslo, Norway
- University of Oslo Institute for Clinical Medicine, Oslo, Norway
| | - Michael Dam Jensen
- Department of Internal Medicine-Gastroenterology, Lillebaelt Hospital, University Hospital of Southern Denmark, Vejle, Denmark
- Institute of Regional Health Research, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | | | - Lene Nyholm Nielsen
- Research Unit of Medical Gastroenterology and Hepatology, Hospital South West Jutland, Esbjerg, Denmark
| | - Martin Rejler
- Jönköping Academy for Improvement in Health and Welfare, Jönköping University, Jönköping, Sweden
- Futurum-Academy for Healthcare, Futurum Academy of Health and Care, Jönköping, Region Jönköping County, Sweden
| | - Dirk Repsilber
- School of Health and Medical Sciences, Örebro University, Örebro, Sweden
| | - Johan D Söderholm
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Östergötland, Sweden
| | - Claus Aalykke
- Internal Medicine and Emergency Department, Odense University Hospital, Svendborg, Denmark
| | - Vibeke Andersen
- Department of Internal Medicine, Molecular Diagnostics and Clinical Research Unit, Institute of Regional Health Research, University Hospital of Southern Denmark, Aabenraa, Denmark
- Institute of Regional Health Research, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
- Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
- OPEN, Open Patient data Explorative Network, University of Southern Denmark, Odense, Denmark
| | - Robin Christensen
- Section for Biostatistics and Evidence-Based Research, Parker Institute, Frederiksberg, Denmark
- Research Unit of Rheumatology, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Jens Kjeldsen
- Department of Medical Gastroenterology, Odense University Hospital, Odense, Denmark
- Research Unit of Medical Gastroenterology, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
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13
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Gyriki D, Nikolaidis C, Stavropoulou E, Bezirtzoglou I, Tsigalou C, Vradelis S, Bezirtzoglou E. Exploring the Gut Microbiome's Role in Inflammatory Bowel Disease: Insights and Interventions. J Pers Med 2024; 14:507. [PMID: 38793089 PMCID: PMC11122163 DOI: 10.3390/jpm14050507] [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: 04/08/2024] [Revised: 05/07/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
Inflammatory Bowel Disease (IBD), encompassing Crohn's disease (CD) and ulcerative colitis (UC), is a chronic and relapsing inflammatory condition of the intestine that significantly impairs quality of life and imposes a heavy burden on healthcare systems globally. While the exact etiology of IBD is unclear, it is influenced by genetic, environmental, immunological, and microbial factors. Recent advances highlight the gut microbiome's pivotal role in IBD pathogenesis. The microbial dysbiosis characteristic of IBD, marked by a decline in beneficial bacteria and an increase in pathogenic microbes, suggests a profound connection between microbial imbalance and disease mechanisms. This review explores diagnostic approaches to IBD that integrate clinical assessment with advanced microbiological analyses, highlighting the potential of microbiome profiling as a non-invasive diagnostic tool. In addition, it evaluates conventional and emerging treatments and discusses microbiome-targeted intervention prospects, such as probiotics, symbiotics, and faecal microbiota transplantation. The necessity for future research to establish their efficacy and safety is emphasised.
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Affiliation(s)
- Despoina Gyriki
- Master Program in “Food, Nutrition and Microbiome”, Department of Medicine, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (C.T.); (S.V.); (E.B.)
- Internal Medicine Department, Vostaneio-General Hospital of Mytilene, 81100 Mytilene, Greece;
| | - Christos Nikolaidis
- Internal Medicine Department, Vostaneio-General Hospital of Mytilene, 81100 Mytilene, Greece;
| | - Elisavet Stavropoulou
- Master Program in “Food, Nutrition and Microbiome”, Department of Medicine, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (C.T.); (S.V.); (E.B.)
- Laboratory of Hygiene and Environmental Protection, Department of Medicine, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | | | - Christina Tsigalou
- Master Program in “Food, Nutrition and Microbiome”, Department of Medicine, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (C.T.); (S.V.); (E.B.)
- Laboratory of Hygiene and Environmental Protection, Department of Medicine, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - Stergios Vradelis
- Master Program in “Food, Nutrition and Microbiome”, Department of Medicine, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (C.T.); (S.V.); (E.B.)
- Department of Gastroenterology, Faculty of Medicine, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - Eugenia Bezirtzoglou
- Master Program in “Food, Nutrition and Microbiome”, Department of Medicine, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (C.T.); (S.V.); (E.B.)
- Laboratory of Hygiene and Environmental Protection, Department of Medicine, Democritus University of Thrace, 68100 Alexandroupolis, Greece
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14
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Guo HX, Wang BB, Wu HY, Feng HY, Zhang HY, Gao W, Yuan B. Turtle peptide and its derivative peptide ameliorated DSS-induced ulcerative colitis by inhibiting inflammation and modulating the composition of the gut microbiota. Int Immunopharmacol 2024; 132:112024. [PMID: 38608475 DOI: 10.1016/j.intimp.2024.112024] [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: 01/16/2024] [Revised: 03/13/2024] [Accepted: 04/04/2024] [Indexed: 04/14/2024]
Abstract
Ulcerative colitis (UC) is a recurrent intestinal disease with an increasing incidence worldwide that seriously affects the life of patients. Turtle peptide (TP) is a bioactive peptide extracted from turtles that has anti-inflammatory, antioxidant and anti-aging properties. However, studies investigating the effect of TP on the progression of UC are lacking. The aim of this study was to investigate effects and underlying mechanisms of TP and its derivative peptide GPAGPIGPV (GP-9) in alleviating UC in mice. The results showed that 500 mg/kg TP treatment significantly ameliorated colitis symptoms and oxidative stress in UC mice. TP alleviated intestinal barrier damage in UC mice by promoting mucosal repair and increasing the expression of tight junction proteins (ZO1, occludin and claudin-1). TP also modulated the composition of the gut microbiota by increasing the abundance of the beneficial bacteria Anaerotignum, Prevotellaceae_UCG-001, Alistipes, and Lachno-spiraceae_NK4A136_group and decreasing the abundance of the harmful bacteria Prevotella_9 and Parasutterella. Furthermore, we characterized the peptide composition of TP and found that GP-9 ameliorated the symptoms of dextran sodium sulfate (DSS)-induced colitis in mice by inhibiting the TLR4/NF-κB signaling pathway. In conclusion, TP and its derivative peptides ameliorated DSS-induced ulcerative colitis by inhibiting the expression of inflammatory factors and modulating the composition of the intestinal microbiota; this study provides a theoretical basis for the application of TP and its derivative peptides for their anti-inflammatory activity.
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Affiliation(s)
- Hai-Xiang Guo
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun 130062, Jilin, China.
| | - Bing-Bing Wang
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun 130062, Jilin, China.
| | - Hong-Yu Wu
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun 130062, Jilin, China; Jilin Academy of Agricultural Sciences, Jilin 132101, Jilin, China.
| | - Hao-Yuan Feng
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun 130062, Jilin, China.
| | - Hong-Yi Zhang
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun 130062, Jilin, China.
| | - Wei Gao
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun 130062, Jilin, China.
| | - Bao Yuan
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun 130062, Jilin, China.
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El Mouzan M, Al Mofarreh M, Alsaleem B, Al Sarkhy A, Alanazi A, Khormi M, Almasoud A, Assiri A. Bacterial dysbiosis in newly diagnosed treatment naïve pediatric ulcerative colitis in Saudi Arabia. Saudi J Gastroenterol 2024:00936815-990000000-00078. [PMID: 38708883 DOI: 10.4103/sjg.sjg_66_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Accepted: 04/01/2024] [Indexed: 05/07/2024] Open
Abstract
BACKGROUND The role of microbiota in the pathogenesis of ulcerative colitis (UC) has been increasingly recognized. However, most of the reports are from Western populations. In Middle Eastern countries, including Saudi Arabia, little is known about the role of microbiota. Therefore, our aim was to describe the bacterial microbiota profile and signature in pediatric UC in Saudi Arabia. METHODS Twenty children with UC and 20 healthy controls enrolled in the study gave stool samples. Twenty rectal mucosal samples were taken from UC and 20 from non-UC controls. Inclusion criteria included newly diagnosed and untreated children and lack of antibiotic exposure for at least 6 months before stool collection was required for children with UC and controls. Bacterial deoxyribonucleic acid was extracted and sequenced using shotgun metagenomic analysis. Statistical analysis included Shannon alpha diversity metrics, Bray-Curtis dissimilarity, DESeq2, and biomarker discovery. RESULTS The demographic characteristics were similar in children with UC and controls. There was a significant reduction in alpha diversity (P = 0.037) and beta diversity in samples from children with UC (P = 0.001). Many taxa were identified with log2 abundance analysis, revealing 110 and 102 species significantly depleted and enriched in UC, respectively. Eleven bacterial species' signatures were identified. CONCLUSIONS In Saudi Arabian children with UC, we demonstrate a dysbiosis similar to reports from Western populations, possibly related to changes of lifestyle. Microbial signature discovery in this report is an important contribution to research, leading to the development of adjunctive non-invasive diagnostic options in unusual cases of UC.
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Affiliation(s)
- Mohammad El Mouzan
- Department of Pediatrics (Gastroenterology Unit), College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | | | - Badr Alsaleem
- King Fahad Medical City, Intestinal Failure Program, Riyadh, Saudi Arabia
| | - Ahmed Al Sarkhy
- Department of Pediatrics (Gastroenterology Unit), College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Aziz Alanazi
- King Abdullah Specialized Children Hospital, Gastroenterology Unit, National Guard, Riyadh, Saudi Arabia
| | - Musa Khormi
- Pediatric Gastroenterology, King Saud Medical City, Riyadh-1 Health Cluster, Riyadh, Saudi Arabia
| | - Abdullah Almasoud
- Department of Pediatrics (Gastroenterology Unit), College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Asaad Assiri
- Department of Pediatrics (Gastroenterology Unit), College of Medicine, King Saud University, Riyadh, Saudi Arabia
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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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Paudel D, Nair DVT, Joseph G, Castro R, Tiwari AK, Singh V. Gastrointestinal microbiota-directed nutritional and therapeutic interventions for inflammatory bowel disease: opportunities and challenges. Gastroenterol Rep (Oxf) 2024; 12:goae033. [PMID: 38690290 PMCID: PMC11057942 DOI: 10.1093/gastro/goae033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 03/01/2024] [Accepted: 03/08/2024] [Indexed: 05/02/2024] Open
Abstract
Evidence-based research has confirmed the role of gastrointestinal microbiota in regulating intestinal inflammation. These data have generated interest in developing microbiota-based therapies for the prevention and management of inflammatory bowel disease (IBD). Despite in-depth understanding of the etiology of IBD, it currently lacks a cure and requires ongoing management. Accumulating data suggest that an aberrant gastrointestinal microbiome, often referred to as dysbiosis, is a significant environmental instigator of IBD. Novel microbiome-targeted interventions including prebiotics, probiotics, fecal microbiota transplant, and small molecule microbiome modulators are being evaluated as therapeutic interventions to attenuate intestinal inflammation by restoring a healthy microbiota composition and function. In this review, the effectiveness and challenges of microbiome-centered interventions that have the potential to alleviate intestinal inflammation and improve clinical outcomes of IBD are explored.
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Affiliation(s)
- Devendra Paudel
- Department of Nutritional Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Divek V T Nair
- Department of Nutritional Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Grace Joseph
- Department of Nutritional Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Rita Castro
- Department of Nutritional Sciences, The Pennsylvania State University, University Park, PA, USA
- Department of Pharmaceutical Sciences and Medicines, Faculty of Pharmacy, Universidade de Lisboa, Lisboa, Portugal
| | - Amit K Tiwari
- College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Vishal Singh
- Department of Nutritional Sciences, The Pennsylvania State University, University Park, PA, USA
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18
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Kruis W, Bokemeyer B, Jessen P, Hoesl M, Mroß M, Morgenstern J, Reimers B, Müller-Grage N, Leifeld L. Prospective Evaluation of the Prediction Score for a Mild Course of Crohn's Disease (PreMiCC) in Newly Diagnosed Patients With Crohn's Disease: The PROGNOS Study. Inflamm Bowel Dis 2024:izae086. [PMID: 38648264 DOI: 10.1093/ibd/izae086] [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: 10/22/2023] [Indexed: 04/25/2024]
Abstract
BACKGROUND AND AIMS The course of Crohn's disease (CD) is highly variable. The Prospektive Evaluation eines Score zur Vorhersage eines milden Verlaufsbei neu diagnostizierten Morbus Crohn-Patienten in gastroenterologischen Fachpraxen (PROGNOS) study aimed to determine the frequency of a mild disease course and validate a proposed prediction score. METHODS The PROGNOS study is a prospective study of CD patients who were newly diagnosed and, except for 1 course of 5-aminosalicylic acid or steroids for ≤10 days, therapy-naïve. Among other predefined inclusion criteria, the initial diagnosis had to be made ≤6 weeks before enrollment. All inception cohort patients were diagnosed and screened consecutively in participating gastroenterology practices in Germany specialized in inflammatory bowel disease. All screened CD patients were scored and, if possible, included in the study for up to 5 years (NCT02193048). RESULTS A total of 201 CD patients were included in the study (43.3% male; mean age 33 years, mean follow-up 38 months). Altogether, 29.5% of the patients had a mild course at 36 months. Among those with a score ≤2, therapy escalation at 36 months was necessary for only 24.2%, whereas in the group with a score >2, therapy escalation was necessary for 70.2% of patients. In the Kaplan-Meier curve showing time to therapy escalation in the 2 groups, there was a pronounced and statistically significant divergence of the curves starting at 3 months and extending to 48 months (P < .001). CONCLUSIONS In this prospective study, about 30% of incident CD patients had a mild disease course. Our suggested PreMiCC (prediction score for a mild course of Crohn's disease) successfully predicted this.
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Affiliation(s)
- Wolfgang Kruis
- Internal Medicine, Protestant Hospital, Cologne, Germany
| | - Bernd Bokemeyer
- Department of Internal Medicine, Interdisciplinary Crohn Colitis Centre, Minden, Germany
- Clinic of General Internal Medicine I, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Petra Jessen
- Gastroenterology Practice, Kiel-Altenholz, Germany
| | - Mark Hoesl
- Gastroenterology Practice Clinic, Nuremberg, Germany
| | | | | | - Birgitta Reimers
- Department of Internal Medicine, Ferring Arzneimittel GmbH, Kiel, Germany
| | - Nike Müller-Grage
- Department of Internal Medicine, Ferring Arzneimittel GmbH, Kiel, Germany
| | - Ludger Leifeld
- Department of Internal Medicine, St. Bernward Hospital, Hildesheim, Germany
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19
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Sun M, Ju J, Xu H, Luo M, Li Z, Wang Y. Antibiotics influence the risk of anti-drug antibody formation during anti-TNF therapy in Chinese inflammatory bowel disease patients. Front Pharmacol 2024; 15:1360835. [PMID: 38655181 PMCID: PMC11035825 DOI: 10.3389/fphar.2024.1360835] [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: 12/24/2023] [Accepted: 03/20/2024] [Indexed: 04/26/2024] Open
Abstract
Aims: The formation of anti-drug antibodies (ADAs) during anti-tumor necrosis factor (anti-TNF) therapy is reported to lead to reducing serum drug levels, which may bring about a loss of response to treatment. Previous research has suggested an association between specific antibiotic classes and ADA formation during anti-TNF therapy. However, there are few studies specifically examining this association in Chinese inflammatory bowel disease (IBD) patients. Therefore, our study aimed to evaluate the possible effect of antibiotic use on ADA formation to anti-TNF therapy in Chinese patients with IBD. Methods: A total of 166 patients with IBD, including 149 with Crohn's disease (CD) and 17 with ulcerative colitis (UC), were included in this retrospective analysis. These patients were initially treated with anti-TNF therapy (infliximab or adalimumab) after January 2018 and reviewed with available ADA levels before October 2023. After univariable analysis of all the variables, a multivariate Cox proportional hazards model was used to assess the association between antibiotic use and ADA development. Results: Among 166 IBD patients treated with infliximab (108/166, 65.1%) or adalimumab (58/166, 34.9%), 31 patients (18.7%) were measured as positive ADA levels. Cox proportional hazard model demonstrated an increased risk of ADA formation in IBD patients who used β-lactam-β-lactamase inhibitor combinations (BL-BLIs) (HR = 5.143, 95%CI 1.136-23.270, p = 0.033), or nitroimidazoles (HR = 4.635, 95%CI 1.641-13.089, p = 0.004) during 12 months before the ADA test. On the contrary, a reduced risk was noted in patients treated with fluoroquinolones (HR = 0.258, 95% CI 0.072-0.924, p = 0.037). Moreover, the median serum infliximab or adalimumab concentration in patients with positive ADA levels was significantly lower than that in patients with negative ADA levels (infliximab: 0.30 vs. 1.85 μg/mL, p < 0.0001; adalimumab: 0.45 vs. 7.55 μg/mL, p = 0.0121). Conclusion: ADA development is associated with various antibiotic classes. BL-BLIs and nitroimidazoles might increase the risk of ADA formation during anti-TNF therapy in Chinese IBD patients, while the treatment with fluoroquinolones could probably reduce such risk. There were certain limitations in the retrospective analysis of the study, therefore, the results are just for reference, and other studies are needed to further confirm our findings.
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Affiliation(s)
| | | | | | | | | | - Yufang Wang
- Department of Gastroenterology and Hepatology, West China Hospital, Sichuan University, Chengdu, China
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20
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Boppana K, Almansouri NE, Bakkannavar S, Faheem Y, Jaiswal A, Shergill K, Nath TS. Alterations in Gut Microbiota as Early Biomarkers for Predicting Inflammatory Bowel Disease Onset and Progression: A Systematic Review. Cureus 2024; 16:e58080. [PMID: 38741828 PMCID: PMC11088963 DOI: 10.7759/cureus.58080] [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: 01/25/2024] [Accepted: 04/11/2024] [Indexed: 05/16/2024] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic ailment impacting the digestive system, triggered by an unusual reaction of the immune system. It includes two types of diseases: ulcerative colitis and Crohn's disease. Nonetheless, the diagnosis and evaluation of disease progression in IBD are difficult due to the absence of distinct indicators. While conventional biomarkers from blood plasma and feces, such as C-reactive protein, fecal calprotectin, and S100A12, can be employed to gauge inflammation, they are not exclusive to IBD. There is a broad consensus that intestinal microorganisms significantly contribute to the onset of intestinal imbalance, a condition intimately linked with the cause and development of IBD. Numerous studies have indicated that the makeup of intestinal microorganisms varies between individuals with IBD and those who are healthy, particularly concerning the diversity of microbes and the proportional prevalence of certain bacteria. A total of 1475 records underwent examination. Following the eligibility assessment, 17 reports were considered. The final review encompassed 12 studies, as five articles were excluded due to insufficient details regarding cases, controls, and comparability. This article suggests that gut microbiota has potential biomarkers for the noninvasive evaluation of IBD activity. Recognizing the microbiome linked with disease activity paves the way for the development of a group of microbiota-derived indicators to evaluate the initiation and advancement of IBD. This article discusses whether changes in gut microbial composition can serve as early indicators of IBD onset and progression.
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Affiliation(s)
- Kusalik Boppana
- Internal Medicine, California Institute of Behavioral Neurosciences & Psychology, Fairfield, USA
- Internal Medicine, Manipal University, Manipal, IND
| | - Naiela E Almansouri
- Internal Medicine, California Institute of Behavioral Neurosciences & Psychology, Fairfield, USA
- Internal Medicine, University of Tripoli, Tripoli, LBY
| | - Saloni Bakkannavar
- Pediatrics, California Institute of Behavioral Neurosciences & Psychology, Fairfield, USA
| | - Youmna Faheem
- Pediatrics, California Institute of Behavioral Neurosciences & Psychology, Fairfield, USA
- Medicine, New Medical Center Royal Hospital, Abu Dhabi, ARE
| | - Amisha Jaiswal
- Internal Medicine, California Institute of Behavioral Neurosciences & Psychology, Fairfield, USA
| | - Kainaat Shergill
- Surgery, California Institute of Behavioral Neurosciences & Psychology, Fairfield, USA
- Medicine, Maharishi Markandeshwar Institute of Medical Sciences and Research, Mullana, IND
| | - Tuheen Sankar Nath
- Surgical Oncology, California Institute of Behavioral Neurosciences & Psychology, Fairfield, USA
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21
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Marshall-Jones ZV, Patel KV, Castillo-Fernandez J, Lonsdale ZN, Haydock R, Staunton R, Amos GCA, Watson P. Conserved signatures of the canine faecal microbiome are associated with metronidazole treatment and recovery. Sci Rep 2024; 14:5277. [PMID: 38438389 PMCID: PMC10912219 DOI: 10.1038/s41598-024-51338-7] [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: 09/29/2023] [Accepted: 01/03/2024] [Indexed: 03/06/2024] Open
Abstract
Antibiotic resistance is recognised as one of the biggest global threats to human and animal health. Understanding the influence of antibiotics on the canine microbiome is important to know the potential mid-to-long term effects on dysbiosis and mitigate side-effects such as antibiotic-associated diarrhoea. In this study, metronidazole was prescribed to 22 dogs for suspected giardiasis after exhibiting gastrointestinal symptoms such as diarrhoea and/or vomiting. Faecal samples were collected before, during seven days of treatment, and six months post-cessation. Faecal microbiota was assessed with 16S rRNA sequencing. Shannon diversity was reduced for up to three days after the treatment ended, and an altered community persisted for four to six weeks. All dogs recovered to a similar microbiome composition as pre-treatment. Immediately after receiving metronidazole, an increase in the relative abundance of the genera Lactobacillus, Bifidobacterium, and Enterococcus was observed. This may be due to antibiotic resistance commonly exhibited by these organisms. One-to-two weeks post-cessation, several other genera that were sensitive to the antibiotic recovered in abundances, with taxa belonging to the Erysipelotrichaceae family particularly driving composition change. Many of the bacteria initially reduced were associated with carbohydrate fermentation. This suggests scope exists to explore interventions to augment gastrointestinal health and support the re-establishment of the microbiome.
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Affiliation(s)
- Zoe V Marshall-Jones
- Waltham Petcare Science Institute, Waltham on the Wolds, Leicestershire, LE14 4RT, UK
| | - Krusha V Patel
- Waltham Petcare Science Institute, Waltham on the Wolds, Leicestershire, LE14 4RT, UK.
| | | | - Zoe N Lonsdale
- Waltham Petcare Science Institute, Waltham on the Wolds, Leicestershire, LE14 4RT, UK
| | - Richard Haydock
- Waltham Petcare Science Institute, Waltham on the Wolds, Leicestershire, LE14 4RT, UK
| | - Ruth Staunton
- Waltham Petcare Science Institute, Waltham on the Wolds, Leicestershire, LE14 4RT, UK
| | - Gregory C A Amos
- Waltham Petcare Science Institute, Waltham on the Wolds, Leicestershire, LE14 4RT, UK
| | - Phillip Watson
- Waltham Petcare Science Institute, Waltham on the Wolds, Leicestershire, LE14 4RT, UK
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22
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Xu C, Shao J. High-throughput omics technologies in inflammatory bowel disease. Clin Chim Acta 2024; 555:117828. [PMID: 38355001 DOI: 10.1016/j.cca.2024.117828] [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: 07/23/2023] [Revised: 02/06/2024] [Accepted: 02/10/2024] [Indexed: 02/16/2024]
Abstract
Inflammatory bowel disease (IBD) is a chronic, relapsing intestinal disease. Elucidation of the pathogenic mechanisms of IBD requires high-throughput technologies (HTTs) to effectively obtain and analyze large amounts of data. Recently, HTTs have been widely used in IBD, including genomics, transcriptomics, proteomics, microbiomics, metabolomics and single-cell sequencing. When combined with endoscopy, the application of these technologies can provide an in-depth understanding on the alterations of intestinal microbe diversity and abundance, the abnormalities of signaling pathway-mediated immune responses and functionality, and the evaluation of therapeutic effects, improving the accuracy of early diagnosis and treatment of IBD. This review comprehensively summarizes the development and advancement of HTTs, and also highlights the challenges and future directions of these technologies in IBD research. Although HTTs have made striking breakthrough in IBD, more standardized methods and large-scale dataset processing are still needed to achieve the goal of personalized medicine.
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Affiliation(s)
- Chen Xu
- Laboratory of Anti-infection and Immunity, College of Integrated Chinese and Western Medicine (College of Life Science), Anhui University of Chinese Medicine, Zhijing Building, 350 Longzihu Road, Xinzhan District, Hefei 230012, Anhui, PR China
| | - Jing Shao
- Laboratory of Anti-infection and Immunity, College of Integrated Chinese and Western Medicine (College of Life Science), Anhui University of Chinese Medicine, Zhijing Building, 350 Longzihu Road, Xinzhan District, Hefei 230012, Anhui, PR China; Institute of Integrated Traditional Chinese and Western Medicine, Anhui Academy of Chinese Medicine, Zhijing Building, 350 Longzihu Road, Xinzhan District, Hefei 230012, Anhui, PR China.
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23
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Xiao P, Cai X, Zhang Z, Guo K, Ke Y, Hu Z, Song Z, Zhao Y, Yao L, Shen M, Li J, Huang Y, Ye L, Huang L, Zhang Y, Liu R, Xu M, Xu X, Zhao Y, Cao Q. Butyrate Prevents the Pathogenic Anemia-Inflammation Circuit by Facilitating Macrophage Iron Export. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306571. [PMID: 38235606 DOI: 10.1002/advs.202306571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 12/15/2023] [Indexed: 01/19/2024]
Abstract
Most patients with inflammatory bowel disease (IBD) develop anemia, which is attributed to the dysregulation of iron metabolism. Reciprocally, impaired iron homeostasis also aggravates inflammation. How this iron-mediated, pathogenic anemia-inflammation crosstalk is regulated in the gut remains elusive. Herein, it is for the first time revealed that anemic IBD patients exhibit impaired production of short-chain fatty acids (SCFAs), particularly butyrate. Butyrate supplementation restores iron metabolism in multiple anemia models. Mechanistically, butyrate upregulates ferroportin (FPN) expression in macrophages by reducing the enrichment of histone deacetylase (HDAC) at the Slc40a1 promoter, thereby facilitating iron export. By preventing iron sequestration, butyrate not only mitigates colitis-induced anemia but also reduces TNF-α production in macrophages. Consistently, macrophage-conditional FPN knockout mice exhibit more severe anemia and inflammation. Finally, it is revealed that macrophage iron overload impairs the therapeutic effectiveness of anti-TNF-α antibodies in colitis, which can be reversed by butyrate supplementation. Hence, this study uncovers the pivotal role of butyrate in preventing the pathogenic circuit between anemia and inflammation.
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Affiliation(s)
- Peng Xiao
- Department of Gastroenterology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, China
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, China
- The Key Laboratory for Immunity and Inflammatory Diseases of Zhejiang Province, Hangzhou, 310058, China
- Inflammatory Bowel Diseases Center, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, China
| | - Xuechun Cai
- Department of Gastroenterology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, China
- Inflammatory Bowel Diseases Center, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, China
| | - Zhou Zhang
- Department of Gastroenterology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, China
- Inflammatory Bowel Diseases Center, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, China
| | - Ke Guo
- Department of Gastroenterology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, China
- Inflammatory Bowel Diseases Center, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, China
| | - Yuehai Ke
- Department of Pathology and Pathophysiology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, China
| | - Ziwei Hu
- Department of Pathology and Pathophysiology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, China
| | - Zhangfa Song
- Department of Colorectal Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, China
| | - Yuening Zhao
- Department of Gastroenterology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, China
- Inflammatory Bowel Diseases Center, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, China
| | - Lingya Yao
- Department of Gastroenterology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, China
- Inflammatory Bowel Diseases Center, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, China
| | - Manlu Shen
- Department of Gastroenterology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, China
- Inflammatory Bowel Diseases Center, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, China
| | - Jingyun Li
- Department of Colorectal Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, China
| | - Youling Huang
- Department of Gastroenterology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, China
- Inflammatory Bowel Diseases Center, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, China
| | - Lingna Ye
- Department of Gastroenterology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, China
- Inflammatory Bowel Diseases Center, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, China
| | - Lingjie Huang
- Department of Gastroenterology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, China
- Inflammatory Bowel Diseases Center, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, China
| | - Yu Zhang
- Department of Gastroenterology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, China
- Inflammatory Bowel Diseases Center, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, China
| | - Rongbei Liu
- Department of Gastroenterology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, China
- Inflammatory Bowel Diseases Center, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, China
| | - Mengque Xu
- Department of Gastroenterology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, China
- Inflammatory Bowel Diseases Center, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, China
| | - Xutao Xu
- Department of Gastroenterology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, China
- Inflammatory Bowel Diseases Center, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, China
| | - Yuan Zhao
- Department of Gastroenterology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, China
- Inflammatory Bowel Diseases Center, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, China
| | - Qian Cao
- Department of Gastroenterology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, China
- Inflammatory Bowel Diseases Center, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310016, China
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24
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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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25
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Arosa L, Camba-Gómez M, Golubnitschaja O, Conde-Aranda J. Predictive, preventive and personalised approach as a conceptual and technological innovation in primary and secondary care of inflammatory bowel disease benefiting affected individuals and populations. EPMA J 2024; 15:111-123. [PMID: 38463620 PMCID: PMC10923750 DOI: 10.1007/s13167-024-00351-x] [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: 01/16/2024] [Accepted: 01/25/2024] [Indexed: 03/12/2024]
Abstract
Inflammatory bowel disease (IBD) is a global health burden which carries lifelong morbidity affecting all age groups in populations with the disease-specific peak of the age groups ranging between 15 and 35 years, which are of great economic importance for the society. An accelerating incidence of IBD is reported for newly industrialised countries, whereas stabilising incidence but increasing prevalence is typical for countries with a Westernised lifestyle, such as the European area and the USA. Although the aetiology of IBD is largely unknown, the interplay between the genetic, environmental, immunological, and microbial components is decisive for the disease manifestation, course, severity and individual outcomes. Contextually, the creation of an individualised patient profile is crucial for the cost-effective disease management in primary and secondary care of IBD. The proposed pathomechanisms include intestinal pathoflora and dysbiosis, chronic inflammation and mitochondrial impairments, amongst others, which collectively may reveal individual molecular signatures defining IBD subtypes and leading to clinical phenotypes, patient stratification and cost-effective protection against health-to-disease transition and treatments tailored to individualised patient profiles-all the pillars of an advanced 3PM approach. The paradigm change from reactive medical services to predictive diagnostics, cost-effective targeted prevention and treatments tailored to individualised patient profiles in overall IBD management holds a promise to meet patient needs in primary and secondary care, to increase the life-quality of affected individuals and to improve health economy in the area of IBD management. This article analyses current achievements and provides the roadmap for future developments in the area in the context of 3P medicine benefiting society at large.
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Affiliation(s)
- Laura Arosa
- Molecular and Cellular Gastroenterology, Health Research Institute of Santiago de Compostela (IDIS), Laboratory 15, Trav. Choupana S/N, Building C, Level -2, 15706 Santiago de Compostela, Spain
| | - Miguel Camba-Gómez
- Molecular and Cellular Gastroenterology, Health Research Institute of Santiago de Compostela (IDIS), Laboratory 15, Trav. Choupana S/N, Building C, Level -2, 15706 Santiago de Compostela, Spain
| | - Olga Golubnitschaja
- 3P Medicine Research Unit, University Hospital, Rheinische Friedrich-Wilhelms Universität Bonn, 53127 Bonn, Germany
| | - Javier Conde-Aranda
- Molecular and Cellular Gastroenterology, Health Research Institute of Santiago de Compostela (IDIS), Laboratory 15, Trav. Choupana S/N, Building C, Level -2, 15706 Santiago de Compostela, Spain
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Vidal-Gallardo A, Méndez Benítez JE, Flores Rios L, Ochoa Meza LF, Mata Pérez RA, Martínez Romero E, Vargas Beltran AM, Beltran Hernandez JL, Banegas D, Perez B, Martinez Ramirez M. The Role of Gut Microbiome in the Pathogenesis and the Treatment of Inflammatory Bowel Diseases. Cureus 2024; 16:e54569. [PMID: 38516478 PMCID: PMC10957260 DOI: 10.7759/cureus.54569] [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] [Accepted: 02/16/2024] [Indexed: 03/23/2024] Open
Abstract
Inflammatory bowel disease (IBD), which includes ulcerative colitis and Crohn's disease, is a chronic condition characterized by inflammation of the gastrointestinal tract. Its exact cause is unknown, but it's thought to result from a dysregulated immune response influenced by various factors, including changes in the intestinal microbiota, diet, lifestyle, and genetics. The gut microbiome, consisting of diverse microorganisms, plays a crucial role in maintaining physiological balance, with its disruption leading to inflammatory responses typical of IBD. Treatments primarily aim at symptom control, employing immunomodulators, corticosteroids, and newer approaches like probiotics, prebiotics, fecal transplants, and dietary modifications, all focusing on leveraging the microbiota's potential in disease management. These strategies aim to restore the delicate balance of the gut microbiome, typically altered in IBD, marked by a decrease in beneficial bacteria and an increase in harmful pathogens. This review underscores the importance of the gut microbiome in the pathogenesis and treatment of IBD, highlighting the shift towards personalized medicine and the necessity for further research in understanding the complex interactions between the gut microbiota, immune system, and genetics in IBD. It points to the potential of emerging treatments and the importance of a multifaceted approach in managing this complex and challenging disease.
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Affiliation(s)
| | | | | | - Luis F Ochoa Meza
- General Surgery, Hospital General ISSSTE Presidente General Lázaro Cárdenas, Chihuahua, MEX
| | - Rodrigo A Mata Pérez
- General Practice, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Ciudad de México, MEX
| | | | | | | | - Douglas Banegas
- General Medicine, Universidad Nacional Autonoma de Honduras, San Pedro Sula, HND
| | - Brenda Perez
- Nutrition, Universidad ICEL, Ciudad de México, MEX
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27
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Wu J, Singleton SS, Bhuiyan U, Krammer L, Mazumder R. Multi-omics approaches to studying gastrointestinal microbiome in the context of precision medicine and machine learning. Front Mol Biosci 2024; 10:1337373. [PMID: 38313584 PMCID: PMC10834744 DOI: 10.3389/fmolb.2023.1337373] [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: 11/15/2023] [Accepted: 12/27/2023] [Indexed: 02/06/2024] Open
Abstract
The human gastrointestinal (gut) microbiome plays a critical role in maintaining host health and has been increasingly recognized as an important factor in precision medicine. High-throughput sequencing technologies have revolutionized -omics data generation, facilitating the characterization of the human gut microbiome with exceptional resolution. The analysis of various -omics data, including metatranscriptomics, metagenomics, glycomics, and metabolomics, holds potential for personalized therapies by revealing information about functional genes, microbial composition, glycans, and metabolites. This multi-omics approach has not only provided insights into the role of the gut microbiome in various diseases but has also facilitated the identification of microbial biomarkers for diagnosis, prognosis, and treatment. Machine learning algorithms have emerged as powerful tools for extracting meaningful insights from complex datasets, and more recently have been applied to metagenomics data via efficiently identifying microbial signatures, predicting disease states, and determining potential therapeutic targets. Despite these rapid advancements, several challenges remain, such as key knowledge gaps, algorithm selection, and bioinformatics software parametrization. In this mini-review, our primary focus is metagenomics, while recognizing that other -omics can enhance our understanding of the functional diversity of organisms and how they interact with the host. We aim to explore the current intersection of multi-omics, precision medicine, and machine learning in advancing our understanding of the gut microbiome. A multidisciplinary approach holds promise for improving patient outcomes in the era of precision medicine, as we unravel the intricate interactions between the microbiome and human health.
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Affiliation(s)
- Jingyue Wu
- Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, United States
| | - Stephanie S. Singleton
- Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, United States
| | - Urnisha Bhuiyan
- Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, United States
| | - Lori Krammer
- Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, United States
- Milken Institute School of Public Health, The George Washington University, Washington, DC, United States
| | - Raja Mazumder
- Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, United States
- The McCormick Genomic and Proteomic Center, The George Washington University, Washington, DC, United States
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28
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Loch FN, Kamphues C, Menzel P, Schwarzer R, Beyer K, Schineis C. Mucosal microbiome of surgically treated terminal ileal Crohn's disease. Front Cell Infect Microbiol 2024; 13:1324668. [PMID: 38282618 PMCID: PMC10811112 DOI: 10.3389/fcimb.2023.1324668] [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: 10/23/2023] [Accepted: 12/15/2023] [Indexed: 01/30/2024] Open
Abstract
Crohn's disease (CD) is associated with changes in the microbiome. The role of these changes and their precise association with disease course and activity remain ambiguous. In this prospective single-center study, the mucosal microbiome of surgical CD and non-CD patients was compared at the time of surgery. Microbial analyses were individually performed for ileal and colonic tissue samples obtained during surgery using 16S-rRNA-gene amplicon sequencing. Three groups out of the 46 included patients were formed: 1) a study group of CD of patients who received ileocecal resection due to CD involvement (CD study, n=10); 2) a control group of non-CD of patients who received intestinal resection due to indications other than CD (non-CD control, n=27); and 3) a second control group of CD who underwent resection of the intestine not affected by CD (CD non-affected control, n=9). Species richness and Shannon diversity were not different between all formed groups and regions analyzed (p>0.05). Several significant taxonomic differences were seen at the phylum-, order-, and genus-levels between the formed groups, such as a decrease of Firmicutes (phylum-level) and an increase of Bacteroides and Escherichia/Shigella/Pseudescherichia (genus-level) in CD study - colon vs. the non-CD control - colon (p ≤ 0.05). The CD non-affected control presented the largest amount of differentially abundant taxa in comparison to the other groups. These results underline that CD is accompanied by changes in affected and non-affected intestinal regions compared to non-CD controls. This study contributes the mucosal microbiome of a well-defined subset of surgical CD patients without confounding aspects of the fecal microbiome or regional microbial differences to the existing literature.
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Affiliation(s)
- Florian N. Loch
- Department of Surgery, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | | | - Peter Menzel
- Labor Berlin – Charité Vivantes GmbH, Berlin, Germany
| | | | - Katharina Beyer
- Department of Surgery, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Christian Schineis
- Department of Surgery, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
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29
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Ye S, Lyu Y, Chen L, Wang Y, He Y, Li Q, Tian L, Liu F, Wang X, Ai F. Construction of a molecular inflammatory predictive model with histone modification-related genes and identification of CAMK2D as a potential response signature to infliximab in ulcerative colitis. Front Immunol 2024; 14:1282136. [PMID: 38274809 PMCID: PMC10808628 DOI: 10.3389/fimmu.2023.1282136] [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: 08/23/2023] [Accepted: 12/19/2023] [Indexed: 01/27/2024] Open
Abstract
Background Ulcerative colitis (UC) is a lifelong inflammatory disease affecting the rectum and colon with numerous treatment options that require an individualized treatment plan. Histone modifications regulate chromosome structure and gene expression, resulting in effects on inflammatory and immune responses. However, the relationship between histone modification-related genes and UC remains unclear. Methods Transcriptomic data from GSE59071 and GSE66407 were obtained from the Gene Expression Omnibus (GEO), encompassing colonic biopsy expression profiles of UC patients in inflamed and non-inflamed status. Differentially expressed gene (DEG) analyses, functional enrichment analyses, weighted gene co-expression network analysis (WGCNA), and random forest were performed to identify histone modification-related core genes associated with UC inflammation. Features were screened through the least absolute shrinkage and selection operator (LASSO) and support vector machine-recursive feature elimination (SVM-RFE), establishing a molecular inflammatory predictive model using logistic regression. The model was validated in the GSE107499 dataset, and the performance of the features was assessed using receiver operating characteristic (ROC) and calibration curves. Immunohistochemistry (IHC) staining of colonic biopsy tissues from UC patients treated with infliximab was used to further confirm the clinical application value. Univariate logistic regression on GSE14580 highlighted features linked to infliximab response. Results A total of 253 histone modification-related DEGs were identified between inflammatory and non-inflammatory patients with UC. Seven key genes (IL-1β, MSL3, HDAC7, IRF4, CAMK2D, AUTS2, and PADI2) were selected using WGCNA and random forest. Through univariate logistic regression, three core genes (CAMK2D, AUTS2, and IL-1β) were further incorporated to construct the molecular inflammatory predictive model. The area under the curve (AUC) of the model was 0.943 in the independent validation dataset. A significant association between CAMK2D protein expression and infliximab response was observed, which was validated in another independent verification set of GSE14580 from the GEO database. Conclusion The molecular inflammatory predictive model based on CAMK2D, AUTS2, and IL-1β could reliably distinguish the mucosal inflammatory status of UC patients. We further revealed that CAMK2D was a predictive marker of infliximab response. These findings are expected to provide a new evidence base for personalized treatment and management strategies for UC patients.
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Affiliation(s)
- Shuyu Ye
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Non-Resolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Yongqing Lyu
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Libin Chen
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Non-Resolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Yiwei Wang
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, China
- Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Yue He
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, China
- Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Quansi Li
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, China
- Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Li Tian
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Non-Resolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Fen Liu
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Non-Resolving Inflammation and Cancer, The Third Xiangya Hospital, 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, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Feiyan Ai
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Non-Resolving Inflammation and Cancer, The Third Xiangya Hospital, Central South University, Changsha, China
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30
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Ananthakrishnan AN. Precision medicine in inflammatory bowel diseases. Intest Res 2024; 22:8-14. [PMID: 37939722 PMCID: PMC10850693 DOI: 10.5217/ir.2023.00087] [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: 07/26/2023] [Revised: 09/16/2023] [Accepted: 10/05/2023] [Indexed: 11/10/2023] Open
Abstract
Inflammatory bowel diseases comprising Crohn's disease and ulcerative colitis have emerged as global diseases. Multiple distinct therapeutic mechanisms have allowed us to increase our rates of achieving remission and reducing permanent disease-related morbidity. However, there is limited data to inform relative positioning of different therapies. This review will summarize existing literature on use of clinical decision models to inform relative efficacy of one therapeutic mechanism compared to the other given individual patient characteristics. It will also demonstrate the value of serologic, transcriptomic (from biopsies), and microbiome-based biomarkers in identifying which therapy is most likely to work for a given patient. We will review the existing gaps in the literature in this field and suggest a path forward for future studies to better inform patient care, incorporating the principles of precision medicine in the management of inflammatory bowel disease.
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Affiliation(s)
- Ashwin N. Ananthakrishnan
- Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
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31
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Arora U, Kedia S, Ahuja V. The practice of fecal microbiota transplantation in inflammatory bowel disease. Intest Res 2024; 22:44-64. [PMID: 37981746 PMCID: PMC10850701 DOI: 10.5217/ir.2023.00085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/10/2023] [Accepted: 09/14/2023] [Indexed: 11/21/2023] Open
Abstract
Current evidence posits a central role for gut microbiota and the metabolome in the pathogenesis and progression of inflammatory bowel disease (IBD). Fecal microbiota transplantation (FMT) has been established as a means to manipulate this microbiome safely and sustainably. Several aspects of the technical improvement including pretreatment with antibiotics, use of frozen stool samples as well as short donor-to-recipient time are proposed to improve its response rates. Its efficacy in ulcerative colitis has been proven in clinical trials while data is emerging for Crohn's disease. This review describes briefly the biology behind FMT, the available evidence for its use in IBD, and the host, recipient and procedural factors which determine the clinical outcomes.
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Affiliation(s)
- Umang Arora
- Department of Gastroenterology and Human Nutrition, All India Institute of Medical Sciences, New Delhi, India
| | - Saurabh Kedia
- Department of Gastroenterology and Human Nutrition, All India Institute of Medical Sciences, New Delhi, India
| | - Vineet Ahuja
- Department of Gastroenterology and Human Nutrition, All India Institute of Medical Sciences, New Delhi, India
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32
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Sosnowski K, Przybyłkowski A. Ethanol-induced changes to the gut microbiome compromise the intestinal homeostasis: a review. Gut Microbes 2024; 16:2393272. [PMID: 39224006 PMCID: PMC11376419 DOI: 10.1080/19490976.2024.2393272] [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: 03/19/2024] [Revised: 08/06/2024] [Accepted: 08/12/2024] [Indexed: 09/04/2024] Open
Abstract
The intestine is the largest organ in terms of surface area in the human body. It is responsible not only for absorbing nutrients but also for protection against the external world. The gut microbiota is essential in maintaining a properly functioning intestinal barrier, primarily through producing its metabolites: short-chain fatty acids, bile acids, and tryptophan derivatives. Ethanol overconsumption poses a significant threat to intestinal health. Not only does it damage the intestinal epithelium, but, maybe foremostly, it changes the gut microbiome. Those ethanol-driven changes shift its metabolome, depriving the host of the protective effect the physiological gut microbiota has. This literature review discusses the impact of ethanol consumption on the gut, the gut microbiota, and its metabolome, providing a comprehensive overview of the mechanisms through which ethanol disrupts intestinal homeostasis and discussing potential avenues for new therapeutic intervention.
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Affiliation(s)
- Konrad Sosnowski
- Department of Gastroenterology and Internal Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Adam Przybyłkowski
- Department of Gastroenterology and Internal Medicine, Medical University of Warsaw, Warsaw, Poland
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33
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Pandey H, Jain D, Tang DWT, Wong SH, Lal D. Gut microbiota in pathophysiology, diagnosis, and therapeutics of inflammatory bowel disease. Intest Res 2024; 22:15-43. [PMID: 37935653 PMCID: PMC10850697 DOI: 10.5217/ir.2023.00080] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 08/23/2023] [Accepted: 08/27/2023] [Indexed: 11/09/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a multifactorial disease, which is thought to be an interplay between genetic, environment, microbiota, and immune-mediated factors. Dysbiosis in the gut microbial composition, caused by antibiotics and diet, is closely related to the initiation and progression of IBD. Differences in gut microbiota composition between IBD patients and healthy individuals have been found, with reduced biodiversity of commensal microbes and colonization of opportunistic microbes in IBD patients. Gut microbiota can, therefore, potentially be used for diagnosing and prognosticating IBD, and predicting its treatment response. Currently, there are no curative therapies for IBD. Microbiota-based interventions, including probiotics, prebiotics, synbiotics, and fecal microbiota transplantation, have been recognized as promising therapeutic strategies. Clinical studies and studies done in animal models have provided sufficient evidence that microbiota-based interventions may improve inflammation, the remission rate, and microscopic aspects of IBD. Further studies are required to better understand the mechanisms of action of such interventions. This will help in enhancing their effectiveness and developing personalized therapies. The present review summarizes the relationship between gut microbiota and IBD immunopathogenesis. It also discusses the use of gut microbiota as a noninvasive biomarker and potential therapeutic option.
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Affiliation(s)
| | | | - Daryl W. T. Tang
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Sunny H. Wong
- Centre for Microbiome Medicine, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Devi Lal
- Department of Zoology, Ramjas College, University of Delhi, Delhi, India
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Balderramo D, Yamamoto-Furusho J, Ponce de León E, de María J, Zubiaurre I, Pedreira S, Lis C, Brion L, de Paula JA. Suboptimal response to tumor necrosis factor antagonists in inflammatory bowel disease in Latin America: EXPLORE LATAM study. GASTROENTEROLOGIA Y HEPATOLOGIA 2024; 47:51-62. [PMID: 37062500 DOI: 10.1016/j.gastrohep.2023.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 03/29/2023] [Accepted: 04/03/2023] [Indexed: 04/18/2023]
Abstract
OBJECTIVE Data on anti-tumor necrosis factor (anti-TNF) treatment and suboptimal response (SOR) among patients with inflammatory bowel diseases (IBD) in Latin America (LATAM) are scarce. This study evaluated the incidence and indicators of SOR to anti-TNF therapy in patients with ulcerative colitis (UC) and Crohn's disease (CD) from Argentina, Colombia and Mexico. PATIENTS AND METHODS We performed retrospective analysis of data from LATAM patients of the EXPLORE study (NCT03090139) including adult patients with IBD who initiated anti-TNF therapy between March 2010 to March 2015. The cumulative incidence of SOR to first-line anti-TNF therapy was assessed. A physician survey to assess barriers to anti-TNF therapies was also carried out. RESULTS We included 185 IBD patients (UC/CD: 99/86) treated with first-line anti-TNF from Argentina (38 UC; 40 CD), Colombia (21 UC; 25 CD) and Mexico (40 UC; 21 CD). 36.4% of patients with UC and 46.5% of patients with CD experienced SOR to anti-TNF therapy during the median (interquartile range) observational period: 49.0 months (37.2-60.1) in UC, and 50.0 months (40.9-60.1) in CD. The most common indicator of SOR among patients was augmentation of non-biologic therapy (UC: 41.7%; CD: 35.0%). Affordability and late referral to IBD specialist care centers were the most common barriers to anti-TNF therapies. CONCLUSIONS SOR to anti-TNF therapy was common in LATAM IBD patients, where augmentation with non-biologic therapy represented the most frequent indicator of SOR across indications. Our findings contribute to the current evidence on the unmet needs associated with anti-TNF in LATAM.
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Affiliation(s)
- Domingo Balderramo
- Gastroenterology Department, Hospital Privado Universitario de Córdoba, Instituto Universitario de Ciencias Biomédicas de Córdoba, X5016 Córdoba, Argentina.
| | - Jesús Yamamoto-Furusho
- Inflammatory Bowel Disease Clinic, Department of Gastroenterology, National Institute of Medical Sciences and Nutrition, 14080 Mexico City, Mexico
| | | | - Julio de María
- Hospital Italiano de La Plata, B1900 La Plata, Argentina
| | | | | | - Camilo Lis
- Takeda Argentina S.A., C1429 Buenos Aires, Argentina
| | - Laura Brion
- Takeda Argentina S.A., C1429 Buenos Aires, Argentina
| | - Juan A de Paula
- Hospital Italiano de Buenos Aires, C1199ABH Buenos Aires, Argentina
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35
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Prins FM, Hidding IJ, Klaassen MA, Collij V, Schultheiss JP, Uniken Venema WT, Bangma A, Aardema JB, Jansen BH, Mares WG, Witteman BJ, Festen EA, Dijkstra G, Visschedijk MC, Fidder HH, Vich Vila A, Oldenburg B, Gacesa R, Weersma RK. Limited predictive value of the gut microbiome and metabolome for response to biological therapy in inflammatory bowel disease. Gut Microbes 2024; 16:2391505. [PMID: 39167702 PMCID: PMC11340771 DOI: 10.1080/19490976.2024.2391505] [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: 06/19/2024] [Accepted: 08/07/2024] [Indexed: 08/23/2024] Open
Abstract
Emerging evidence suggests the gut microbiome's potential in predicting response to biologic treatments in patients with inflammatory bowel disease (IBD). In this prospective study, we aimed to predict treatment response to vedolizumab and ustekinumab, integrating clinical data, gut microbiome profiles based on metagenomic sequencing, and untargeted fecal metabolomics. We aimed to identify predictive biomarkers and attempted to replicate microbiome-based signals from previous studies. We found that the predictive utility of the gut microbiome and fecal metabolites for treatment response was marginal compared to clinical features alone. Testing our identified microbial ratios in an external cohort reinforced the lack of predictive power of the microbiome. Additionally, we could not confirm previously published predictive signals observed in similar sized cohorts. Overall, these findings highlight the importance of external validation and larger sample sizes, to better understand the microbiome's impact on therapy outcomes in the setting of biologicals in IBD before potential clinical implementation.
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Affiliation(s)
- Femke M. Prins
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Cardiology, 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
| | - Marjolein A.Y. Klaassen
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Valerie Collij
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Johannes P.D. Schultheiss
- Department of Gastroenterology and Hepatology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Werna T.C. Uniken Venema
- 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
| | - Jurne B. Aardema
- Department of Gastroenterology and Hepatology, 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
| | - Wout G.N. Mares
- Gastroenterology and Hepatology Department, Hospital Gelderse Vallei, Ede, The Netherlands
| | - Ben J.M. Witteman
- Gastroenterology and Hepatology Department, Hospital Gelderse Vallei, Ede, The Netherlands
| | - Eleonora A.M. Festen
- 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
| | - Marijn C. Visschedijk
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Herma H. Fidder
- Department of Gastroenterology and Hepatology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Arnau Vich Vila
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Bas Oldenburg
- Department of Gastroenterology and Hepatology, University Medical Center Utrecht, Utrecht, 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
| | - Rinse K. Weersma
- 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
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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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Zeng Z, Jiang M, Li X, Yuan J, Zhang H. Precision medicine in inflammatory bowel disease. PRECISION CLINICAL MEDICINE 2023; 6:pbad033. [PMID: 38638127 PMCID: PMC11025389 DOI: 10.1093/pcmedi/pbad033] [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] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 12/13/2023] [Indexed: 04/20/2024] Open
Abstract
Inflammatory bowel disease (IBD) is an incurable disease characterized by remission-relapse cycles throughout its course. Both Crohn's disease (CD) and ulcerative colitis (UC), the two main forms of IBD, exhibit tendency to develop complications and substantial heterogeneity in terms of frequency and severity of relapse, thus posing great challenges to the clinical management for IBD. Current treatment strategies are effective in different ways in induction and maintenance therapies for IBD. Recent advances in studies of genetics, pharmacogenetics, proteomics and microbiome provide a strong driving force for identifying molecular markers of prognosis and treatment response, which should help clinicians manage IBD patients more effectively, and then, improve clinical outcomes and reduce treatment costs of patients. In this review, we summarize and discuss precision medicine in IBD, focusing on predictive markers of disease course and treatment response, and monitoring indices during therapeutic drug monitoring.
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Affiliation(s)
- Zhen Zeng
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu 610041, China
- Centre for Inflammatory Bowel Disease, West China Hospital, Sichuan University, Chengdu 610041, China
- Lab of Inflammatory Bowel Disease, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Mingshan Jiang
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu 610041, China
- Centre for Inflammatory Bowel Disease, West China Hospital, Sichuan University, Chengdu 610041, China
- Lab of Inflammatory Bowel Disease, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xi Li
- Lab of Inflammatory Bowel Disease, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
- General Practice Ward/International Medical Center Ward, General Practice Medical Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Jing Yuan
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu 610041, China
- Centre for Inflammatory Bowel Disease, West China Hospital, Sichuan University, Chengdu 610041, China
- Lab of Inflammatory Bowel Disease, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Hu Zhang
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu 610041, China
- Centre for Inflammatory Bowel Disease, West China Hospital, Sichuan University, Chengdu 610041, China
- Lab of Inflammatory Bowel Disease, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
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38
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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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Yu S, Guo H, Ji Z, Zheng Y, Wang B, Chen Q, Tang H, Yuan B. Sea Cucumber Peptides Ameliorate DSS-Induced Ulcerative Colitis: The Role of the Gut Microbiota, the Intestinal Barrier, and Macrophage Polarization. Nutrients 2023; 15:4813. [PMID: 38004208 PMCID: PMC10674221 DOI: 10.3390/nu15224813] [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: 10/27/2023] [Revised: 11/14/2023] [Accepted: 11/16/2023] [Indexed: 11/26/2023] Open
Abstract
The incidence of ulcerative colitis (UC) is increasing annually. There are few treatments for UC patients, and some drugs have serious side effects. Sea cucumber peptide (SCP) has anti-inflammatory, antioxidant and other biological activities, and various sea cucumber species are in pharmaceutical development. However, relevant studies on the effects of SCP on UC progression are still lacking. In this study, a mouse model of acute colitis was induced by 3% dextran sulfate (DSS), and the effect of 500 mg/kg SCP on colitis was investigated. The results showed that SCP can alleviate DSS-induced colon damage and intestinal barrier damage. SCP significantly inhibited the expression of inflammatory factors and oxidative stress in UC mice. SCP reversed the intestinal microbiota dysregulation induced by DSS, inhibited the growth of Sutterella, Prevotella_9 and Escherichia-Shigella harmful bacteria, and increased the abundance of Lachnospiraceae_NK4A136_group. At the same time, SCP treatment significantly inhibited the LPS-induced polarization of M1 macrophages, which may be mediated by two monopeptides, IPGAPGVP and TGPIGPPGSP, via FPR2. In conclusion, SCP can protect against colitis by modulating the intestinal microbiota composition and the intestinal barrier and inhibiting the polarization of M1 macrophages.
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Affiliation(s)
- Song Yu
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun 130062, China; (S.Y.); (H.G.); (Z.J.); (Y.Z.); (B.W.); (Q.C.)
| | - Haixiang Guo
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun 130062, China; (S.Y.); (H.G.); (Z.J.); (Y.Z.); (B.W.); (Q.C.)
| | - Zhonghao Ji
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun 130062, China; (S.Y.); (H.G.); (Z.J.); (Y.Z.); (B.W.); (Q.C.)
- Department of Basic Medicine, Changzhi Medical College, Changzhi 046000, China
| | - Yi Zheng
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun 130062, China; (S.Y.); (H.G.); (Z.J.); (Y.Z.); (B.W.); (Q.C.)
| | - Bingbing Wang
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun 130062, China; (S.Y.); (H.G.); (Z.J.); (Y.Z.); (B.W.); (Q.C.)
| | - Qingqing Chen
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun 130062, China; (S.Y.); (H.G.); (Z.J.); (Y.Z.); (B.W.); (Q.C.)
| | - Hongyu Tang
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun 130062, China; (S.Y.); (H.G.); (Z.J.); (Y.Z.); (B.W.); (Q.C.)
| | - Bao Yuan
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun 130062, China; (S.Y.); (H.G.); (Z.J.); (Y.Z.); (B.W.); (Q.C.)
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Gorelik Y, Ghersin I, Shlon D, Friss C, Lujan R, Loewenberg Weisband Y, Greenfeld S, Kariv R, Ledderman N, Matz E, Dotan I, Bar-Yoseph H, Chowers Y, Turner D. Association of Antibiotic Use with Durability of Biologic Agents in Inflammatory Bowel Disease: a Report from the epi-IIRN. J Crohns Colitis 2023; 17:1410-1417. [PMID: 37084088 DOI: 10.1093/ecco-jcc/jjad070] [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: 11/11/2022] [Indexed: 04/22/2023]
Abstract
BACKGROUND Different antibiotic classes were reported to have variable effects on immunogenicity towards anti-tumour necrosis factor [TNF] agents. However, the impact of antibiotic administration on biologic treatment durability was not investigated. We aimed to assess the association between antibiotic treatment and persistence of different classes of biologic therapy in inflammatory bowel disease [IBD] patients. METHODS Data from the epi-IIRN, a nationwide registry of all Israeli IBD patients were analysed. All patients who filled a prescription of either infliximab, adalimumab, vedolizumab, or ustekinumab, were included. Treatment cessation was defined as drug discontinuation of at least 6 months. Macrolides, cephalosporins, fluoroquinolones, and penicillins with beta-lactamase inhibitors were selected as primary exposure variables. Survival analysis was performed using marginal structural models for each drug separately. RESULTS In all 13 513 IBD patients, with a total of 39 600 patient-years, were included. Significant differences of overall treatment persistence were demonstrated, with highest persistence rates for ustekinumab and the lowest for infliximab treatment. Macrolides were found to be significantly associated with reduced risk of infliximab cessation (adjusted hazard ratio [aHR] 0.72, 95% CI 0.62-0.89]. Fluoroquinolones and cephalosporins were associated with an elevated risk of adalimumab treatment cessation [aHR 1.33, 95% CI 1.22-1.46; and aHR 1.20, 95% CI 1.08-1.34, respectively]. No significant effects of the studied antibiotics were observed in ustekinumab and vedolizumab users. CONCLUSIONS Specific antibiotic classes are associated with duration of anti-TNF treatment, but not with durability of vedolizumab or ustekinumab treatments. Further research is required to study the effect of specific antibiotics on response to biologics.
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Affiliation(s)
- Yuri Gorelik
- Department of Gastroenterology, Rambam Health Care Campus, Haifa, Israel
| | - Itai Ghersin
- Department of Gastroenterology, Rambam Health Care Campus, Haifa, Israel
| | - Deema Shlon
- Department of Gastroenterology, Rambam Health Care Campus, Haifa, Israel
| | - Chagit Friss
- Juliet Keidan Institute of Pediatric Gastroenterology Hepatology and Nutrition, Shaare Zedek Medical Center, Hebrew University of Jerusalem, Israel
| | - Rona Lujan
- Juliet Keidan Institute of Pediatric Gastroenterology Hepatology and Nutrition, Shaare Zedek Medical Center, Hebrew University of Jerusalem, Israel
| | | | - Shira Greenfeld
- Maccabi Health Services, Tel-Aviv, Israel
- The Sackler Faculty of Medicine, Tel Aviv University, Israel
| | - Revital Kariv
- Maccabi Health Services, Tel-Aviv, Israel
- The Sackler Faculty of Medicine, Tel Aviv University, Israel
| | - Natan Ledderman
- Meuhedet Health Services, Meuhedet Research Institue, Tel-Aviv, Israel
| | - Eran Matz
- Leumit Health Services, Leumit Research Institue, Tel-Aviv, Israel
| | - Iris Dotan
- Division of Gastroenterology, Rabin Medical Center, Petah Tikva, Israel
| | - Haggai Bar-Yoseph
- Department of Gastroenterology, Rambam Health Care Campus, Haifa, Israel
| | - Yehuda Chowers
- Department of Gastroenterology, Rambam Health Care Campus, Haifa, Israel
- Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Dan Turner
- Juliet Keidan Institute of Pediatric Gastroenterology Hepatology and Nutrition, Shaare Zedek Medical Center, Hebrew University of Jerusalem, Israel
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Li X, Luo J, Han C, Lu X. Nanoplastics enhance the intestinal damage and genotoxicity of sulfamethoxazole to medaka juveniles (Oryzias melastigma) in coastal environment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 894:164943. [PMID: 37329919 DOI: 10.1016/j.scitotenv.2023.164943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/28/2023] [Accepted: 06/14/2023] [Indexed: 06/19/2023]
Abstract
Antibiotics and nanoplastics are widely detected in the coastal ecosystem. However, the transcriptome mechanism elucidating the effect of antibiotics and nanoplastics co-exposure on the gene expression of aquatic organisms in coastal environment is still unclear. Here, single and joint effects of sulfamethoxazole (SMX) and polystyrene nanoplastics (PS-NPs) on the intestinal health and gene expression of medaka juveniles (Oryzias melastigma), which live in coastal environment, were investigated. The SMX and PS-NPs co-exposure decreased intestinal microbiota diversity compared to the PS-NPs, and caused more adverse effect on the intestinal microbiota composition and intestinal damage compared to the SMX, indicating that PS-NPs might enhance the toxicity of SMX on the medaka intestine. The increased abundance of Proteobacteria in the intestine was observed in the co-exposure group, which might induce the intestinal epithelium damage. In addition, the differentially expressed genes (DEGs) were mainly involved in the drug metabolism-other enzymes, drug metabolism-cytochrome P450, metabolism of xenobiotics by cytochrome P450 pathways in visceral tissue after the co-exposure. The expression of the host immune system genes (e.g., ifi30) could be associated with the increased pathogens in intestinal microbiota. This study is useful for understanding the toxicity effect of antibiotics and NPs on aquatic organisms in coastal ecosystem.
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Affiliation(s)
- Xue Li
- Tianjin Key Laboratory of Environmental Technology for Complex Trans-Media Pollution, Tianjin International Joint Research Center for Environmental Biogeochemical Technology, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Jiwei Luo
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, Hainan University, Haikou 570228, China
| | - Chenglong Han
- Tianjin Key Laboratory of Environmental Technology for Complex Trans-Media Pollution, Tianjin International Joint Research Center for Environmental Biogeochemical Technology, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Xueqiang Lu
- Tianjin Key Laboratory of Environmental Technology for Complex Trans-Media Pollution, Tianjin International Joint Research Center for Environmental Biogeochemical Technology, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China.
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Koneru S, Thiruvadi V, Ramesh M. Gut microbiome and its clinical implications: exploring the key players in human health. Curr Opin Infect Dis 2023; 36:353-359. [PMID: 37593952 DOI: 10.1097/qco.0000000000000958] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Abstract
PURPOSE OF REVIEW The human gut harbors a diverse community of microorganisms known as the gut microbiota. Extensive research in recent years has shed light on the profound influence of the gut microbiome on human health and disease. This review aims to explore the role of the gut microbiome in various clinical conditions and highlight the emerging therapeutic potential of targeting the gut microbiota for disease management. RECENT FINDINGS Knowledge of the influence of gut microbiota on human physiology led to the development of various therapeutic possibilities such as fecal microbiota transplant (FMT), phage therapy, prebiotics, and probiotics. Recently, the U.S. FDA approved two FMT products for the treatment of recurrent Clostridioides difficile infection with ongoing research for the treatment of various disease conditions. SUMMARY Advancement in the knowledge of the association between gut microbiota and various disease processes has paved the way for novel therapeutics.
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Affiliation(s)
- Sindhuja Koneru
- Division of Infectious Diseases, Henry Ford Hospital, Detroit, Michigan, USA
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Bi Z, Chen J, Chang X, Li D, Yao Y, Cai F, Xu H, Cheng J, Hua Z, Zhuang H. ADT-OH improves intestinal barrier function and remodels the gut microbiota in DSS-induced colitis. Front Med 2023; 17:972-992. [PMID: 37507636 DOI: 10.1007/s11684-023-0990-1] [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: 05/04/2022] [Accepted: 01/31/2023] [Indexed: 07/30/2023]
Abstract
Owing to the increasing incidence and prevalence of inflammatory bowel disease (IBD) worldwide, effective and safe treatments for IBD are urgently needed. Hydrogen sulfide (H2S) is an endogenous gasotransmitter and plays an important role in inflammation. To date, H2S-releasing agents are viewed as potential anti-inflammatory drugs. The slow-releasing H2S donor 5-(4-hydroxyphenyl)-3H-1,2-dithiole-3-thione (ADT-OH), known as a potent therapeutic with chemopreventive and cytoprotective properties, has received attention recently. Here, we reported its anti-inflammatory effects on dextran sodium sulfate (DSS)-induced acute (7 days) and chronic (30 days) colitis. We found that ADT-OH effectively reduced the DSS-colitis clinical score and reversed the inflammation-induced shortening of colon length. Moreover, ADT-OH reduced intestinal inflammation by suppressing the nuclear factor kappa-B pathway. In vivo and in vitro results showed that ADT-OH decreased intestinal permeability by increasing the expression of zonula occludens-1 and occludin and blocking increases in myosin II regulatory light chain phosphorylation and epithelial myosin light chain kinase protein expression levels. In addition, ADT-OH restored intestinal microbiota dysbiosis characterized by the significantly increased abundance of Muribaculaceae and Alistipes and markedly decreased abundance of Helicobacter, Mucispirillum, Parasutterella, and Desulfovibrio. Transplanting ADT-OH-modulated microbiota can alleviate DSS-induced colitis and negatively regulate the expression of local and systemic proinflammatory cytokines. Collectively, ADT-OH is safe without any short-term (5 days) or long-term (30 days) toxicological adverse effects and can be used as an alternative therapeutic agent for IBD treatment.
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Affiliation(s)
- Zhiqian Bi
- The State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Jia Chen
- The State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Xiaoyao Chang
- The State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Dangran Li
- The State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Yingying Yao
- The State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Fangfang Cai
- The State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, 210023, China
- School of Biopharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Huangru Xu
- The State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Jian Cheng
- Institute of Neuroscience, Soochow University, Suzhou, 215123, China.
| | - Zichun Hua
- The State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, 210023, China.
- Changzhou High-Tech Research Institute of Nanjing University and Jiangsu TargetPharma Laboratories Inc., Changzhou, 213164, China.
- School of Biopharmacy, China Pharmaceutical University, Nanjing, 211198, China.
| | - Hongqin Zhuang
- The State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, 210023, China.
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Chang CC, Liu TC, Lu CJ, Chiu HC, Lin WN. Machine learning strategy for identifying altered gut microbiomes for diagnostic screening in myasthenia gravis. Front Microbiol 2023; 14:1227300. [PMID: 37829445 PMCID: PMC10565662 DOI: 10.3389/fmicb.2023.1227300] [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: 05/23/2023] [Accepted: 09/06/2023] [Indexed: 10/14/2023] Open
Abstract
Myasthenia gravis (MG) is a neuromuscular junction disease with a complex pathophysiology and clinical variation for which no clear biomarker has been discovered. We hypothesized that because changes in gut microbiome composition often occur in autoimmune diseases, the gut microbiome structures of patients with MG would differ from those without, and supervised machine learning (ML) analysis strategy could be trained using data from gut microbiota for diagnostic screening of MG. Genomic DNA from the stool samples of MG and those without were collected and established a sequencing library by constructing amplicon sequence variants (ASVs) and completing taxonomic classification of each representative DNA sequence. Four ML methods, namely least absolute shrinkage and selection operator, extreme gradient boosting (XGBoost), random forest, and classification and regression trees with nested leave-one-out cross-validation were trained using ASV taxon-based data and full ASV-based data to identify key ASVs in each data set. The results revealed XGBoost to have the best predicted performance. Overlapping key features extracted when XGBoost was trained using the full ASV-based and ASV taxon-based data were identified, and 31 high-importance ASVs (HIASVs) were obtained, assigned importance scores, and ranked. The most significant difference observed was in the abundance of bacteria in the Lachnospiraceae and Ruminococcaceae families. The 31 HIASVs were used to train the XGBoost algorithm to differentiate individuals with and without MG. The model had high diagnostic classification power and could accurately predict and identify patients with MG. In addition, the abundance of Lachnospiraceae was associated with limb weakness severity. In this study, we discovered that the composition of gut microbiomes differed between MG and non-MG subjects. In addition, the proposed XGBoost model trained using 31 HIASVs had the most favorable performance with respect to analyzing gut microbiomes. These HIASVs selected by the ML model may serve as biomarkers for clinical use and mechanistic study in the future. Our proposed ML model can identify several taxonomic markers and effectively discriminate patients with MG from those without with a high accuracy, the ML strategy can be applied as a benchmark to conduct noninvasive screening of MG.
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Affiliation(s)
- Che-Cheng Chang
- PhD Program in Nutrition and Food Science, Fu Jen Catholic University, New Taipei City, Taiwan
- Department of Neurology, Fu Jen Catholic University Hospital, Fu Jen Catholic University, New Taipei City, Taiwan
- Graduate Institute of Biomedical and Pharmaceutical Science, Fu Jen Catholic University, New Taipei City, Taiwan
| | - Tzu-Chi Liu
- Graduate Institute of Business Administration, Fu Jen Catholic University, New Taipei City, Taiwan
| | - Chi-Jie Lu
- Graduate Institute of Business Administration, Fu Jen Catholic University, New Taipei City, Taiwan
- Artificial Intelligence Development Center, Fu Jen Catholic University, New Taipei City, Taiwan
- Department of Information Management, Fu Jen Catholic University, New Taipei City, Taiwan
| | - Hou-Chang Chiu
- School of Medicine, Fu Jen Catholic University, New Taipei City, Taiwan
- Department of Neurology, Taipei Medical University, Shuang-Ho Hospital, New Taipei City, Taiwan
| | - Wei-Ning Lin
- Graduate Institute of Biomedical and Pharmaceutical Science, Fu Jen Catholic University, New Taipei City, Taiwan
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Fang M, Hu W, Liu B. Effects of nano-selenium on cecum microbial community and metabolomics in chickens challenged with Ochratoxin A. Front Vet Sci 2023; 10:1228360. [PMID: 37732141 PMCID: PMC10507861 DOI: 10.3389/fvets.2023.1228360] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 08/22/2023] [Indexed: 09/22/2023] Open
Abstract
Introduction Ochratoxin A (OTA) is a widely distributed mycotoxin. Nano-selenium (Nano-Se) is an emerging form of selenium known for its superior bioavailability, remarkable catalytic efficiency, and robust adsorbing capacity. Despite these characteristics, its impact on the microbial community and metabolomics in the cecum of chickens exposed to OTA has been infrequently investigated. This research examined the microbiota and metabolomic alterations linked to OTA in chickens, with or without Nano-Se present. Methods A cohort of 80 healthy chickens at the age of 1 day was randomly distributed into four groups of equal numbers, namely the Se cohort (1 mg/kg Nano-Se), the OTA cohort (50 μg/kg OTA), the OTA-Se cohort (50 μg/kg OTA + 1 mg/kg Nano-Se), and the control group. Each chicken group's caecal microbiome and metabolome were characterized using 16S rRNA sequencing and Liquid chromatography coupled with mass spectrometry (LC-MS) analyses. Results and discussion Our results showed that the on day 21, the final body weight was significantly reduced in response to OTA treatments (p < 0.05), the average daily gain in the OTA group was found to be inferior to the other groups (p < 0.01). In addition, Nano-Se supplementation could reduce the jejunum and liver pathological injuries caused by OTA exposure. The 16S rRNA sequencing suggest that Nano-Se supplementation in OTA-exposed chickens mitigated gut microbiota imbalances by promoting beneficial microbiota and suppressing detrimental bacteria. Moreover, untargeted metabolomics revealed a significant difference in caecal metabolites by Nano-Se pretreatment. Collectively, the dataset outcomes highlighted that Nano-Se augmentation regulates intestinal microbiota and associated metabolite profiles, thus influencing critical metabolic pathways, and points to a possible food-additive product.
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Affiliation(s)
- Manxin Fang
- College of Life Science and Resources and Environment, Yichun University, Yichun, China
- Engineering Technology Research Center of Jiangxi Universities and Colleges for Selenium Agriculture, Yichun University, Yichun, China
| | - Wei Hu
- College of Life Science and Resources and Environment, Yichun University, Yichun, China
- Engineering Technology Research Center of Jiangxi Universities and Colleges for Selenium Agriculture, Yichun University, Yichun, China
| | - Ben Liu
- College of Life Science and Resources and Environment, Yichun University, Yichun, China
- Engineering Technology Research Center of Jiangxi Universities and Colleges for Selenium Agriculture, Yichun University, Yichun, China
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Zhang J, Sun S, Chen H, Feng Y, Li Y, Dong Z. Advances in natural compound-based nanomedicine and the interaction with gut microbiota in ulcerative colitis therapy. Front Pharmacol 2023; 14:1197144. [PMID: 37521480 PMCID: PMC10372797 DOI: 10.3389/fphar.2023.1197144] [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: 04/04/2023] [Accepted: 06/28/2023] [Indexed: 08/01/2023] Open
Abstract
Ulcerative colitis (UC) is a chronic inflammatory bowel disorder of the large intestine. Previous studies have indicated that the gut microbiota plays an important role in the triggers, development, and treatment response of UC. Natural active molecules and their nanoformulations show huge potential for treating UC. The nanoparticles can regulate the gut microbiota and metabolites, whereas gut microbiota-mediated effects on nanomedicines can also bring additional therapeutic benefits. Therefore, this review aims to integrate current research on natural active molecule-based nanomedicines for UC therapy and their interaction with the gut microbiota. Here, this discussion focuses on the effects and functions of gut microbiota and metabolites in UC. The use of active molecules and the nanoformulation from natural compounds for UC therapy have been provided. The interactions between the gut microbiota and nanomedicines are derived from natural products and elucidate the possible biological mechanisms involved. Finally, the challenges and future directions for enhancing the therapeutic efficacy of nanomedicine in treating UC are proposed.
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Affiliation(s)
- Jinlan Zhang
- Drug Delivery Research Center, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of New Drug Discovery Based on Classic Chinese Medicine Prescription, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory of Innovative Drug Discovery of Traditional Chinese Medicine (Natural Medicine) and Translational Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Shuhui Sun
- Drug Delivery Research Center, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of New Drug Discovery Based on Classic Chinese Medicine Prescription, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory of Innovative Drug Discovery of Traditional Chinese Medicine (Natural Medicine) and Translational Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Huan Chen
- Drug Delivery Research Center, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of New Drug Discovery Based on Classic Chinese Medicine Prescription, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory of Innovative Drug Discovery of Traditional Chinese Medicine (Natural Medicine) and Translational Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yifan Feng
- Drug Delivery Research Center, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of New Drug Discovery Based on Classic Chinese Medicine Prescription, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory of Innovative Drug Discovery of Traditional Chinese Medicine (Natural Medicine) and Translational Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Ying Li
- Drug Delivery Research Center, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of New Drug Discovery Based on Classic Chinese Medicine Prescription, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory of Innovative Drug Discovery of Traditional Chinese Medicine (Natural Medicine) and Translational Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Zhengqi Dong
- Drug Delivery Research Center, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of New Drug Discovery Based on Classic Chinese Medicine Prescription, Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory of Innovative Drug Discovery of Traditional Chinese Medicine (Natural Medicine) and Translational Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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Wang F, Yang H, Wu Y, Peng L, Li X. SAELGMDA: Identifying human microbe-disease associations based on sparse autoencoder and LightGBM. Front Microbiol 2023; 14:1207209. [PMID: 37415823 PMCID: PMC10320730 DOI: 10.3389/fmicb.2023.1207209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 05/18/2023] [Indexed: 07/08/2023] Open
Abstract
Introduction Identification of complex associations between diseases and microbes is important to understand the pathogenesis of diseases and design therapeutic strategies. Biomedical experiment-based Microbe-Disease Association (MDA) detection methods are expensive, time-consuming, and laborious. Methods Here, we developed a computational method called SAELGMDA for potential MDA prediction. First, microbe similarity and disease similarity are computed by integrating their functional similarity and Gaussian interaction profile kernel similarity. Second, one microbe-disease pair is presented as a feature vector by combining the microbe and disease similarity matrices. Next, the obtained feature vectors are mapped to a low-dimensional space based on a Sparse AutoEncoder. Finally, unknown microbe-disease pairs are classified based on Light Gradient boosting machine. Results The proposed SAELGMDA method was compared with four state-of-the-art MDA methods (MNNMDA, GATMDA, NTSHMDA, and LRLSHMDA) under five-fold cross validations on diseases, microbes, and microbe-disease pairs on the HMDAD and Disbiome databases. The results show that SAELGMDA computed the best accuracy, Matthews correlation coefficient, AUC, and AUPR under the majority of conditions, outperforming the other four MDA prediction models. In particular, SAELGMDA obtained the best AUCs of 0.8358 and 0.9301 under cross validation on diseases, 0.9838 and 0.9293 under cross validation on microbes, and 0.9857 and 0.9358 under cross validation on microbe-disease pairs on the HMDAD and Disbiome databases. Colorectal cancer, inflammatory bowel disease, and lung cancer are diseases that severely threat human health. We used the proposed SAELGMDA method to find possible microbes for the three diseases. The results demonstrate that there are potential associations between Clostridium coccoides and colorectal cancer and one between Sphingomonadaceae and inflammatory bowel disease. In addition, Veillonella may associate with autism. The inferred MDAs need further validation. Conclusion We anticipate that the proposed SAELGMDA method contributes to the identification of new MDAs.
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Affiliation(s)
- Feixiang Wang
- School of Computer Science, Hunan University of Technology, Zhuzhou, China
| | - Huandong Yang
- Department of Gastrointestinal Surgery, Yidu Central Hospital of Weifang, Weifang, China
| | - Yan Wu
- Geneis (Beijing) Co., Ltd., Beijing, China
| | - Lihong Peng
- School of Computer Science, Hunan University of Technology, Zhuzhou, China
| | - Xiaoling Li
- The Second Department of Oncology, Beidahuang Industry Group General Hospital, Harbin, China
- The Second Department of Oncology, Heilongjiang Second Cancer Hospital, Harbin, China
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Li X, Mo K, Tian G, Zhou J, Gong J, Li L, Huang X. Shikimic Acid Regulates the NF-κB/MAPK Signaling Pathway and Gut Microbiota to Ameliorate DSS-Induced Ulcerative Colitis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37257042 DOI: 10.1021/acs.jafc.3c00283] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Shikimic acid (SA) is a compound extracted from the plant anise and has anti-inflammatory effects. However, any impact on intestinal inflammation or mechanisms involved has not been investigated. The present study used a dextran sulfate sodium (DSS)-induced mouse colitis model to investigate the effects of SA on intestinal inflammation. Intragastric administration of SA slowed DSS-induced weight loss, reduced disease activity index (DAI) score, enhanced the intestinal barrier, reduced the destruction of the colonic structure, inhibited the phosphorylation of key proteins in MAPK and NF-κB signaling pathways, inhibited the expression of inflammatory factors TNF-α, IL-1β, and MPO (P < 0.05), decreased IFN-γ expression (P < 0.05), and increased immunoglobulin IgG content (P < 0.05). After 50 mg/kg SA treatment, the content of Bacteroidetes increased and Proteobacteria decreased in the cecal feces of mice with colitis (P < 0.05) and the richness of gut species increased. In conclusion, SA could improve intestinal inflammation and enhance intestinal immunity, indicating its suitability as a therapeutic candidate.
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Affiliation(s)
- Xin Li
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Kaibin Mo
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Ge Tian
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Jiaxin Zhou
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Jiongzhou Gong
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Li Li
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Xianhui Huang
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
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Liang Y, Xie R, Xiong X, Hu Z, Mao X, Wang X, Zhang J, Sun P, Yue Z, Wang W, Zhang G. Alterations of nasal microbiome in eosinophilic chronic rhinosinusitis. J Allergy Clin Immunol 2023; 151:1286-1295.e2. [PMID: 36736796 DOI: 10.1016/j.jaci.2022.11.031] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 10/16/2022] [Accepted: 11/04/2022] [Indexed: 02/04/2023]
Abstract
BACKGROUND Exposure to microbes may be important in the development of chronic rhinosinusitis (CRS). Dysbiosis of the nasal microbiome is considered to be related to CRS with nasal polyps (CRSwNP). The link between the nasal microbiota and eosinophilic CRSwNP (eCRSwNP) has rarely been studied. OBJECTIVE The aim of this study was to rigorously characterize nasal dysbiosis in a cohort of patients with eCRSwNP and compare the nasal microbiomes of these patients with those of healthy controls (HCs). METHODS We performed a cross-sectional study of 34 patients with eCRSwNP, 10 patients without CRSwNP, and 44 HCs by using 16S rRNA gene sequencing. An independent cohort of 14 patients with eCRSwNP, 9 patients without CRSwNP, and 11 HCs was used to validate the results. RESULTS Compared with the nasal microbiome of healthy controls, the nasal microbiome of patients with eCRSwNP was characterized by higher α-diversity (Shannon and Chao1 index) and a distinct composition of microbes. Notably, the distinct differences in microbial composition between patients with eCRSwNP and HCs were significantly correlated with eCRSwNP disease status. Furthermore, in a diagnostic model generated by using these differences, a combination of 15 genera could be used to distinguish patients with eCRSwNP from HCs, with an area under the curve of approximately 0.8 in both the exploration and validation cohorts. CONCLUSION Our study establishes the compositional alterations in the nasal microbiome in eCRSwNP and suggests the potential for using the nasal microbiota as a noninvasive predictive classifier for the diagnosis of eCRSwNP.
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Affiliation(s)
- Yibo Liang
- Department of Otorhinolaryngology Head and Neck Surgery, Tianjin First Central Hospital, Tianjin, China; Institute of Otolaryngology of Tianjin, Tianjin, China; Key Laboratory of Auditory Speech and Balance Medicine, Tianjin; Key Medical Discipline of Tianjin (Otolaryngology), Tianjin, China; Quality Control Centre of Otolaryngology, Tianjin, China
| | - Runxiang Xie
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Xin Xiong
- Department of Otorhinolaryngology Head and Neck Surgery, Tianjin First Central Hospital, Tianjin, China; Institute of Otolaryngology of Tianjin, Tianjin, China; Key Laboratory of Auditory Speech and Balance Medicine, Tianjin; Key Medical Discipline of Tianjin (Otolaryngology), Tianjin, China; Quality Control Centre of Otolaryngology, Tianjin, China
| | - Zhanjun Hu
- Department of Pathology, Tianjin First Central Hospital, Tianjin, China
| | - Xiang Mao
- Department of Otorhinolaryngology Head and Neck Surgery, Tianjin First Central Hospital, Tianjin, China; Institute of Otolaryngology of Tianjin, Tianjin, China; Key Laboratory of Auditory Speech and Balance Medicine, Tianjin; Key Medical Discipline of Tianjin (Otolaryngology), Tianjin, China; Quality Control Centre of Otolaryngology, Tianjin, China
| | - Xiaoyu Wang
- Department of Otorhinolaryngology Head and Neck Surgery, Tianjin First Central Hospital, Tianjin, China; Institute of Otolaryngology of Tianjin, Tianjin, China; Key Laboratory of Auditory Speech and Balance Medicine, Tianjin; Key Medical Discipline of Tianjin (Otolaryngology), Tianjin, China; Quality Control Centre of Otolaryngology, Tianjin, China
| | - Jinmei Zhang
- Department of Otorhinolaryngology Head and Neck Surgery, Tianjin First Central Hospital, Tianjin, China; Institute of Otolaryngology of Tianjin, Tianjin, China; Key Laboratory of Auditory Speech and Balance Medicine, Tianjin; Key Medical Discipline of Tianjin (Otolaryngology), Tianjin, China; Quality Control Centre of Otolaryngology, Tianjin, China
| | - Peiyong Sun
- Department of Otorhinolaryngology Head and Neck Surgery, Tianjin First Central Hospital, Tianjin, China; Institute of Otolaryngology of Tianjin, Tianjin, China; Key Laboratory of Auditory Speech and Balance Medicine, Tianjin; Key Medical Discipline of Tianjin (Otolaryngology), Tianjin, China; Quality Control Centre of Otolaryngology, Tianjin, China
| | - Zhenzhong Yue
- Department of Otorhinolaryngology Head and Neck Surgery, Tianjin First Central Hospital, Tianjin, China; Institute of Otolaryngology of Tianjin, Tianjin, China; Key Laboratory of Auditory Speech and Balance Medicine, Tianjin; Key Medical Discipline of Tianjin (Otolaryngology), Tianjin, China; Quality Control Centre of Otolaryngology, Tianjin, China
| | - Wei Wang
- Department of Otorhinolaryngology Head and Neck Surgery, Tianjin First Central Hospital, Tianjin, China; Institute of Otolaryngology of Tianjin, Tianjin, China; Key Laboratory of Auditory Speech and Balance Medicine, Tianjin; Key Medical Discipline of Tianjin (Otolaryngology), Tianjin, China; Quality Control Centre of Otolaryngology, Tianjin, China
| | - Guimin Zhang
- Department of Otorhinolaryngology Head and Neck Surgery, Tianjin First Central Hospital, Tianjin, China; Institute of Otolaryngology of Tianjin, Tianjin, China; Key Laboratory of Auditory Speech and Balance Medicine, Tianjin; Key Medical Discipline of Tianjin (Otolaryngology), Tianjin, China; Quality Control Centre of Otolaryngology, Tianjin, China.
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Clarke TH, Greco C, Brinkac L, Nelson KE, Singh H. MPrESS: An R-Package for Accurately Predicting Power for Comparisons of 16S rRNA Microbiome Taxa Distributions including Simulation by Dirichlet Mixture Modeling. Microorganisms 2023; 11:1166. [PMID: 37317139 DOI: 10.3390/microorganisms11051166] [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: 02/27/2023] [Revised: 04/24/2023] [Accepted: 04/27/2023] [Indexed: 06/16/2023] Open
Abstract
Deep sequencing has revealed that the 16S rRNA gene composition of the human microbiome can vary between populations. However, when existing data are insufficient to address the desired study questions due to limited sample sizes, Dirichlet mixture modeling (DMM) can simulate 16S rRNA gene predictions from experimental microbiome data. We examined the extent to which simulated 16S rRNA gene microbiome data can accurately reflect the diversity within that identified from experimental data and calculate the power. Even when experimental and simulated datasets differed by less than 10%, simulation by DMM consistently overestimates power, except when using only highly discriminating taxa. Admixtures of DMM with experimental data performed poorly compared to pure simulation and did not show the same correlation with experimental data p-value and power values. While multiple replications of random sampling remain the favored method of determining the power, when the estimated sample size required to achieve a certain power exceeds the sample number, then simulated samples based on DMM can be used. We introduce an R-Package, MPrESS, to assist in power calculation and sample size estimation for a 16S rRNA gene microbiome dataset to detect a difference between populations. MPrESS can be downloaded from GitHub.
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Affiliation(s)
- Thomas H Clarke
- J. Craig Venter Institute, 9605 Medical Center Drive, Suite #150, Rockville, MD 20850, USA
| | - Chris Greco
- J. Craig Venter Institute, 9605 Medical Center Drive, Suite #150, Rockville, MD 20850, USA
| | - Lauren Brinkac
- J. Craig Venter Institute, 9605 Medical Center Drive, Suite #150, Rockville, MD 20850, USA
- Noblis, Reston, VA 20191, USA
| | - Karen E Nelson
- J. Craig Venter Institute, 9605 Medical Center Drive, Suite #150, Rockville, MD 20850, USA
| | - Harinder Singh
- J. Craig Venter Institute, 9605 Medical Center Drive, Suite #150, Rockville, MD 20850, USA
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