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Chen W, Li Y, Wang W, Gao S, Hu J, Xiang B, Wu D, Jiao N, Xu T, Zhi M, Zhu L, Zhu R. Enhanced microbiota profiling in patients with quiescent Crohn's disease through comparison with paired healthy first-degree relatives. Cell Rep Med 2024; 5:101624. [PMID: 38942021 PMCID: PMC11293350 DOI: 10.1016/j.xcrm.2024.101624] [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: 11/04/2023] [Revised: 04/09/2024] [Accepted: 06/07/2024] [Indexed: 06/30/2024]
Abstract
Prior studies indicate no correlation between the gut microbes of healthy first-degree relatives (HFDRs) of patients with Crohn's disease (CD) and the development of CD. Here, we utilize HFDRs as controls to examine the microbiota and metabolome in individuals with active (CD-A) and quiescent (CD-R) CD, thereby minimizing the influence of genetic and environmental factors. When compared to non-relative controls, the use of HFDR controls identifies fewer differential taxa. Faecalibacterium, Dorea, and Fusicatenibacter are decreased in CD-R, independent of inflammation, and correlated with fecal short-chain fatty acids (SCFAs). Validation with a large multi-center cohort confirms decreased Faecalibacterium and other SCFA-producing genera in CD-R. Classification models based on these genera distinguish CD from healthy individuals and demonstrate superior diagnostic power than models constructed with markers identified using unrelated controls. Furthermore, these markers exhibited limited discriminatory capabilities for other diseases. Finally, our results are validated across multiple cohorts, underscoring their robustness and potential for diagnostic and therapeutic applications.
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Affiliation(s)
- Wanning Chen
- Department of Gastroenterology, the Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200072, P.R. China
| | - Yichen Li
- Medical College, Jiaying University, Meizhou 514031, P. R. China; Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, P.R. China; Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, P.R. China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology; Biomedical Innovation Center; The Sixth Affiliated Hospital, Sun Yat-sen University; Key Laboratory of Human Microbiome and Chronic Diseases (Sun Yat-sen University), Ministry of Education, Guangzhou 510655, P.R. China
| | - Wenxia Wang
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, P.R. China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology; Biomedical Innovation Center; The Sixth Affiliated Hospital, Sun Yat-sen University; Key Laboratory of Human Microbiome and Chronic Diseases (Sun Yat-sen University), Ministry of Education, Guangzhou 510655, P.R. China
| | - Sheng Gao
- Department of Gastroenterology, the Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200072, P.R. China
| | - Jun Hu
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology; Biomedical Innovation Center; The Sixth Affiliated Hospital, Sun Yat-sen University; Key Laboratory of Human Microbiome and Chronic Diseases (Sun Yat-sen University), Ministry of Education, Guangzhou 510655, P.R. China; Department of Gastroenterology, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, P.R. China
| | - Bingjie Xiang
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology; Biomedical Innovation Center; The Sixth Affiliated Hospital, Sun Yat-sen University; Key Laboratory of Human Microbiome and Chronic Diseases (Sun Yat-sen University), Ministry of Education, Guangzhou 510655, P.R. China; Department of Gastroenterology, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, P.R. China
| | - Dingfeng Wu
- Department of Nephrology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310058, Zhejiang, P.R. China
| | - Na Jiao
- Department of Nephrology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310058, Zhejiang, P.R. China
| | - Tao Xu
- Medical College, Jiaying University, Meizhou 514031, P. R. China; Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, P.R. China
| | - Min Zhi
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology; Biomedical Innovation Center; The Sixth Affiliated Hospital, Sun Yat-sen University; Key Laboratory of Human Microbiome and Chronic Diseases (Sun Yat-sen University), Ministry of Education, Guangzhou 510655, P.R. China; Department of Gastroenterology, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, P.R. China.
| | - Lixin Zhu
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, P.R. China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology; Biomedical Innovation Center; The Sixth Affiliated Hospital, Sun Yat-sen University; Key Laboratory of Human Microbiome and Chronic Diseases (Sun Yat-sen University), Ministry of Education, Guangzhou 510655, P.R. China.
| | - Ruixin Zhu
- Department of Gastroenterology, the Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200072, P.R. China.
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Ghusn W, Loftus EV, Johnson AM. Reviewing the impact of obesity on inflammatory bowel disease and considerations for optimizing management. Curr Opin Gastroenterol 2024; 40:268-275. [PMID: 38662340 DOI: 10.1097/mog.0000000000001025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
PURPOSE OF REVIEW This review examines the complex relationship between obesity and inflammatory bowel disease (IBD), encompassing their potentially shared pathogenesis, the impact of obesity on the natural history and treatment outcomes of IBD, and the management of obesity in the patient with IBD. RECENT FINDINGS Obesity represents a state of chronic inflammation that may not only contribute to IBD pathogenesis, but also influence disease progression, complications, and response to treatment. Increased visceral adiposity may carry negative prognostic implications for disease and treatment-specific outcomes. Antiobesity medications, endoscopic bariatric therapies, and even bariatric surgery may be effective and well tolerated in selected patients with IBD. SUMMARY The intersection of obesity and IBD presents a significant clinical challenge, with obesity influencing the natural history of IBD and potentially affecting treatment efficacy. As obesity prevalence among IBD patients rises, a tailored approach to management is crucial, taking into account the individualized risks and benefits of various treatment strategies, including lifestyle interventions, pharmacotherapy, endoscopic procedures, and bariatric surgery.
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Affiliation(s)
- Wissam Ghusn
- Department of Internal Medicine, Boston Medical Center, Boston, Massachusetts
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
| | - Edward V Loftus
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
| | - Amanda M Johnson
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
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3
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Foppa C, Rizkala T, Repici A, Hassan C, Spinelli A. Microbiota and IBD: Current knowledge and future perspectives. Dig Liver Dis 2024; 56:911-922. [PMID: 38008696 DOI: 10.1016/j.dld.2023.11.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 10/18/2023] [Accepted: 11/09/2023] [Indexed: 11/28/2023]
Abstract
Inflammatory Bowel Disease (IBD) is a chronic relapsing-remitting disease with a remarkable increase in incidence worldwide and a substantial disease burden. Although the pathophysiology is not fully elucidated yet an aberrant immune reaction against the intestinal microbiota and the gut microbial dysbiosis have been identified to play a major role. The composition of gut microbiota in IBD patients is distinct from that of healthy individuals, with certain organisms predominating over others. Differences in the microbial dysbiosis have been also observed between Crohn Disease (CD) and Ulcerative Colitis (UC). A disruption of the microbiota's balance can lead to inflammation and intestinal damage. Microbiota composition in IBD can be affected both by endogenous (i.e., interaction with the immune system and intestinal epithelial cells) and exogenous (i.e., medications, surgery, diet) factors. The complex interplay between the gut microbiota and IBD is an area of great interest for understanding disease pathogenesis and developing new treatments. The purpose of this review is to summarize the latest evidence on the role of microbiota in IBD pathogenesis and to explore possible future areas of research.
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Affiliation(s)
- Caterina Foppa
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele, 20090, Milan, Italy; IRCCS Humanitas Research Hospital, Division of Colon and Rectal Surgery, via Manzoni 56, Rozzano, 20089, Milan, Italy
| | - Tommy Rizkala
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele, 20090, Milan, Italy
| | - Alessandro Repici
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele, 20090, Milan, Italy; IRCCS Humanitas Research Hospital, Division of Gastroenterology and Digestive Endoscopy Unit, via Manzoni 56, Rozzano, 20089, Milan, Italy
| | - Cesare Hassan
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele, 20090, Milan, Italy; IRCCS Humanitas Research Hospital, Division of Gastroenterology and Digestive Endoscopy Unit, via Manzoni 56, Rozzano, 20089, Milan, Italy
| | - Antonino Spinelli
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele, 20090, Milan, Italy; IRCCS Humanitas Research Hospital, Division of Colon and Rectal Surgery, via Manzoni 56, Rozzano, 20089, Milan, Italy.
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Zeng L, Yang K, He Q, Zhu X, Long Z, Wu Y, Chen J, Li Y, Zeng J, Cui G, Xiang W, Hao W, Sun L. Efficacy and safety of gut microbiota-based therapies in autoimmune and rheumatic diseases: a systematic review and meta-analysis of 80 randomized controlled trials. BMC Med 2024; 22:110. [PMID: 38475833 PMCID: PMC10935932 DOI: 10.1186/s12916-024-03303-4] [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: 06/27/2023] [Accepted: 02/13/2024] [Indexed: 03/14/2024] Open
Abstract
BACKGROUND Previous randomized controlled trials (RCTs) suggested that gut microbiota-based therapies may be effective in treating autoimmune diseases, but a systematic summary is lacking. METHODS Pubmed, EMbase, Sinomed, and other databases were searched for RCTs related to the treatment of autoimmune diseases with probiotics from inception to June 2022. RevMan 5.4 software was used for meta-analysis after 2 investigators independently screened literature, extracted data, and assessed the risk of bias of included studies. RESULTS A total of 80 RCTs and 14 types of autoimmune disease [celiac sprue, SLE, and lupus nephritis (LN), RA, juvenile idiopathic arthritis (JIA), spondyloarthritis, psoriasis, fibromyalgia syndrome, MS, systemic sclerosis, type 1 diabetes mellitus (T1DM), oral lichen planus (OLP), Crohn's disease, ulcerative colitis] were included. The results showed that gut microbiota-based therapies may improve the symptoms and/or inflammatory factor of celiac sprue, SLE and LN, JIA, psoriasis, PSS, MS, systemic sclerosis, Crohn's disease, and ulcerative colitis. However, gut microbiota-based therapies may not improve the symptoms and/or inflammatory factor of spondyloarthritis and RA. Gut microbiota-based therapies may relieve the pain of fibromyalgia syndrome, but the effect on fibromyalgia impact questionnaire score is not significant. Gut microbiota-based therapies may improve HbA1c in T1DM, but its effect on total insulin requirement does not seem to be significant. These RCTs showed that probiotics did not increase the incidence of adverse events. CONCLUSIONS Gut microbiota-based therapies may improve several autoimmune diseases (celiac sprue, SLE and LN, JIA, psoriasis, fibromyalgia syndrome, PSS, MS, T1DM, Crohn's disease, and ulcerative colitis).
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Affiliation(s)
- Liuting Zeng
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Graduate School of Peking Union Medical College, Nanjing, China.
| | - Kailin Yang
- Hunan University of Chinese Medicine, Changsha, China
| | - Qi He
- People's Hospital of Ningxiang City, Ningxiang, China
| | | | - Zhiyong Long
- Department of Rehabilitation Medicine, Guangzhou Panyu Central Hospital, Guangzhou, China
| | - Yang Wu
- Department of Rheumatology, National Clinical Research Center for Dermatologic and Immunologic Diseases, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | | | - Yuwei Li
- Hunan University of Science and Technology, Xiangtan, China
| | - Jinsong Zeng
- Department of Rheumatology, National Clinical Research Center for Dermatologic and Immunologic Diseases, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Ge Cui
- Department of Epidemiology and Statistics, School of Public Health, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Wang Xiang
- Department of Rheumatology, The First People's Hospital Changde City, Changde, China
| | - Wensa Hao
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lingyun Sun
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Graduate School of Peking Union Medical College, Nanjing, China.
- Department of Rheumatology and Immunology, The First Affiliated Hospital of Anhui Medical University, Hefei, China.
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Amara J, Itani T, Hajal J, Bakhos JJ, Saliba Y, Aboushanab SA, Kovaleva EG, Fares N, Mondragon AC, Miranda JM. Circadian Rhythm Perturbation Aggravates Gut Microbiota Dysbiosis in Dextran Sulfate Sodium-Induced Colitis in Mice. Nutrients 2024; 16:247. [PMID: 38257139 PMCID: PMC10819604 DOI: 10.3390/nu16020247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
Circadian rhythm disruption is increasingly considered an environmental risk factor for the development and exacerbation of inflammatory bowel disease. We have reported in a previous study that nychthemeral dysregulation is associated with an increase in intestinal barrier permeability and inflammation in mice with dextran sulfate sodium (DSS)-induced colitis. To investigate the effect of circadian rhythm disruption on the composition and diversity of the gut microbiota (GM), sixty male C57BL/6J mice were initially divided to two groups, with the shifted group (n = 30) exposed to circadian shifts for three months and the non-shifted group (n = 30) kept under a normal light-dark cycle. The mice of the shifted group were cyclically housed for five days under the normal 12:12 h light-dark cycle, followed by another five days under a reversed light-dark cycle. At the end of the three months, a colitis was induced by 2% DSS given in the drinking water of 30 mice. Animals were then divided into four groups (n = 15 per group): sham group non-shifted (Sham-NS), sham group shifted (Sham-S), DSS non-shifted (DSS-NS) and DSS shifted (DSS-S). Fecal samples were collected from rectal content to investigate changes in GM composition via DNA extraction, followed by high-throughput sequencing of the bacterial 16S rRNA gene. The mouse GM was dominated by three phyla: Firmicutes, Bacteroidetes and Actinobacteria. The Firmicutes/Bacteroidetes ratio decreased in mice with induced colitis. The richness and diversity of the GM were reduced in the colitis group, especially in the group with inverted circadian rhythm. Moreover, the GM composition was modified in the inverted circadian rhythm group, with an increase in Alloprevotella, Turicibacter, Bacteroides and Streptococcus genera. Circadian rhythm inversion exacerbates GM dysbiosis to a less rich and diversified extent in a DSS-induced colitis model. These findings show possible interplay between circadian rhythm disruption, GM dynamics and colitis pathogenesis.
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Affiliation(s)
- Joseph Amara
- Laboratoire de Recherche en Physiologie et Physiopathologie, Pôle Technologie Santé, Faculté de Médecine, Université Saint Joseph, Beirut 1104 2020, Lebanon; (J.A.); (J.H.); (Y.S.)
| | - Tarek Itani
- Laboratoire de Microbiologie, Faculté de Pharmacie, Université Saint Joseph, Beirut 1104 2020, Lebanon;
| | - Joelle Hajal
- Laboratoire de Recherche en Physiologie et Physiopathologie, Pôle Technologie Santé, Faculté de Médecine, Université Saint Joseph, Beirut 1104 2020, Lebanon; (J.A.); (J.H.); (Y.S.)
| | - Jules-Joel Bakhos
- Laboratoire de Recherche en Physiologie et Physiopathologie, Pôle Technologie Santé, Faculté de Médecine, Université Saint Joseph, Beirut 1104 2020, Lebanon; (J.A.); (J.H.); (Y.S.)
| | - Youakim Saliba
- Laboratoire de Recherche en Physiologie et Physiopathologie, Pôle Technologie Santé, Faculté de Médecine, Université Saint Joseph, Beirut 1104 2020, Lebanon; (J.A.); (J.H.); (Y.S.)
| | - Saied A. Aboushanab
- Institute of Chemical Engineering, Ural Federal University Named after the First President of Russia B. N. Yeltsin, Mira 19, Yekaterinburg 620002, Russia; (S.A.A.); (E.G.K.)
| | - Elena G. Kovaleva
- Institute of Chemical Engineering, Ural Federal University Named after the First President of Russia B. N. Yeltsin, Mira 19, Yekaterinburg 620002, Russia; (S.A.A.); (E.G.K.)
| | - Nassim Fares
- Laboratoire de Recherche en Physiologie et Physiopathologie, Pôle Technologie Santé, Faculté de Médecine, Université Saint Joseph, Beirut 1104 2020, Lebanon; (J.A.); (J.H.); (Y.S.)
| | - Alicia C. Mondragon
- Laboratorio de Higiene, Inspección y Control de Alimentos, Departamento de Química Analítica, Nutrición y Bromatología, Campus Terra, Universidade da Santiago de Compostela, 27002 Lugo, Spain;
| | - Jose Manuel Miranda
- Laboratorio de Higiene, Inspección y Control de Alimentos, Departamento de Química Analítica, Nutrición y Bromatología, Campus Terra, Universidade da Santiago de Compostela, 27002 Lugo, Spain;
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6
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Ma R, Zhu Y, Li X, Hu S, Zheng D, Xiong S, Xu S, Xiang L, Zhao M, Tang C, Zeng Z, Chen M, Feng R. A Novel Serum Metabolomic Panel for the Diagnosis of Crohn's Disease. Inflamm Bowel Dis 2023; 29:1524-1535. [PMID: 37195904 DOI: 10.1093/ibd/izad080] [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: 01/04/2023] [Indexed: 05/19/2023]
Abstract
BACKGROUND A distinctive metabolic phenotype provides the opportunity to discover noninvasive biomarkers for the diagnosis of Crohn's disease (CD) and for differentiating it from other intestinal inflammatory diseases. The study sought to identify new biomarkers for CD diagnosis. METHODS Serum metabolites from 68 newly diagnosed and treatment-naïve patients with CD and 56 healthy control (HC) subjects were profiled using targeted liquid chromatography-mass spectrometry. Five metabolic biomarkers were identified to distinguish patients with CD from the HC subjects and validated in a separate cohort consisting of 110 patients with CD and 90 HC subjects using a combination of univariate analysis, orthogonal partial least-squares discriminant analysis, and receiver-operating characteristic curve analysis. Differences in the 5 metabolites were evaluated among patients with CD and patients with ulcerative colitis (n = 62), intestinal tuberculosis (n = 48), and Behçet's disease (n = 31). RESULTS Among the 185 quantified metabolites, a panel of 5 (pyruvate, phenylacetylglutamine, isolithocholic acid, taurodeoxycholic acid, and glycolithocholic acid) were found to distinguish patients with CD with high accuracy from HC subjects, with an area under the curve of 0.861 (P < .001). The performance of the model in assessing clinical disease activity was comparable to that of the present biomarkers: C-reactive protein and erythrocyte sedimentation rate. The 5 metabolites were significantly different among the patients and were valuable in the differentiation between CD and other chronic intestinal inflammatory diseases. CONCLUSIONS The combination of 5 serum metabolite biomarkers for the diagnosis of CD has the potential to provide an accurate, noninvasive, and inexpensive alternative to conventional tests and might be valuable for the differentiation from other diagnostically challenging intestinal inflammatory diseases.
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Affiliation(s)
- Ruiqi Ma
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yijun Zhu
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xiaozhi Li
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Shixian Hu
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Danping Zheng
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Shanshan Xiong
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Shu Xu
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Liyuan Xiang
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Min Zhao
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ce Tang
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zhirong Zeng
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Minhu Chen
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Rui Feng
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Department of Gastroenterology, Guangxi Hospital Division of The First Affiliated Hospital, Sun Yat-sen University, Nanning, China
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7
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Kaliora AC. Nutrition in inflammatory bowel diseases; Is there a role? Best Pract Res Clin Gastroenterol 2023; 62-63:101827. [PMID: 37094912 DOI: 10.1016/j.bpg.2023.101827] [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: 12/31/2022] [Revised: 02/10/2023] [Accepted: 02/15/2023] [Indexed: 04/26/2023]
Abstract
Nutrition is of paramount importance not only for healthy individuals, but all the more for the ones with pathologies interlinked with the diet. In that light, diet, when used accordingly can act in a protective manner in inflammatory bowel diseases. The interplay of diet and IBD is not thoroughly defined, and guidelines are a work in progress. However, significant knowledge has been gained with regard to foods and nutrients that may exacerbate or alleviate the core symptoms. Patients with IBD restrict from their diet a plethora of foods often arbitrary, thus depriving themselves from valuable constituents. Careful navigation into the newfound field of genetic variants and personalization of diet should be employed with avoidance of the Westernized diet, processed foods and additives, and focus on a holistic approach with a balanced diet rich in bioactive compounds in order to improve the quality of life of these patients and address diet-related deficiencies.
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Affiliation(s)
- Andriana C Kaliora
- Human Nutrition and Foods, Department of Dietetics-Nutrition Science, School of Health and Education Sciences, Harokopio University, 70 El. Venizelou Ave., 17676, Athens, Greece.
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8
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Becker HEF, Demers K, Derijks LJJ, Jonkers DMAE, Penders J. Current evidence and clinical relevance of drug-microbiota interactions in inflammatory bowel disease. Front Microbiol 2023; 14:1107976. [PMID: 36910207 PMCID: PMC9996055 DOI: 10.3389/fmicb.2023.1107976] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 02/06/2023] [Indexed: 02/25/2023] Open
Abstract
Background Inflammatory bowel disease (IBD) is a chronic relapsing-remitting disease. An adverse immune reaction toward the intestinal microbiota is involved in the pathophysiology and microbial perturbations are associated with IBD in general and with flares specifically. Although medical drugs are the cornerstone of current treatment, responses vary widely between patients and drugs. The intestinal microbiota can metabolize medical drugs, which may influence IBD drug (non-)response and side effects. Conversely, several drugs can impact the intestinal microbiota and thereby host effects. This review provides a comprehensive overview of current evidence on bidirectional interactions between the microbiota and relevant IBD drugs (pharmacomicrobiomics). Methods Electronic literature searches were conducted in PubMed, Web of Science and Cochrane databases to identify relevant publications. Studies reporting on microbiota composition and/or drug metabolism were included. Results The intestinal microbiota can both enzymatically activate IBD pro-drugs (e.g., in case of thiopurines), but also inactivate certain drugs (e.g., mesalazine by acetylation via N-acetyltransferase 1 and infliximab via IgG-degrading enzymes). Aminosalicylates, corticosteroids, thiopurines, calcineurin inhibitors, anti-tumor necrosis factor biologicals and tofacitinib were all reported to alter the intestinal microbiota composition, including changes in microbial diversity and/or relative abundances of various microbial taxa. Conclusion Various lines of evidence have shown the ability of the intestinal microbiota to interfere with IBD drugs and vice versa. These interactions can influence treatment response, but well-designed clinical studies and combined in vivo and ex vivo models are needed to achieve consistent findings and evaluate clinical relevance.
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Affiliation(s)
- Heike E F Becker
- Division Gastroenterology-Hepatology, Department of Internal Medicine, NUTRIM School of Translational Research in Metabolism, Maastricht University Medical Centre+, Maastricht, Netherlands.,Department of Medical Microbiology, Infectious Diseases and Infection Prevention, NUTRIM School of Translational Research in Metabolism, Maastricht University Medical Centre+, Maastricht, Netherlands
| | - Karlijn Demers
- Division Gastroenterology-Hepatology, Department of Internal Medicine, NUTRIM School of Translational Research in Metabolism, Maastricht University Medical Centre+, Maastricht, Netherlands
| | - Luc J J Derijks
- Department of Clinical Pharmacy and Pharmacology, Máxima Medical Center, Veldhoven, Netherlands.,Department of Clinical Pharmacy and Toxicology, Maastricht University Medical Centre+, Maastricht, Netherlands
| | - Daisy M A E Jonkers
- Division Gastroenterology-Hepatology, Department of Internal Medicine, NUTRIM School of Translational Research in Metabolism, Maastricht University Medical Centre+, Maastricht, Netherlands
| | - John Penders
- Department of Medical Microbiology, Infectious Diseases and Infection Prevention, NUTRIM School of Translational Research in Metabolism, Maastricht University Medical Centre+, Maastricht, Netherlands.,Department of Medical Microbiology, Infectious Diseases and Infection Prevention, CAPHRI School of Public Health and Primary Care, Maastricht University Medical Centre+, Maastricht, Netherlands
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9
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Ma X, Lu X, Zhang W, Yang L, Wang D, Xu J, Jia Y, Wang X, Xie H, Li S, Zhang M, He Y, Jin P, Sheng J. Gut microbiota in the early stage of Crohn’s disease has unique characteristics. Gut Pathog 2022; 14:46. [DOI: 10.1186/s13099-022-00521-0] [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: 06/20/2022] [Accepted: 12/06/2022] [Indexed: 12/15/2022] Open
Abstract
Abstract
Background
Emerging evidence suggests that gut microbiota plays a predominant role in Crohn’s disease (CD). However, the microbiome alterations in the early stage of CD patients still remain unclear. The present study aimed to identify dysbacteriosis in patients with early CD and explore specific gut bacteria related to the progression of CD.
Methods
This study was nested within a longitudinal prospective Chinese CD cohort, and it included 18 early CD patients, 22 advanced CD patients and 30 healthy controls. The microbiota communities were investigated using high-throughput Illumina HiSeq sequencing targeting the V3–V4 region of 16S ribosomal DNA (rDNA) gene. The relationship between the gut microbiota and clinical characteristics of CD was analyzed.
Results
Differential microbiota compositions were observed in CD samples (including early and advanced CD samples) and healthy controls samples. Notably, Lachnospiracea_incertae_sedis and Parabacteroides were enriched in the early CD patients, Escherichia/Shigella, Enterococcus and Proteus were enriched in the advanced CD patients, and Roseburia, Gemmiger, Coprococcus, Ruminococcus 2, Butyricicoccus, Dorea, Fusicatenibacter, Anaerostipes, Clostridium IV were enriched in the healthy controls [LDA score (log10) > 2]. Furthermore, Kruskal–Wallis Rank sum test results showed that Blautia, Clostridium IV, Coprococcus, Dorea, Fusicatenibacter continued to significantly decrease in early and advanced CD patients, and Escherichia/Shigella and Proteus continued to significantly increase compared with healthy controls (P < 0.05). The PICRUSt analysis identified 16 remarkably different metabolic pathways [LDA score (log10) > 2]. Some genera were significantly correlated with various clinical parameters, such as fecal calprotectin, erythrocyte sedimentation rate, C-reactive protein, gland reduce, goblet cells decreased, clinical symptoms (P < 0.05).
Conclusions
Dysbacteriosis occurs in the early stage of CD and is associated with the progression of CD. This data provides a foundation that furthers the understanding of the role of gut microbiota in CD’s pathogenesis.
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Functional Plasmon-Activated Water Increases Akkermansia muciniphila Abundance in Gut Microbiota to Ameliorate Inflammatory Bowel Disease. Int J Mol Sci 2022; 23:ijms231911422. [PMID: 36232724 PMCID: PMC9570201 DOI: 10.3390/ijms231911422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/22/2022] [Accepted: 09/22/2022] [Indexed: 11/16/2022] Open
Abstract
Inflammatory bowel disease (IBD) is associated with dysbiosis and intestinal barrier dysfunction, as indicated by epithelial hyperpermeability and high levels of mucosal-associated bacteria. Changes in gut microbiota may be correlated with IBD pathogenesis. Additionally, microbe-based treatments could mitigate clinical IBD symptoms. Plasmon-activated water (PAW) is known to have an anti-inflammatory potential. In this work, we studied the association between the anti-inflammatory ability of PAW and intestinal microbes, thereby improving IBD treatment. We examined the PAW-induced changes in the colonic immune activity and microbiota of mice by immunohistochemistry and next generation sequencing, determined whether drinking PAW can mitigate IBD induced by 2,4,6-trinitrobenzene sulfonic acid (TNBS) and dysbiosis through mice animal models. The effects of specific probiotic species on mice with TNBS-induced IBD were also investigated. Experimental results indicated that PAW could change the local inflammation in the intestinal microenvironment. Moreover, the abundance of Akkermansia spp. was degraded in the TNBS-treated mice but elevated in the PAW-drinking mice. Daily rectal injection of Akkermansia muciniphila, a potential probiotic species in Akkermansia spp., also improved the health of the mice. Correspondingly, both PAW consumption and increasing the intestinal abundance of Akkermansia muciniphila can mitigate IBD in mice. These findings indicate that increasing the abundance of Akkermansia muciniphila in the gut through PAW consumption or other methods may mitigate IBD in mice with clinically significant IBD.
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11
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Gubatan J, Boye TL, Temby M, Sojwal RS, Holman DR, Sinha SR, Rogalla SR, Nielsen OH. Gut Microbiome in Inflammatory Bowel Disease: Role in Pathogenesis, Dietary Modulation, and Colitis-Associated Colon Cancer. Microorganisms 2022; 10:1371. [PMID: 35889090 PMCID: PMC9316834 DOI: 10.3390/microorganisms10071371] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/03/2022] [Accepted: 07/05/2022] [Indexed: 12/11/2022] Open
Abstract
The gut microbiome has increasingly been recognized as a critical and central factor in inflammatory bowel disease (IBD). Here, we review specific microorganisms that have been suggested to play a role in the pathogenesis of IBD and the current state of fecal microbial transplants as a therapeutic strategy in IBD. We discuss specific nutritional and dietary interventions in IBD and their effects on gut microbiota composition. Finally, we examine the role and mechanisms of the gut microbiome in mediating colitis-associated colon cancer.
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Affiliation(s)
- John Gubatan
- Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA 94305, USA; (M.T.); (R.S.S.); (D.R.H.); (S.R.S.); (S.R.R.)
| | - Theresa Louise Boye
- Department of Gastroenterology, Medical Section, Herlev Hospital, University of Copenhagen, DK-2730 Copenhagen, Denmark; (T.L.B.); or (O.H.N.)
| | - Michelle Temby
- Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA 94305, USA; (M.T.); (R.S.S.); (D.R.H.); (S.R.S.); (S.R.R.)
| | - Raoul S. Sojwal
- Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA 94305, USA; (M.T.); (R.S.S.); (D.R.H.); (S.R.S.); (S.R.R.)
| | - Derek R. Holman
- Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA 94305, USA; (M.T.); (R.S.S.); (D.R.H.); (S.R.S.); (S.R.R.)
| | - Sidhartha R. Sinha
- Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA 94305, USA; (M.T.); (R.S.S.); (D.R.H.); (S.R.S.); (S.R.R.)
| | - Stephan R. Rogalla
- Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA 94305, USA; (M.T.); (R.S.S.); (D.R.H.); (S.R.S.); (S.R.R.)
| | - Ole Haagen Nielsen
- Department of Gastroenterology, Medical Section, Herlev Hospital, University of Copenhagen, DK-2730 Copenhagen, Denmark; (T.L.B.); or (O.H.N.)
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12
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Zhu R, Tang J, Xing C, Nan Q, Liang G, Luo J, Zhou J, Miao Y, Cao Y, Dai S, Lan D. The Distinguishing Bacterial Features From Active and Remission Stages of Ulcerative Colitis Revealed by Paired Fecal Metagenomes. Front Microbiol 2022; 13:883495. [PMID: 35801108 PMCID: PMC9253600 DOI: 10.3389/fmicb.2022.883495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 05/23/2022] [Indexed: 11/13/2022] Open
Abstract
Ulcerative colitis (UC) is a serious chronic intestinal inflammatory disease, with an increased incidence in recent years. The intestinal microbiota plays a key role in the pathogenesis of UC. However, there is no unified conclusion on how the intestinal microbiota changes. Most studies focus on the change between UC patients and healthy individuals, rather than the active and remission stage of the same patient. To minimize the influences of genetic differences, environmental and dietary factors, we studied the intestinal microbiota of paired fecal samples from 42 UC patients at the active and remission stages. We identified 175 species of microbes from 11 phyla and found no difference of the alpha and beta diversities between the active and remission stages. Paired t-test analysis revealed differential microbiota at levels of the phyla, class, order, family, genus, and species, including 13 species with differential abundance. For example, CAG-269 sp001916005, Eubacterium F sp003491505, Lachnospira sp000436475, et al. were downregulated in the remission, while the species of Parabacteroides distasonis, Prevotellamassilia sp900540885, CAG-495 sp001917125, et al. were upregulated in the remission. The 13 species can effectively distinguish the active and remission stages. Functional analysis showed that the sporulation and biosynthesis were downregulated, and the hydrogen peroxide catabolic process was upregulated in remission of UC. Our study suggests that the 13 species together may serve as a biomarker panel contributing to identify the active and remission stages of UC, which provides a valuable reference for the treatment of UC patients by FMT or other therapeutic methods.
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Affiliation(s)
- Ran Zhu
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
| | - Junrui Tang
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Yunnan Province Clinical Research Center for Digestive Diseases, Kunming, China
| | - Chengfeng Xing
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Yunnan Province Clinical Research Center for Digestive Diseases, Kunming, China
| | - Qiong Nan
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Yunnan Province Clinical Research Center for Digestive Diseases, Kunming, China
| | - Guili Liang
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Yunnan Province Clinical Research Center for Digestive Diseases, Kunming, China
| | - Juan Luo
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Yunnan Province Clinical Research Center for Digestive Diseases, Kunming, China
| | - Jiao Zhou
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Yunnan Province Clinical Research Center for Digestive Diseases, Kunming, China
| | - Yinglei Miao
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Yunnan Province Clinical Research Center for Digestive Diseases, Kunming, China
| | - Yu Cao
- Department of Cardiac Surgery, The First People’s Hospital of Yunnan Province, Kunming, China
- Yu Cao,
| | - Shaoxing Dai
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
- Shaoxing Dai,
| | - Danfeng Lan
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Yunnan Province Clinical Research Center for Digestive Diseases, Kunming, China
- *Correspondence: Danfeng Lan,
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13
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Krela-Kaźmierczak I, Zakerska-Banaszak O, Skrzypczak-Zielińska M, Łykowska-Szuber L, Szymczak-Tomczak A, Zawada A, Rychter AM, Ratajczak AE, Skoracka K, Skrzypczak D, Marcinkowska E, Słomski R, Dobrowolska A. Where Do We Stand in the Behavioral Pathogenesis of Inflammatory Bowel Disease? The Western Dietary Pattern and Microbiota-A Narrative Review. Nutrients 2022; 14:nu14122520. [PMID: 35745251 PMCID: PMC9230670 DOI: 10.3390/nu14122520] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/13/2022] [Accepted: 06/15/2022] [Indexed: 02/06/2023] Open
Abstract
Despite the increasing knowledge with regard to IBD (inflammatory bowel disease), including ulcerative colitis (UC) and Crohn’s disease (CD), the etiology of these conditions is still not fully understood. Apart from immunological, environmental and nutritional factors, which have already been well documented, it is worthwhile to look at the possible impact of genetic factors, as well as the composition of the microbiota in patients suffering from IBD. New technologies in biochemistry allow to obtain information that can add to the current state of knowledge in IBD etiology.
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Affiliation(s)
- Iwona Krela-Kaźmierczak
- Department of Gastroenterology, Dietetics and Internal Medicine, Poznan University of Medical Sciences, 60-355 Poznań, Poland; (L.Ł.-S.); (A.S.-T.); (A.Z.); (A.M.R.); (A.E.R.); (K.S.); (E.M.); (A.D.)
- Correspondence: (I.K.-K.); (O.Z.-B.); (D.S.)
| | - Oliwia Zakerska-Banaszak
- Institute of Human Genetics, Polish Academy of Sciences, 60-479 Poznań, Poland; (M.S.-Z.); (R.S.)
- Correspondence: (I.K.-K.); (O.Z.-B.); (D.S.)
| | | | - Liliana Łykowska-Szuber
- Department of Gastroenterology, Dietetics and Internal Medicine, Poznan University of Medical Sciences, 60-355 Poznań, Poland; (L.Ł.-S.); (A.S.-T.); (A.Z.); (A.M.R.); (A.E.R.); (K.S.); (E.M.); (A.D.)
| | - Aleksandra Szymczak-Tomczak
- Department of Gastroenterology, Dietetics and Internal Medicine, Poznan University of Medical Sciences, 60-355 Poznań, Poland; (L.Ł.-S.); (A.S.-T.); (A.Z.); (A.M.R.); (A.E.R.); (K.S.); (E.M.); (A.D.)
| | - Agnieszka Zawada
- Department of Gastroenterology, Dietetics and Internal Medicine, Poznan University of Medical Sciences, 60-355 Poznań, Poland; (L.Ł.-S.); (A.S.-T.); (A.Z.); (A.M.R.); (A.E.R.); (K.S.); (E.M.); (A.D.)
| | - Anna Maria Rychter
- Department of Gastroenterology, Dietetics and Internal Medicine, Poznan University of Medical Sciences, 60-355 Poznań, Poland; (L.Ł.-S.); (A.S.-T.); (A.Z.); (A.M.R.); (A.E.R.); (K.S.); (E.M.); (A.D.)
- Doctoral School, Poznan University of Medical Sciences, 61-701 Poznań, Poland
| | - Alicja Ewa Ratajczak
- Department of Gastroenterology, Dietetics and Internal Medicine, Poznan University of Medical Sciences, 60-355 Poznań, Poland; (L.Ł.-S.); (A.S.-T.); (A.Z.); (A.M.R.); (A.E.R.); (K.S.); (E.M.); (A.D.)
- Doctoral School, Poznan University of Medical Sciences, 61-701 Poznań, Poland
| | - Kinga Skoracka
- Department of Gastroenterology, Dietetics and Internal Medicine, Poznan University of Medical Sciences, 60-355 Poznań, Poland; (L.Ł.-S.); (A.S.-T.); (A.Z.); (A.M.R.); (A.E.R.); (K.S.); (E.M.); (A.D.)
- Doctoral School, Poznan University of Medical Sciences, 61-701 Poznań, Poland
| | - Dorota Skrzypczak
- Department of Gastroenterology, Dietetics and Internal Medicine, Poznan University of Medical Sciences, 60-355 Poznań, Poland; (L.Ł.-S.); (A.S.-T.); (A.Z.); (A.M.R.); (A.E.R.); (K.S.); (E.M.); (A.D.)
- Correspondence: (I.K.-K.); (O.Z.-B.); (D.S.)
| | - Emilia Marcinkowska
- Department of Gastroenterology, Dietetics and Internal Medicine, Poznan University of Medical Sciences, 60-355 Poznań, Poland; (L.Ł.-S.); (A.S.-T.); (A.Z.); (A.M.R.); (A.E.R.); (K.S.); (E.M.); (A.D.)
| | - Ryszard Słomski
- Institute of Human Genetics, Polish Academy of Sciences, 60-479 Poznań, Poland; (M.S.-Z.); (R.S.)
| | - Agnieszka Dobrowolska
- Department of Gastroenterology, Dietetics and Internal Medicine, Poznan University of Medical Sciences, 60-355 Poznań, Poland; (L.Ł.-S.); (A.S.-T.); (A.Z.); (A.M.R.); (A.E.R.); (K.S.); (E.M.); (A.D.)
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14
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Stockdale SR, Harrington RS, Shkoporov AN, Khokhlova EV, Daly KM, McDonnell SA, O'Reagan O, Nolan JA, Sheehan D, Lavelle A, Draper LA, Shanahan F, Ross RP, Hill C. Metagenomic assembled plasmids of the human microbiome vary across disease cohorts. Sci Rep 2022; 12:9212. [PMID: 35654877 PMCID: PMC9163076 DOI: 10.1038/s41598-022-13313-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 05/17/2022] [Indexed: 12/15/2022] Open
Abstract
We compiled a human metagenome assembled plasmid (MAP) database and interrogated differences across multiple studies that were originally designed to investigate the composition of the human microbiome across various lifestyles, life stages and events. This was performed as plasmids enable bacteria to rapidly expand their functional capacity through mobilisation, yet their contribution to human health and disease is poorly understood. We observed that inter-sample β-diversity differences of plasmid content (plasmidome) could distinguish cohorts across a multitude of conditions. We also show that reduced intra-sample plasmidome α-diversity is consistent amongst patients with inflammatory bowel disease (IBD) and Clostridioides difficile infections. We also show that faecal microbiota transplants can restore plasmidome diversity. Overall plasmidome diversity, specific plasmids, and plasmid-encoded functions can all potentially act as biomarkers of IBD or its severity. The human plasmidome is an overlooked facet of the microbiome and should be integrated into investigations regarding the role of the microbiome in promoting health or disease. Including MAP databases in analyses will enable a greater understanding of the roles of plasmid-encoded functions within the gut microbiome and will inform future human metagenome analyses.
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Affiliation(s)
- S R Stockdale
- APC Microbiome Ireland, University College Cork, Co. Cork, Ireland.
| | - R S Harrington
- School of Microbiology, University College Cork, Co. Cork, Ireland
| | - A N Shkoporov
- APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
| | - E V Khokhlova
- APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
| | - K M Daly
- APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
| | - S A McDonnell
- APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
| | - O O'Reagan
- APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
| | - J A Nolan
- APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
| | - D Sheehan
- Department of Medicine, University College Cork, Co. Cork, Ireland
| | - A Lavelle
- APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
- Department of Medicine, University College Cork, Co. Cork, Ireland
| | - L A Draper
- APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
| | - F Shanahan
- APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
- Department of Medicine, University College Cork, Co. Cork, Ireland
| | - R P Ross
- APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
| | - C Hill
- APC Microbiome Ireland, University College Cork, Co. Cork, Ireland.
- School of Microbiology, University College Cork, Co. Cork, Ireland.
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15
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Adamkova P, Hradicka P, Kupcova Skalnikova H, Cizkova V, Vodicka P, Farkasova Iannaccone S, Kassayova M, Gancarcikova S, Demeckova V. Dextran Sulphate Sodium Acute Colitis Rat Model: A Suitable Tool for Advancing Our Understanding of Immune and Microbial Mechanisms in the Pathogenesis of Inflammatory Bowel Disease. Vet Sci 2022; 9:238. [PMID: 35622766 PMCID: PMC9147231 DOI: 10.3390/vetsci9050238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/11/2022] [Accepted: 05/12/2022] [Indexed: 01/27/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a group of disorders causing inflammation in the digestive tract. Recent data suggest that dysbiosis may play a pivotal role in the IBD pathogenesis. As microbiome-based therapeutics that modulate the gut ecology have been proposed as a novel strategy for preventing IBD, the aim of presenting study was to evaluate the dextran sulphate sodium (DSS) rat model mainly in terms of microbial shifts to confirm its suitability for dysbiosis study in IBD. Acute colitis was induced using 5% DSS solution for seven days and rats were euthanized five days after DSS removal. The faecal/caecal microbiota was analyzed by next generation sequencing. Disease activity index (DAI) score was evaluated daily. Blood and colon tissue immunophenotyping was assessed by flow cytometry and histological, haematological, and biochemical parameters were also evaluated. The colitis induction was reflected in a significantly higher DAI score and changes in all parameters measured. This study demonstrated significant shifts in the colitis-related microbial species after colitis induction. The characteristic inflammation-associated microbiota could be detected even after a five day-recovery period. Moreover, the DSS-model might contribute to an understanding of the effect of different treatments on extraintestinal organ impairments. The observation that certain bacterial species in the gut microbiota are associated with colitis raises the question of whether these organisms are contributors to, or a consequence of the disease. Despite some limitations, we confirmed the suitability of DSS-induced colitis model to monitor microbial changes during acute colitis, in order to test attractive new microbiome-based therapies.
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Affiliation(s)
- Petra Adamkova
- Faculty of Science, Institute of Biology and Ecology, Pavol Jozef Safarik University in Kosice, 041 54 Kosice, Slovakia; (P.A.); (P.H.); (M.K.)
| | - Petra Hradicka
- Faculty of Science, Institute of Biology and Ecology, Pavol Jozef Safarik University in Kosice, 041 54 Kosice, Slovakia; (P.A.); (P.H.); (M.K.)
| | - Helena Kupcova Skalnikova
- Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, 277 21 Libechov, Czech Republic; (H.K.S.); (V.C.); (P.V.)
| | - Veronika Cizkova
- Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, 277 21 Libechov, Czech Republic; (H.K.S.); (V.C.); (P.V.)
| | - Petr Vodicka
- Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, 277 21 Libechov, Czech Republic; (H.K.S.); (V.C.); (P.V.)
| | - Silvia Farkasova Iannaccone
- Department of Forensic Medicine, Faculty of Medicine, Pavol Jozef Safarik University in Kosice, 040 11 Kosice, Slovakia;
| | - Monika Kassayova
- Faculty of Science, Institute of Biology and Ecology, Pavol Jozef Safarik University in Kosice, 041 54 Kosice, Slovakia; (P.A.); (P.H.); (M.K.)
| | - Sona Gancarcikova
- Department of Microbiology and Immunology, University of Veterinary Medicine and Pharmacy in Kosice, 041 81 Kosice, Slovakia;
| | - Vlasta Demeckova
- Faculty of Science, Institute of Biology and Ecology, Pavol Jozef Safarik University in Kosice, 041 54 Kosice, Slovakia; (P.A.); (P.H.); (M.K.)
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16
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Bosch S, Wintjens DSJ, Wicaksono A, Pierik M, Covington JA, de Meij TGJ, de Boer NKH. Prediction of Inflammatory Bowel Disease Course Based on Fecal Scent. SENSORS 2022; 22:s22062316. [PMID: 35336485 PMCID: PMC8948784 DOI: 10.3390/s22062316] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/28/2022] [Accepted: 03/05/2022] [Indexed: 02/05/2023]
Abstract
The early prediction of changes in disease state allows timely treatment of patients with inflammatory bowel disease (IBD) to be performed, which improves disease outcome. The aim of this pilot study is to explore the potential of fecal volatile organic compound (VOC) profiles to predict disease course. In this prospective cohort, IBD patients were asked to collect two fecal samples and fill in a questionnaire at set intervals. Biochemically, active disease was defined by FCP ≥ 250 mg/g and remission was defined by FCP < 100 mg/g. Clinically, active disease was defined by a Harvey Bradshaw Index (HBI) ≥ 5 for Crohn’s disease or by a Simple Clinical Colitis Activity Index (SCCAI) ≥ 3 for ulcerative colitis. Clinical remission was defined by an HBI < 4 or SCCAI ≤ 2. Fecal VOC profiles were measured using gas chromatography-ion mobility spectrometry (GC-IMS). The fecal samples collected first were included for VOC analysis to predict disease state at the following collection. A total of 182 subsequently collected samples met the disease-state criteria. The fecal VOC profiles of samples displaying low FCP levels at the first measurements differed between patients preceding exacerbation versus those who remained in remission (AUC 0.75; p < 0.01). Samples with FCP levels at the first time point displayed different VOC profiles in patients preceding remission compared with those whose disease remained active (AUC 0.86; p < 0.01). Based on disease activity scores, there were no significant differences in any of the comparisons. Alterations in fecal VOC profiles preceding changes in FCP levels may be useful to detect disease-course alterations at an early stage. This could lead to earlier treatment, decreased numbers of complications, surgery and hospital admission.
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Affiliation(s)
- Sofie Bosch
- Department of Gastroenterology and Hepatology, AG&M Research Institute, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands;
- Correspondence: or
| | - Dion S. J. Wintjens
- Department of Gastroenterology and Hepatology, MUMC+, Maastricht University, 6229 HX Maastricht, The Netherlands; (D.S.J.W.); (M.P.)
| | - Alfian Wicaksono
- School of Engineering, University of Warwick, Coventry CV4 7AL, UK; (A.W.); (J.A.C.)
| | - Marieke Pierik
- Department of Gastroenterology and Hepatology, MUMC+, Maastricht University, 6229 HX Maastricht, The Netherlands; (D.S.J.W.); (M.P.)
| | - James A. Covington
- School of Engineering, University of Warwick, Coventry CV4 7AL, UK; (A.W.); (J.A.C.)
| | - Tim G. J. de Meij
- Department of Pediatric Gastroenterology, AG&M Research Institute, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands;
| | - Nanne K. H. de Boer
- Department of Gastroenterology and Hepatology, AG&M Research Institute, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands;
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17
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Guo X, Huang C, Xu J, Xu H, Liu L, Zhao H, Wang J, Huang W, Peng W, Chen Y, Nie Y, Zhou Y, Zhou Y. Gut Microbiota Is a Potential Biomarker in Inflammatory Bowel Disease. Front Nutr 2022; 8:818902. [PMID: 35127797 PMCID: PMC8814525 DOI: 10.3389/fnut.2021.818902] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 12/29/2021] [Indexed: 12/12/2022] Open
Abstract
Inflammatory bowel disease (IBD), which includes ulcerative colitis (UC) and Crohn's disease (CD), is characterized by relapse and remission alternately. It remains a great challenge to diagnose and assess disease activity during IBD due to the lack of specific markers. While traditional biomarkers from plasma and stool, such as C-reactive protein (CRP), fecal calprotectin (FC), and S100A12, can be used to measure inflammation, they are not specific to IBD and difficult to determine an effective cut-off value. There is consensus that gut microbiota is crucial for intestinal dysbiosis is closely associated with IBD etiopathology and pathogenesis. Multiple studies have documented differences in the composition of gut microbiota between patients with IBD and healthy individuals, particularly regarding microbial diversity and relative abundance of specific bacteria. Patients with IBD have higher levels of Proteobacteria and lower amounts of Bacteroides, Eubacterium, and Faecalibacterium than healthy individuals. This review summarizes the pros and cons of using traditional and microbiota biomarkers to assess disease severity and treatment outcomes and addresses the possibility of using microbiota-focused interventions during IBD treatment. Understanding the role of microbial biomarkers in the assessment of disease activity and treatment outcomes has the potential to change clinical practice and lead to the development of more personalized therapies.
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Affiliation(s)
- Xue Guo
- Department of Gastroenterology and Hepatology, The Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, China
- Department of Gastroenterology and Hepatology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Chen Huang
- Department of Gastroenterology and Hepatology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Jing Xu
- Department of Gastroenterology and Hepatology, The Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, China
- Department of Gastroenterology and Hepatology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Haoming Xu
- Department of Gastroenterology and Hepatology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Le Liu
- Department of Gastroenterology, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Hailan Zhao
- Department of Gastroenterology and Hepatology, The Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, China
- Department of Gastroenterology and Hepatology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Jiaqi Wang
- Department of Gastroenterology and Hepatology, The Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, China
- Department of Gastroenterology and Hepatology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Wenqi Huang
- Department of Gastroenterology and Hepatology, The Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, China
- Department of Gastroenterology and Hepatology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Wu Peng
- Department of Gastroenterology and Hepatology, The Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, China
- Department of Gastroenterology and Hepatology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Ye Chen
- Department of Gastroenterology, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Yuqiang Nie
- Department of Gastroenterology and Hepatology, The Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, China
- Department of Gastroenterology and Hepatology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Yongjian Zhou
- Department of Gastroenterology and Hepatology, The Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, China
- Department of Gastroenterology and Hepatology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
- Yongjian Zhou
| | - Youlian Zhou
- Department of Gastroenterology and Hepatology, The Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, China
- Department of Gastroenterology and Hepatology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
- *Correspondence: Youlian Zhou
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18
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Pedroso AA, Lee MD, Maurer JJ. Strength Lies in Diversity: How Community Diversity Limits Salmonella Abundance in the Chicken Intestine. Front Microbiol 2021; 12:694215. [PMID: 34211451 PMCID: PMC8239400 DOI: 10.3389/fmicb.2021.694215] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 05/24/2021] [Indexed: 12/12/2022] Open
Abstract
The transfer of the intestinal microbiota from adult to juvenile animals reduces Salmonella prevalence and abundance. The mechanism behind this exclusion is unknown, however, certain member species may exclude or promote pathogen colonization and Salmonella abundance in chickens correlates with intestinal community composition. In this study, newly hatched chicks were colonized with Salmonella Typhimurium and 16S rRNA libraries were generated from the cecal bacterial community at 21, 28, 35, and 42 days of age. Salmonella was quantified by real-time PCR. Operational taxonomic units (OTUs) were assigned, and taxonomic assignments were made, using the Ribosomal Database Project. Bacterial diversity was inversely proportional to the Salmonella abundance in the chicken cecum (p < 0.01). In addition, cecal communities with no detectable Salmonella (exclusive community) displayed an increase in the abundance of OTUs related to specific clostridial families (Ruminococcaceae, Eubacteriaceae, and Oscillospiraceae), genera (Faecalibacterium and Turicibacter) and member species (Ethanoligenens harbinense, Oscillibacter ruminantium, and Faecalibacterium prausnitzii). For cecal communities with high Salmonella abundance (permissive community), there was a positive correlation with the presence of unclassified Lachnospiraceae, clostridial genera Blautia and clostridial species Roseburia hominis, Eubacterium biforme, and Robinsoniella peoriensis. These findings strongly support the link between the intestinal bacterial species diversity and the presence of specific member species with Salmonella abundance in the chicken ceca. Exclusive bacterial species could prove effective as direct-fed microbials for reducing Salmonella in poultry while permissive species could be used to predict which birds will be super-shedders.
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Affiliation(s)
- Adriana A Pedroso
- Department of Population Health, University of Georgia, Athens, GA, United States
| | - Margie D Lee
- Department of Population Health, University of Georgia, Athens, GA, United States.,Department of Biomedical Sciences and Pathobiology, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - John J Maurer
- Department of Population Health, University of Georgia, Athens, GA, United States.,Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
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19
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Singh A, D'Amico D, Andreux PA, Dunngalvin G, Kern T, Blanco-Bose W, Auwerx J, Aebischer P, Rinsch C. Direct supplementation with Urolithin A overcomes limitations of dietary exposure and gut microbiome variability in healthy adults to achieve consistent levels across the population. Eur J Clin Nutr 2021; 76:297-308. [PMID: 34117375 PMCID: PMC8821002 DOI: 10.1038/s41430-021-00950-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 05/07/2021] [Accepted: 05/18/2021] [Indexed: 01/22/2023]
Abstract
BACKGROUND Urolithin A (UA) is produced by gut microflora from foods rich in ellagitannins. UA has been shown to improve mitochondrial health preclinically and in humans. Not everyone has a microbiome capable of producing UA, making supplementation with UA an appealing strategy. OBJECTIVE This is the first detailed investigation of the prevalence of UA producers in a healthy population and the ability of direct UA supplementation to overcome both microbiome and dietary variability. Dietary intake of a glass of pomegranate juice (PJ) was used to assess UA producer status (n = 100 participants) and to characterize differences in gut microbiome between UA producers from non-producers. METHODS Subjects were randomized (1:1) to either PJ or a food product containing UA (500 mg). Prevalence of UA producers and non-producers were determined in the PJ group. Diet questionnaires and fecal samples were collected to compare differences between UA producers and non-producers along with plasma samples at different time points to assess levels of UA and its conjugates between the interventions. RESULTS Only 12% of subjects had detectable levels of UA at baseline. Following PJ intake ~40% of the subjects converted significantly the precursor compounds into UA. UA producers were distinguished by a significantly higher gut microbiome diversity and ratio of Firmicutes to Bacteroides. Direct supplementation with UA significantly increased plasma levels and provided a >6-fold exposure to UA vs. PJ (p < 0.0001). CONCLUSIONS Differences in gut microbiome and diet that dictate natural exposure to UA can be overcome via direct dietary UA supplementation.
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Affiliation(s)
- Anurag Singh
- Amazentis SA, EPFL Innovation Park, Lausanne, Switzerland.
| | - Davide D'Amico
- Amazentis SA, EPFL Innovation Park, Lausanne, Switzerland
| | | | | | - Timo Kern
- Clinical Microbiomics, København, Denmark
| | | | - Johan Auwerx
- Laboratory of Integrative Systems Physiology, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | | | - Chris Rinsch
- Amazentis SA, EPFL Innovation Park, Lausanne, Switzerland
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20
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Becker HEF, Jamin C, Bervoets L, Boleij A, Xu P, Pierik MJ, Stassen FRM, Savelkoul PHM, Penders J, Jonkers DMAE. Higher Prevalence of Bacteroides fragilis in Crohn's Disease Exacerbations and Strain-Dependent Increase of Epithelial Resistance. Front Microbiol 2021; 12:598232. [PMID: 34168621 PMCID: PMC8219053 DOI: 10.3389/fmicb.2021.598232] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 04/30/2021] [Indexed: 12/12/2022] Open
Abstract
Bacteroides fragilis has previously been linked to Crohn's disease (CD) exacerbations, but results are inconsistent and underlying mechanisms unknown. This study investigates the epidemiology of B. fragilis and its virulence factors bft (enterotoxin) and ubiquitin among 181 CD patients and the impact on the intestinal epithelial barrier in vitro. The prevalence of B. fragilis was significantly higher in active (n = 69/88, 78.4%) as compared to remissive (n = 58/93, 62.4%, p = 0.018) CD patients. Moreover, B. fragilis was associated with intestinal strictures. Interestingly, the intestinal barrier function, as examined by transepithelial electrical resistance (TEER) measurements of Caco-2 monolayers, increased when exposed to secretomes of bft-positive (bft-1 and bft-2 isotype; increased TEER ∼160%, p < 0.001) but not when exposed to bft-negative strains. Whole metagenome sequencing and metabolomics, respectively, identified nine coding sequences and two metabolites that discriminated TEER-increasing from non-TEER-increasing strains. This study revealed a higher B. fragilis prevalence during exacerbation. Surprisingly, bft-positive secretomes increased epithelial resistance, but we excluded Bft as the likely causative factor.
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Affiliation(s)
- Heike E. F. Becker
- Department of Medical Microbiology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre+, Maastricht, Netherlands
- Division of Gastroenterology/Hepatology, Department of Internal Medicine, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre+, Maastricht, Netherlands
| | - Casper Jamin
- Department of Medical Microbiology, Caphri School for Public Health and Primary Care, Maastricht University Medical Centre+, Maastricht, Netherlands
| | - Liene Bervoets
- Department of Medical Microbiology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre+, Maastricht, Netherlands
| | - Annemarie Boleij
- Department of Pathology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, Netherlands
| | - Pan Xu
- Division of Gastroenterology/Hepatology, Department of Internal Medicine, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre+, Maastricht, Netherlands
| | - Marie J. Pierik
- Division of Gastroenterology/Hepatology, Department of Internal Medicine, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre+, Maastricht, Netherlands
| | - Frank R. M. Stassen
- Department of Medical Microbiology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre+, Maastricht, Netherlands
| | - Paul H. M. Savelkoul
- Department of Medical Microbiology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre+, Maastricht, Netherlands
- Department of Medical Microbiology and Infection Control, Amsterdam University Medical Center, Location VUMC, Amsterdam, Netherlands
| | - John Penders
- Department of Medical Microbiology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre+, Maastricht, Netherlands
- Department of Medical Microbiology, Caphri School for Public Health and Primary Care, Maastricht University Medical Centre+, Maastricht, Netherlands
| | - Daisy M. A. E. Jonkers
- Division of Gastroenterology/Hepatology, Department of Internal Medicine, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre+, Maastricht, Netherlands
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21
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Microbiome Responses to Vancomycin Treatment in a Child With Primary Sclerosing Cholangitis and Ulcerative Colitis. ACG Case Rep J 2021; 8:e00577. [PMID: 33997090 PMCID: PMC8116036 DOI: 10.14309/crj.0000000000000577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 12/02/2020] [Indexed: 12/02/2022] Open
Abstract
The therapeutic effects of off-label oral vancomycin in pediatric and adult primary sclerosing cholangitis (PSC)-inflammatory bowel disease, more commonly PSC-ulcerative colitis (UC), indicate the translational relevance of disease-associated microbiome findings. This is the first report on longitudinal salivary and fecal microbiome changes in a pediatric PSC-UC patient over the first 90 days of vancomycin therapy. Increase in bacterial diversity and abundance changes in Fusobacterium, Haemophilus, and Neisseria were observed. Our findings highlight the importance of longitudinal microbiome sampling in PSC-UC and serve as a nidus for larger-scale observations toward advancing microbial therapeutics for PSC.
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22
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Öhman L, Lasson A, Strömbeck A, Isaksson S, Hesselmar M, Simrén M, Strid H, Magnusson MK. Fecal microbiota dynamics during disease activity and remission in newly diagnosed and established ulcerative colitis. Sci Rep 2021; 11:8641. [PMID: 33883600 PMCID: PMC8060394 DOI: 10.1038/s41598-021-87973-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 04/07/2021] [Indexed: 12/19/2022] Open
Abstract
Patients with ulcerative colitis (UC) have an altered gut microbiota composition, but the microbial relationship to disease activity needs to be further elucidated. Therefore, temporal dynamics of the fecal microbial community during remission and flare was determined. Fecal samples were collected at 2–6 time-points from UC patients during established disease (cohort EST) and at diagnosis (cohort NEW). Sampling range for cohort EST was 3–10 months and for cohort NEW 36 months. Relapses were monitored for an additional three years for cohort EST. Microbial composition was assessed by Genetic Analysis GA-map Dysbiosis Test, targeting ≥ 300 bacteria. Eighteen patients in cohort EST (8 with maintained remission and 10 experiencing a flare), provided 71 fecal samples. In cohort NEW, 13 patients provided 49 fecal samples. The microbial composition showed no clustering related to disease activity in any cohort. Microbial dissimilarity was higher between than within patients for both cohorts, irrespective of presence of a flare. Microbial stability within patients was constant over time with no major shift in overall composition nor modification in the abundance of any specific species. Microbial composition was not affected by intensified medical treatment or linked to future disease course. Thus in UC, the gut microbiota is highly stable irrespective of disease stage, disease activity or treatment escalation. This suggests that prolonged dietary interventions or repeated fecal transplantations are needed to be able to induce permanent alterations of the gut microbiota.
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Affiliation(s)
- Lena Öhman
- Department of Microbiology and Immunology, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Box 435, 405 30, Gothenburg, Sweden.,Department of Internal Medicine and Clinical Nutrition, Institute for Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anders Lasson
- Department of Internal Medicine, Södra Älvsborg Hospital, Borås, Sweden
| | - Anna Strömbeck
- Department of Microbiology and Immunology, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Box 435, 405 30, Gothenburg, Sweden
| | - Stefan Isaksson
- Department of Microbiology and Immunology, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Box 435, 405 30, Gothenburg, Sweden
| | - Marcus Hesselmar
- Department of Internal Medicine and Clinical Nutrition, Institute for Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Magnus Simrén
- Department of Internal Medicine and Clinical Nutrition, Institute for Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Center for Functional Gastrointestinal and Motility Disorders, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Hans Strid
- Department of Internal Medicine, Södra Älvsborg Hospital, Borås, Sweden
| | - Maria K Magnusson
- Department of Microbiology and Immunology, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Box 435, 405 30, Gothenburg, Sweden.
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23
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Weng YJ, Jiang DX, Liang J, Ye SC, Tan WK, Yu CY, Zhou Y. Effects of Pretreatment with Bifidobacterium bifidum Using 16S Ribosomal RNA Gene Sequencing in a Mouse Model of Acute Colitis Induced by Dextran Sulfate Sodium. Med Sci Monit 2021; 27:e928478. [PMID: 33686049 PMCID: PMC7959103 DOI: 10.12659/msm.928478] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Background Bifidobacterium is a potentially effective and safe treatment for patients with inflammatory bowel disease (IBD), including ulcerative colitis and Crohn’s disease. However, information on the influence of B. bifidum on gut microbial diversity of treated and pretreated IBD patients is limited. Material/Methods Our study investigated therapeutic and preventive effects of B. bifidum ATCC 29521 on C57BL/6 mice with dextran sulfate sodium (DSS)-induced acute colitis via 16S ribosomal ribonucleic acid (rRNA) gene sequencing. Results Treatment and pretreatment of mice with B. bifidum ATCC 29521 significantly alleviated the severity of acute colitis on the basis of clinical and pathologic indicators. 16S rRNA gene sequencing showed that administration of B. bifidum shifted composition of the gut microbiome in mice with DSS-induced colitis in both treated and pretreated groups. Mice pretreated with B. bifidum ATCC 29521 for 21 days exhibited a significant increase in diversity of the gut microbiome. Principal coordinate analysis showed that gut microbiota structure was shaped by different treatments and time points. On the basis of linear discriminant analysis of effect size, the abundance of the genus Escherichia-Shigella, belonging to the family Enterobacteriaceae, was reduced in the B. bifidum-treated group, indicating that pathogens were inhibited by the B. bifidum treatment. Furthermore, the genera Intestinimonas and Bacteroides were significantly associated with the B. bifidum-pretreated group. Conclusions 16S rRNA gene sequencing showed that pretreatment with B. bifidum ATCC 29521 reduced intestinal inflammation and altered the gut microbiota to favor the genera Intestinimonas and Bacteroides.
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Affiliation(s)
- Yi-Jie Weng
- Department of Gastroenterology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China (mainland)
| | - Dan-Xian Jiang
- Department of Medical Oncology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China (mainland)
| | - Jian Liang
- Department of Gastroenterology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China (mainland)
| | - Shi-Cai Ye
- Department of Gastroenterology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China (mainland)
| | - Wen-Kai Tan
- Department of Gastroenterology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China (mainland)
| | - Cai-Yuan Yu
- Department of Gastroenterology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China (mainland)
| | - Yu Zhou
- Department of Gastroenterology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China (mainland)
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24
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Hu S, Png E, Gowans M, Ong DEH, de Sessions PF, Song J, Nagarajan N. Ectopic gut colonization: a metagenomic study of the oral and gut microbiome in Crohn's disease. Gut Pathog 2021; 13:13. [PMID: 33632307 PMCID: PMC7905567 DOI: 10.1186/s13099-021-00409-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 02/18/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND This study aims to characterize, the gut and oral microbiome in Asian subjects with Crohn's disease (CD) using whole genome shotgun sequencing, thereby allowing for strain-level comparison. METHODS A case-control study with age, sex and ethnicity matched healthy controls was conducted. CD subjects were limited to well-controlled patients without oral manifestations. Fecal and saliva samples were collected for characterization of gut and oral microbiome respectively. Microbial DNA were extracted, libraries prepared and sequenced reads profiled. Taxonomic diversity, taxonomic association, strain typing and microbial gene pathway analyses were conducted. RESULTS The study recruited 25 subjects with CD and 25 healthy controls. The oral microbe Streptococcus salivarius was found to be enriched and of concordant strains in the gut and oral microbiome of Crohn's disease subjects. This was more likely in CD subjects with higher Crohn's Disease Activity Index (184.3 ± 2.9 vs 67.1 ± 82.5, p = 0.012) and active disease status (Diarrhoea/abdominal pain/blood-in-stool/fever and fatigue) (p = 0.016). Gut species found to be significantly depleted in CD compared to control (Relative abundance: Median[Range]) include: Faecalibacterium prausnitzii (0.03[0.00-4.56] vs 13.69[5.32-18.71], p = 0.010), Roseburia inulinivorans (0.00[0.00-0.03] vs 0.21[0.01-0.53], p = 0.010) and Alistipes senegalensis (0.00[0.00-0.00] vs 0.00[0.00-0.02], p = 0.029). While Clostridium nexile (0.00[0.00-0.12] vs 0.00[0.00-0.00], p = 0.038) and Ruminococcus gnavus (0.43[0.02-0.33] vs 0.00[0.00-0.13], p = 0.043) were found to be enriched. C. nexile enrichment was not found in CD subjects of European descent. Microbial arginine (Linear-discriminant-analysis: 3.162, p = 0.001) and isoprene (Linear-discriminant-analysis: 3.058, p < 0.001) pathways were found at a higher relative abundance level in gut microbiome of Crohn's disease. CONCLUSIONS There was evidence of ectopic gut colonization by oral bacteria, especially during the active phase of CD. Previously studied gut microbial differences were detected, in addition to novel associations which could have resulted from geographical/ethnic differences to subjects of European descent. Differences in microbial pathways provide possible targets for microbiome modification.
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Affiliation(s)
- Shijia Hu
- Discipline of Orthodontics and Paediatric Dentistry, Faculty of Dentistry, National University of Singapore, 9 Lower Kent Ridge Road, Singapore, 119085, Singapore.
| | - Eileen Png
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis St, Singapore, 138672, Singapore
| | - Michelle Gowans
- Division of Gastroenterology & Hepatology, National University Hospital, 5 Lower Kent Ridge Rd, Singapore, 119074, Singapore
| | - David E H Ong
- Division of Gastroenterology & Hepatology, National University Hospital, 5 Lower Kent Ridge Rd, Singapore, 119074, Singapore
| | - Paola Florez de Sessions
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis St, Singapore, 138672, Singapore
| | - Jie Song
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis St, Singapore, 138672, Singapore
| | - Niranjan Nagarajan
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis St, Singapore, 138672, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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25
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Franzin M, Stefančič K, Lucafò M, Decorti G, Stocco G. Microbiota and Drug Response in Inflammatory Bowel Disease. Pathogens 2021; 10:211. [PMID: 33669168 PMCID: PMC7919657 DOI: 10.3390/pathogens10020211] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 02/10/2021] [Accepted: 02/11/2021] [Indexed: 02/06/2023] Open
Abstract
A mutualistic relationship between the composition, function and activity of the gut microbiota (GM) and the host exists, and the alteration of GM, sometimes referred as dysbiosis, is involved in various immune-mediated diseases, including inflammatory bowel disease (IBD). Accumulating evidence suggests that the GM is able to influence the efficacy of the pharmacological therapy of IBD and to predict whether individuals will respond to treatment. Additionally, the drugs used to treat IBD can modualate the microbial composition. The review aims to investigate the impact of the GM on the pharmacological therapy of IBD and vice versa. The GM resulted in an increase or decrease in therapeutic responses to treatment, but also to biotransform drugs to toxic metabolites. In particular, the baseline GM composition can help to predict if patients will respond to the IBD treatment with biologic drugs. On the other hand, drugs can affect the GM by incrementing or reducing its diversity and richness. Therefore, the relationship between the GM and drugs used in the treatment of IBD can be either beneficial or disadvantageous.
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Affiliation(s)
- Martina Franzin
- Department of Medicine, Surgery and Health Sciences, University of Trieste, 34127 Trieste, Italy;
| | - Katja Stefančič
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (K.S.); (G.S.)
| | - Marianna Lucafò
- Institute for Maternal and Child Health—IRCCS “Burlo Garofolo”, 34137 Trieste, Italy;
| | - Giuliana Decorti
- Department of Medicine, Surgery and Health Sciences, University of Trieste, 34127 Trieste, Italy;
- Institute for Maternal and Child Health—IRCCS “Burlo Garofolo”, 34137 Trieste, Italy;
| | - Gabriele Stocco
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (K.S.); (G.S.)
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26
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Abstract
Epidemiological studies have consistently demonstrated the benefits of dietary fibre on gastrointestinal health through consumption of unrefined whole foods, such as wholegrains, legumes, vegetables and fruits. Mechanistic studies and clinical trials on isolated and extracted fibres have demonstrated promising regulatory effects on the gut (for example, digestion and absorption, transit time, stool formation) and microbial effects (changes in gut microbiota composition and fermentation metabolites) that have important implications for gastrointestinal disorders. In this Review, we detail the major physicochemical properties and functional characteristics of dietary fibres, the importance of dietary fibres and current evidence for their use in the management of gastrointestinal disorders. It is now well-established that the physicochemical properties of different dietary fibres (such as solubility, viscosity and fermentability) vary greatly depending on their origin and processing and are important determinants of their functional characteristics and clinical utility. Although progress in understanding these relationships has uncovered potential therapeutic opportunities for dietary fibres, many clinical questions remain unanswered such as clarity on the optimal dose, type and source of fibre required in both the management of clinical symptoms and the prevention of gastrointestinal disorders. The use of novel fibres and/or the co-administration of fibres is an additional therapeutic approach yet to be extensively investigated.
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27
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Gao Y, Li T, Duan S, Lyu L, Li Y, Xu L, Wang Y. Impact of titanium dioxide nanoparticles on intestinal community in 2,4,6-trinitrobenzenesulfonic acid (TNBS)-induced acute colitis mice and the intervention effect of vitamin E. NANOSCALE 2021; 13:1842-1862. [PMID: 33438704 DOI: 10.1039/d0nr08106j] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Titanium dioxide nanoparticles (TiO2-NPs) are widely applied as additives in foods due to their excellent whitening and brightening capability. Although the toxicity and antibacterial activity of TiO2-NPs have been extensively studied, their impact on the gut microbiota in vivo still remains unclear, especially in animals with gastrointestinal disorders. In the present study, healthy mice and TNBS-induced colitis mice were administered with TiO2-NPs (38.3 ± 9.3 nm) orally at a dose of 100 mg per kg bw daily for 10 days to study the impact of TiO2-NPs on the gut microbiota and colitis development. Moreover, the mechanism of TiO2-NPs on the gut microbiota was also discussed when the colitis mice were additionally administered with vitamin E to remove ROS. Changes in the microbiota community structure and gut-associated function prediction were analyzed through bioinformatics. The result showed that the oral administration of TiO2-NPs mitigated colitis symptoms by reducing the DAI and CMDI scores and TNF-α level. Furthermore, 16S rDNA sequencing analysis showed that the structure and function prediction of gut microbiota could be modified in healthy mice and colitis mice after exposure to TiO2-NPs, but the opposite physiological effect occurred since the dominant flora varied in these two groups. Moreover, vitamin E intervention did not change the effects of TiO2-NPs on the microbiota community structure and gut-associated function, which indicates that the mechanism of the biological effects of TiO2-NPs on the gut microbiota may not be associated with their ability to induce the generation of ROS. In summary, our work firstly found that TiO2-NPs could regulate the gut microbiota of colitis mice and participate in the mitigation of TNBS-induced acute colitis, and the capability of TiO2-NPs to induce the generation of ROS inducement did not contribute to this process.
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Affiliation(s)
- Yanjun Gao
- Department of Occupational and Environmental Health Sciences School of Public Health Peking University, Beijing 100191, China.
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Hattori S, Nakamura M, Yamamura T, Maeda K, Sawada T, Mizutani Y, Yamamoto K, Ishikawa T, Furukawa K, Ohno E, Honda T, Kawashima H, Ishigami M, Hirooka Y, Fujishiro M. The microbiome can predict mucosal healing in small intestine in patients with Crohn's disease. J Gastroenterol 2020; 55:1138-1149. [PMID: 33067682 DOI: 10.1007/s00535-020-01728-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 09/10/2020] [Indexed: 02/04/2023]
Abstract
BACKGROUND Mucosal healing is the main treatment goal for Crohn's disease. In this situation, some patients have difficulty with endoscopic evaluation of the entire small intestine. Crohn's disease is closely associated with the gut microbiota, but the relationship between the microbiome and disease activity in the small intestine remains unclear. We examined the association between the microbiome and endoscopic findings in the small intestine and determined whether the microbiome can predict mucosal healing. METHODS The patients with Crohn's disease who were scheduled for capsule or balloon-assisted endoscopy were included in this prospective study. Patients whose entire small intestine was evaluated were divided into two groups based on ulcerative findings. The microbiomes in the fecal samples were analyzed using 16S rRNA sequencing. RESULTS The 38 enrolled patients were divided into the ulcer group (24) and mucosal healing group (14). The ulcer group exhibited lower α diversity. Six genera, namely Faecalibacterium (P = 0.008), Lachnospira (P = 0.009), Paraprevotella (P = 0.01), Dialister (P = 0.012), Streptococcus (P = 0.025), and Clostridium (P = 0.028) were enriched in the mucosal healing group. A predictive score for mucosal healing was defined using these six genera. The area under the curve was 0.795 and the sensitivity and specificity for predicting mucosal healing were 0.643 and 0.917, respectively. CONCLUSIONS Fecal microbiome is corelated with disease activity in the entire small intestine in Crohn's disease patients. The predictive score proposed by microbiota characteristics was a potential biomarker for mucosal healing in the small intestine.
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Affiliation(s)
- Shun Hattori
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Japan
| | - Masanao Nakamura
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Japan.
| | - Takeshi Yamamura
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Japan
| | - Keiko Maeda
- Department of Endoscopy, Nagoya University Hospital, 65 Tsurumai-cho, Showa-ku, Nagoya, Japan
| | - Tsunaki Sawada
- Department of Endoscopy, Nagoya University Hospital, 65 Tsurumai-cho, Showa-ku, Nagoya, Japan
| | - Yasuyuki Mizutani
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Japan
| | - Kenta Yamamoto
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Japan
| | - Takuya Ishikawa
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Japan
| | - Kazuhiro Furukawa
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Japan
| | - Eizaburo Ohno
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Japan
| | - Takashi Honda
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Japan
| | - Hiroki Kawashima
- Department of Endoscopy, Nagoya University Hospital, 65 Tsurumai-cho, Showa-ku, Nagoya, Japan
| | - Masatoshi Ishigami
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Japan
| | - Yoshiki Hirooka
- Department of Liver, Biliary Tract, and Pancreas Diseases, Fujita Health University School of Medicine, Aichi, Japan
| | - Mitsuhiro Fujishiro
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Japan
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Caenepeel C, Sadat Seyed Tabib N, Vieira-Silva S, Vermeire S. Review article: how the intestinal microbiota may reflect disease activity and influence therapeutic outcome in inflammatory bowel disease. Aliment Pharmacol Ther 2020; 52:1453-1468. [PMID: 32969507 DOI: 10.1111/apt.16096] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/08/2020] [Accepted: 09/03/2020] [Indexed: 12/13/2022]
Abstract
BACKGROUND Intestinal bacteria produce metabolites and by-products necessary for homeostasis. Imbalance in this equilibrium is linked to multiple pathologies including inflammatory bowel disease (IBD). The role of the gut microbiota in determining treatment response is becoming apparent, and may act as biomarker for efficacy. AIM To describe knowledge about the intestinal microbiota on disease severity and treatment outcomes in IBD METHODS: Descriptive review using PubMed to identify literature on the intestinal microbiota in IBD RESULTS: Severe IBD has a less diverse microbiota with fewer commensal microbiota communities and more opportunistic pathogenic bacteria originating from the oral cavity or respiratory tract. IBD treatments can alter gut microbiota composition, but in vitro/in vivo studies are needed to prove causation. A diversification of the microbiota is observed during remission. Patients with a more diverse baseline microbiome and higher microbial diversity show better response to anti-tumour necrosis factor-α, vedolizumab and ustekinumab therapy. Higher abundance of short chain fatty acid-producing bacteria, fewer mucus-colonising bacteria and lower abundance of pro-inflammatory bacteria have also been associated with a favourable outcome. Predictive models, based on a combination of microbiota, clinical data and serological markers, have good accuracy for treatment outcome and disease severity. CONCLUSION The intestinal microbiota in IBD carries a set of promising biomarkers of disease activity and prediction of therapeutic outcome. Current insights may also help in designing microbiota modulation strategies to improve outcomes in IBD.
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Affiliation(s)
| | | | - Sara Vieira-Silva
- Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, Rega Institute for Medical Research, VIB, KU Leuven, Leuven, Belgium
| | - Séverine Vermeire
- Department of Chronic Diseases & Metabolism, Translational Research Center for Gastrointestinal Disorders, KU Leuven, Leuven, Belgium.,Department of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium
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30
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In search for interplay between stool microRNAs, microbiota and short chain fatty acids in Crohn's disease - a preliminary study. BMC Gastroenterol 2020; 20:307. [PMID: 32958038 PMCID: PMC7507689 DOI: 10.1186/s12876-020-01444-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 09/09/2020] [Indexed: 12/19/2022] Open
Abstract
Background Inflammatory bowel diseases are classic polygenic disorders, with genetic loads that reflect immunopathological processes in response to the intestinal microbiota. Herein we performed the multiomics analysis by combining the large scale surveys of gut bacterial community, stool microRNA (miRNA) and short chain fatty acid (SCFA) signatures to correlate their association with the activity of Crohn’s disease (CD). Methods DNA, miRNA, and metabolites were extracted from stool samples of 15 CD patients, eight with active disease and seven in remission, and nine healthy individuals. Microbial, miRNA and SCFA profiles were assessed using datasets from 16S rRNA sequencing, Nanostring miRNA and GC-MS targeted analysis, respectively. Results Pairwise comparisons showed that 9 and 23 taxa differed between controls and CD patients with active and inactive disease, respectively. Six taxa were common to both comparisons, whereas four taxa differed in CD patients. α-Diversity was lower in both CD groups than in controls. The levels of 13 miRNAs differed (p-value < 0.05; FC > 1.5) in CD patients and controls before FDR correction and 4 after. Of six SCFAs, the levels of two differed significantly (p-value < 0.05, FC > 1.5) in CD patients and controls, and the levels of four differed in patients with active and inactive CD. PLS-DA revealed models with smallest error rate for controls in bacterial component and inactive disease in metabolites. Conclusion A complex interrelationship may exist between gut dysbiosis, miRNA profiling and SCFA level in response to intestinal inflammation.
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31
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Constructing bi-plots for random forest: Tutorial. Anal Chim Acta 2020; 1131:146-155. [PMID: 32928475 DOI: 10.1016/j.aca.2020.06.043] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 06/15/2020] [Accepted: 06/16/2020] [Indexed: 01/29/2023]
Abstract
Current technological developments have allowed for a significant increase and availability of data. Consequently, this has opened enormous opportunities for the machine learning and data science field, translating into the development of new algorithms in a wide range of applications in medical, biomedical, daily-life, and national security areas. Ensemble techniques are among the pillars of the machine learning field, and they can be defined as approaches in which multiple, complex, independent/uncorrelated, predictive models are subsequently combined by either averaging or voting to yield a higher model performance. Random forest (RF), a popular ensemble method, has been successfully applied in various domains due to its ability to build predictive models with high certainty and little necessity of model optimization. RF provides both a predictive model and an estimation of the variable importance. However, the estimation of the variable importance is based on thousands of trees, and therefore, it does not specify which variable is important for which sample group. The present study demonstrates an approach based on the pseudo-sample principle that allows for construction of bi-plots (i.e. spin plots) associated with RF models. The pseudo-sample principle for RF. is explained and demonstrated by using two simulated datasets, and three different types of real data, which include political sciences, food chemistry and the human microbiome data. The pseudo-sample bi-plots, associated with RF and its unsupervised version, allow for a versatile visualization of multivariate models, and the variable importance and the relation among them.
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32
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Cruz-Lebrón A, D’argenio Garcia L, Talla A, Joussef-Piña S, Quiñones-Mateu ME, Sékaly RP, de Carvalho KIL, Levine AD. Decreased Enteric Bacterial Composition and Diversity in South American Crohn's Disease Vary With the Choice of Treatment Strategy and Time Since Diagnosis. J Crohns Colitis 2020; 14:791-800. [PMID: 31758685 PMCID: PMC7346893 DOI: 10.1093/ecco-jcc/jjz189] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND AND AIMS The symptomology of Crohn's disease [CD], a chronic inflammatory disease of the digestive tract, correlates poorly with clinical, endoscopic or immunological assessments of disease severity. The prevalence of CD in South America is rising, reflecting changes in socio-economic stability. Many treatment options are available to CD patients, including biological agents and corticosteroids, each of which offers variable efficacy attributed to host genetics and environmental factors associated with alterations in the gut microbiota. METHODS Based on 16S rRNA gene sequencing and taxonomic differences, we compared the faecal microbial population of Brazilian patients with CD treated with corticosteroid or anti-tumour necrosis factor [anti-TNF] immunotherapy. Faecal calprotectin and plasma sCD14 levels were quantified as markers for local and systemic inflammation, respectively. RESULTS Anti-TNF treatment led to an increased relative abundance of Proteobacteria and a decreased level of Bacteroidetes. In contrast, corticoid treatment was associated with an increase in the relative abundance of Actinobacteria, which has been linked to inflammation in CD. Disruption of the faecal microbiota was related to decreased bacterial diversity and composition. Moreover, the choice of clinical regimen and time since diagnosis modulate the character of the resulting dysbiosis. CONCLUSIONS Enteric microbial populations in CD patients who have been treated are modulated by disease pathogenesis, local inflammatory microenvironment and treatment strategy. The dysbiosis that remains after anti-TNF treatment due to decreased bacterial diversity and composition abates restoration of the microbiota to a healthy state, suggesting that the identification and development of new clinical treatments for CD must include their capacity to normalize the gut microbiota.
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Affiliation(s)
- Angélica Cruz-Lebrón
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, USA
| | | | - Aarthi Talla
- Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
| | - Samira Joussef-Piña
- Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
| | | | | | | | - Alan D Levine
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, USA
- Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
- Departments of Pharmacology, Medicine, and Pediatrics, Case Western Reserve University, Cleveland, OH, USA
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33
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Bosch S, Wintjens DSJ, Wicaksono A, Kuijvenhoven J, van der Hulst R, Stokkers P, Daulton E, Pierik MJ, Covington JA, de Meij TGJ, de Boer NKH. The faecal scent of inflammatory bowel disease: Detection and monitoring based on volatile organic compound analysis. Dig Liver Dis 2020; 52:745-752. [PMID: 32402741 DOI: 10.1016/j.dld.2020.03.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 03/07/2020] [Accepted: 03/10/2020] [Indexed: 12/11/2022]
Abstract
BACKGROUND Inflammatory bowel disease (IBD) is diagnosed and monitored using endoscopic assessment, which is invasive and costly. In this study, potential of faecal volatile organic compounds (VOC) analysis for IBD detection and identification of disease activity was evaluated. METHODS IBD patients visiting outpatient clinics of participating tertiary hospitals were included. Active disease was defined as FCP ≥250 mg/g, remission as FCP <100 mg/g with Harvey Bradshaw Index <4 for Crohn's disease (CD) or Simple Clinical Colitis Activity Index <3 for ulcerative colitis (UC). Healthy controls (HC) were patients without mucosal abnormalities during colonoscopy. Faecal samples were measured using gas chromatography-ion mobility spectrometry. RESULTS A total of 280 IBD patients collected 107 CDa, 84 CDr, 80 UCa and 63 UCr samples. Additionally, 227 HC provided one faecal sample. UC and CD were discriminated from HC with high accuracy (AUC (95%CI): UCa vs HC 0.96(0.94-0.99); UCr vs HC 0.95(0.93-0.98); CDa vs HC 0.96(0.94-0.99); CDr vs HC 0.95(0.93-0.98)). There were small differences between UC and CD (0.55(0.50-0.6)) and no differences between active disease and remission (UCa vs UCr 0.63(0.44-0.82); CDa vs CDr 0.52(0.39-0.65)). CONCLUSION Our study outcomes imply that faecal VOC analysis holds potential for identifying biomarkers for IBD detection but not for monitoring disease activity.
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Affiliation(s)
- Sofie Bosch
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Gastroenterology and Hepatology, AG&M research institute, Amsterdam, The Netherlands.
| | - Dion S J Wintjens
- MUMC+, Maastricht University, Department of Gastroenterology and Hepatology, Maastricht, The Netherlands
| | - Alfian Wicaksono
- University of Warwick, School of Engineering, Coventry, United Kingdom
| | - Johan Kuijvenhoven
- Spaarne Gasthuis, Department of Gastroenterology and Hepatology, Hoofddorp and Haarlem, The Netherlands
| | - René van der Hulst
- Spaarne Gasthuis, Department of Gastroenterology and Hepatology, Hoofddorp and Haarlem, The Netherlands
| | - Pieter Stokkers
- OLVG West, Department of Gastroenterology and hepatology, Amsterdam, The Netherlands
| | - Emma Daulton
- University of Warwick, School of Engineering, Coventry, United Kingdom
| | - Marieke J Pierik
- MUMC+, Maastricht University, Department of Gastroenterology and Hepatology, Maastricht, The Netherlands
| | - James A Covington
- University of Warwick, School of Engineering, Coventry, United Kingdom
| | - Tim G J de Meij
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pediatric Gastroenterology, AG&M research institute, Amsterdam, The Netherlands
| | - Nanne K H de Boer
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Gastroenterology and Hepatology, AG&M research institute, Amsterdam, The Netherlands
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Khafipour A, Eissa N, Munyaka PM, Rabbi MF, Kapoor K, Kermarrec L, Khafipour E, Bernstein CN, Ghia JE. Denosumab Regulates Gut Microbiota Composition and Cytokines in Dinitrobenzene Sulfonic Acid (DNBS)-Experimental Colitis. Front Microbiol 2020; 11:1405. [PMID: 32670246 PMCID: PMC7331113 DOI: 10.3389/fmicb.2020.01405] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 05/29/2020] [Indexed: 12/11/2022] Open
Abstract
The pro-inflammatory mediator receptor activator of nuclear factor-kappa B ligand (RANKL) plays a significant role in the development of rheumatoid arthritis; however, its role in inflammatory bowel disease is unknown. Genome-wide association meta-analysis for Crohn's disease (CD) identified a variant near the TNFSF11 gene that encodes RANKL and CD risk allele increased expression of RANKL in specific cell lines. This study aims to elucidate if the RANKL inhibitor denosumab can reduce the severity of experimental colitis and modify the gut microbiota composition using murine dinitrobenzenesulfonic acid (DNBS)-experimental model of colitis mimicking CD. In colitic conditions, denosumab treatment significantly decreased the pro-inflammatory cytokines IL-6, IL-1β, and TNF-α within the colonic mucosa. Moreover, colitis was accompanied by disruption of gut microbiota, and preventative treatment with denosumab modulated this disruption. Denosumab treatment also modified the alpha- and beta diversity of colonic mucosa and fecal microbiota. These results provide a rationale for considering denosumab as a future potential therapy in CD; however, more detailed experimental and clinical studies are warranted.
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Affiliation(s)
- Azin Khafipour
- Department of Immunology, University of Manitoba, Winnipeg, MB, Canada
| | - Nour Eissa
- Department of Immunology, University of Manitoba, Winnipeg, MB, Canada.,Children's Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, MB, Canada.,Section of Gastroenterology, Department of Internal Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada.,University of Manitoba IBD Clinical and Research Centre, University of Manitoba, Winnipeg, MB, Canada
| | - Peris M Munyaka
- Department of Immunology, University of Manitoba, Winnipeg, MB, Canada.,Section of Gastroenterology, Department of Internal Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada.,Department of Animal Science, University of Manitoba, Winnipeg, MB, Canada
| | - Mohammad F Rabbi
- Department of Immunology, University of Manitoba, Winnipeg, MB, Canada.,Children's Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, MB, Canada.,Section of Gastroenterology, Department of Internal Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada.,University of Manitoba IBD Clinical and Research Centre, University of Manitoba, Winnipeg, MB, Canada
| | - Kunal Kapoor
- Department of Immunology, University of Manitoba, Winnipeg, MB, Canada.,Section of Gastroenterology, Department of Internal Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada.,University of Manitoba IBD Clinical and Research Centre, University of Manitoba, Winnipeg, MB, Canada
| | - Laetitia Kermarrec
- Department of Immunology, University of Manitoba, Winnipeg, MB, Canada.,Section of Gastroenterology, Department of Internal Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada.,University of Manitoba IBD Clinical and Research Centre, University of Manitoba, Winnipeg, MB, Canada
| | - Ehsan Khafipour
- Department of Animal Science, University of Manitoba, Winnipeg, MB, Canada
| | - Charles N Bernstein
- Section of Gastroenterology, Department of Internal Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada.,University of Manitoba IBD Clinical and Research Centre, University of Manitoba, Winnipeg, MB, Canada
| | - Jean-Eric Ghia
- Department of Immunology, University of Manitoba, Winnipeg, MB, Canada.,Children's Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, MB, Canada.,Section of Gastroenterology, Department of Internal Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada.,University of Manitoba IBD Clinical and Research Centre, University of Manitoba, Winnipeg, MB, Canada
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35
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Liu Z, Liu F, Wang W, Sun C, Gao D, Ma J, Hussain MA, Xu C, Jiang Z, Hou J. Study of the alleviation effects of a combination of Lactobacillus rhamnosus and inulin on mice with colitis. Food Funct 2020; 11:3823-3837. [PMID: 32329478 DOI: 10.1039/c9fo02992c] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Ulcerative colitis (UC) is a common inflammatory bowel disease (IBD) that has serious harmful effects on human health. Lactobacillus rhamnosus, a probiotic, has a strong colonization and adhesion effect and improves the intestinal health of the host. Inulin has good anti-inflammatory effects and can promote the proliferation of beneficial intestinal bacteria. The purpose of this study was to investigate the alleviating effects of L. rhamnosus 1.0320 in combination with inulin on UC, examining the resulting changes in intestinal flora. A UC model was established by having mice freely drink a 3% (w/v) dextran sodium sulphate (DSS) solution for seven days. After successful modeling, the mice were given antibiotics, L. rhamnosus 1.0320 by itself, inulin by itself, and L. rhamnosus 1.0320 combined with inulin as an intragastric intervention for 28 days. The abundance and structural changes of bacteria in the intestinal content of mice were analyzed by 16S rDNA high-throughput sequencing. The study found that male BALB/c mice can successfully establish a typical model of small intestinal inflammation by freely drinking a 3% DSS solution for one week. L. rhamnosus 1.0320 combined with inulin can alleviate DSS-induced colitis, reduce the Disease Activity Index (DAI) score of the pathological damage of colon tissue, decrease myeloperoxidase (MPO) activity, increase hemoglobin content, and regulate the expression levels of inflammatory cytokines IL-1β, IL-6, TNF-α and IL-10. The intestinal flora of mice is reduced after enteritis, and its structure gets disordered. The combination of L. rhamnosus 1.0320 and inulin can increase the abundance and diversity of intestinal flora, and increase the content of beneficial bacteria. Prebiotics promote the colonization ability of probiotics. L. rhamnosus 1.0320 combined with inulin can change the intestinal flora to relieve ulcerative colitis, providing a new theoretical basis for the study of UC mechanism.
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Affiliation(s)
- Zhijing Liu
- Key Laboratory of Dairy Science, Northeast Agricultural University, College of Food Science, Harbin 150030, People's Republic of China.
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36
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Blanco-Míguez A, Fdez-Riverola F, Sánchez B, Lourenço A. Resources and tools for the high-throughput, multi-omic study of intestinal microbiota. Brief Bioinform 2020; 20:1032-1056. [PMID: 29186315 DOI: 10.1093/bib/bbx156] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 10/23/2017] [Indexed: 12/18/2022] Open
Abstract
The human gut microbiome impacts several aspects of human health and disease, including digestion, drug metabolism and the propensity to develop various inflammatory, autoimmune and metabolic diseases. Many of the molecular processes that play a role in the activity and dynamics of the microbiota go beyond species and genic composition and thus, their understanding requires advanced bioinformatics support. This article aims to provide an up-to-date view of the resources and software tools that are being developed and used in human gut microbiome research, in particular data integration and systems-level analysis efforts. These efforts demonstrate the power of standardized and reproducible computational workflows for integrating and analysing varied omics data and gaining deeper insights into microbe community structure and function as well as host-microbe interactions.
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Affiliation(s)
| | | | | | - Anália Lourenço
- Dpto. de Informática - Universidade de Vigo, ESEI - Escuela Superior de Ingeniería Informática, Edificio politécnico, Campus Universitario As Lagoas s/n, 32004 Ourense, Spain
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37
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Lucafò M, Franzin M, Lagatolla C, Franca R, Bramuzzo M, Stocco G, Decorti G. Emerging Insights on the Interaction Between Anticancer and Immunosuppressant Drugs and Intestinal Microbiota in Pediatric Patients. Clin Transl Sci 2020; 13:238-259. [PMID: 31675176 PMCID: PMC7070880 DOI: 10.1111/cts.12722] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 10/23/2019] [Indexed: 02/06/2023] Open
Abstract
Diseases affecting the immune system, such as inflammatory bowel disease (IBD), juvenile idiopathic arthritis (JIA), and acute lymphoblastic leukemia (ALL), are pathological conditions affecting the pediatric population and are often associated with alterations in the intestinal microbiota, such as a decrease in bacterial diversity. Growing evidence suggests that gut microbiota can interfere with chemotherapeutic and immunosuppressant drugs, used in the treatment of these diseases, reducing or facilitating drug efficacy. In particular, the effect of intestinal microflora through translocation, immunomodulation, metabolism, enzymatic degradation, and reduction of bacterial diversity seems to be one of the reasons of interindividual variability in the therapeutic response. Although the extent of the role of intestinal microflora in chemotherapy and immunosuppression remains still unresolved, current evidence on bacterial compositional shifts will be taken in consideration together with clinical response to drugs for a better and personalized therapy. This review is focused on the effect of the intestinal microbiota on the efficacy of pharmacological therapy of agents used to treat IBD, JIA, and ALL.
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Affiliation(s)
- Marianna Lucafò
- Institute for Maternal and Child Health – IRCCS “Burlo Garofolo”TriesteItaly
| | - Martina Franzin
- PhD Course in Reproductive and Developmental SciencesUniversity of TriesteTriesteItaly
| | | | - Raffaella Franca
- Department of Medical, Surgical and Health SciencesUniversity of TriesteTriesteItaly
| | - Matteo Bramuzzo
- Institute for Maternal and Child Health – IRCCS “Burlo Garofolo”TriesteItaly
| | - Gabriele Stocco
- Department of Life SciencesUniversity of TriesteTriesteItaly
| | - Giuliana Decorti
- Institute for Maternal and Child Health – IRCCS “Burlo Garofolo”TriesteItaly
- Department of Medical, Surgical and Health SciencesUniversity of TriesteTriesteItaly
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38
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Busbee PB, Menzel L, Alrafas HR, Dopkins N, Becker W, Miranda K, Tang C, Chatterjee S, Singh UP, Nagarkatti M, Nagarkatti PS. Indole-3-carbinol prevents colitis and associated microbial dysbiosis in an IL-22-dependent manner. JCI Insight 2020; 5:127551. [PMID: 31941837 PMCID: PMC7030851 DOI: 10.1172/jci.insight.127551] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 12/04/2019] [Indexed: 12/11/2022] Open
Abstract
Colitis, an inflammatory bowel disease, is caused by a variety of factors, but luminal microbiota are thought to play crucial roles in disease development and progression. Indole is produced by gut microbiota and is believed to protect the colon from inflammatory damage. In the current study, we investigated whether indole-3-carbinol (I3C), a naturally occurring plant product found in numerous cruciferous vegetables, can prevent colitis-associated microbial dysbiosis and attempted to identify the mechanisms. Treatment with I3C led to repressed colonic inflammation and prevention of microbial dysbiosis caused by colitis, increasing a subset of gram-positive bacteria known to produce butyrate. I3C was shown to increase production of butyrate, and when mice with colitis were treated with butyrate, there was reduced colonic inflammation accompanied by suppression of Th17 and induction of Tregs, protection of the mucus layer, and upregulation in Pparg expression. Additionally, IL-22 was increased only after I3C but not butyrate administration, and neutralization of IL-22 prevented the beneficial effects of I3C against colitis, as well as blocked I3C-mediated dysbiosis and butyrate induction. This study suggests that I3C attenuates colitis primarily through induction of IL-22, which leads to modulation of gut microbiota that promote antiinflammatory butyrate.
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Affiliation(s)
- Philip B. Busbee
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, South Carolina, USA
| | - Lorenzo Menzel
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, South Carolina, USA
| | - Haider Rasheed Alrafas
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, South Carolina, USA
| | - Nicholas Dopkins
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, South Carolina, USA
| | - William Becker
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, South Carolina, USA
| | - Kathryn Miranda
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, South Carolina, USA
| | - Chaunbing Tang
- Department of Chemistry and Biochemistry, University of South Carolina College of Arts and Sciences, Columbia, South Carolina, USA
| | - Saurabh Chatterjee
- Environmental Health and Disease Laboratory, Department of Environmental Health Sciences, Arnold School of Public Health, University of South Carolina Columbia, South Carolina, USA
| | - Udai P. Singh
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, South Carolina, USA
| | - Mitzi Nagarkatti
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, South Carolina, USA
| | - Prakash S. Nagarkatti
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, South Carolina, USA
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History of Inflammatory Bowel Diseases. J Clin Med 2019; 8:jcm8111970. [PMID: 31739460 PMCID: PMC6912289 DOI: 10.3390/jcm8111970] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Revised: 11/02/2019] [Accepted: 11/12/2019] [Indexed: 12/19/2022] Open
Abstract
Inflammatory bowel diseases (IBD) are characterized by chronic inflammation of the intestinal mucosa and unknown etiology. In this review, we identified three main eras in the IBD history. Between the 19th and the 20th century, the primary task had been the definition of the diagnostic criteria in order to differentiate the new entity from intestinal tuberculosis. In the 20th century, an intense and prolific therapeutic research prevailed, culminating in the introduction of biological drugs in the clinical setting. Since the beginning of the 21st century, traditional definition criteria have been challenged by holistic criteria in an effort to seek a still unattained cure. Centuries of worldwide efforts on IBD etiology and therapy search have culminated in this novel strategy.
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Liu S, Pan J, Meng X, Zhu J, Zhou J, Zhu X. Trichinella spiralis infection decreases the diversity of the intestinal flora in the infected mouse. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2019; 54:490-500. [PMID: 31708483 DOI: 10.1016/j.jmii.2019.09.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/20/2019] [Accepted: 09/30/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND Trichinella spiralis is a kind of intestinal nematode that can strongly modulate the host immune system. However, the effects of T. spiralis infection on the intestinal flora are poorly understood. This study aimed to explore the effect of T. spiralis infection on the intestinal flora. METHODS The intestinal contents of T. spiralis infected mice were examined through high-throughput sequencing (Illumina) of the V3-V4 hypervariable region in bacterial 16S rRNA gene. The sequences were analyzed using the QIIME software package and other bioinformatics methods. RESULTS Altogether 2,899,062 sequences were generated from the samples collected from different intestinal regions at various infection time points; the 44,843 Operational Taxonomic Unit (OTUs) analysis showed that T. spiralis infection would decrease the diversity of intestinal flora in the infected mice relative to that in the uninfected ones, especially in the large intestine and feces. Further analysis indicated that, the genera Oscillospira from the phylum Firmicutes showed a higher abundance in the helminth-infected small and larger intestines; the genera Bacteroides from the phyla Bacteroides, the genera Lactobacillus from the phyla Firmicutes, the genera Escherichia from the phyla Proteobacteria, and the genera Akkermansia from the phyla Verrucomicrobia displayed increased abundances in the T. spiralis positive fecal samples compared with those in the negative samples. CONCLUSIONS T. spiralis infection decreases the diversity of the intestinal flora in the infected mouse. However, it remains unclear about the association between the changes in intestinal flora caused by T. spiralis infection and the parasite pathogenesis, which should be further examined.
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Affiliation(s)
- Sha Liu
- Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, PR China
| | - Jin Pan
- Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, PR China
| | - Xiangli Meng
- Ningbo International Travel Healthcare Center, Ningbo Customs District People's Republic of China, Ningbo 315012, PR China
| | - Junping Zhu
- Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, PR China
| | - Jie Zhou
- Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, PR China
| | - Xinping Zhu
- Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, PR China.
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Abstract
Introduction: Inflammatory bowel diseases (IBD) are on the rise worldwide. This review covers the current concepts of the etiology of Crohn´s disease and ulcerative colitis by focusing on an unbalanced interaction between the intestinal microbiota and the mucosal barrier. Understanding these issues is of paramount importance for the development of targeted therapies aiming at the disease cause.Area covered: Gut microbiota alterations and a dysfunctional intestinal mucosa are associated with IBD. Here we focus on specific defense structures of the mucosal barrier, namely antimicrobial peptides and the mucus layer, which keep the gut microbiota at a distance under healthy conditions and are defective in IBD.Expert commentary: The microbiology of both forms of IBD is different but characterized by a reduced bacterial diversity and richness. Abundance of certain bacterial species is altered, and the compositional changes are related to disease activity. In IBD the mucus layer above the epithelium is contaminated by bacteria and the immune reaction is dominated by the antibacterial response. Human genetics suggest that many of the basic deficiencies in the mucosal response, due to Paneth cell, defensin and mucus defects, are primary. Nutrition may also be important but so far there is no therapy targeting the mucosal barrier.
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Affiliation(s)
- Eduard F Stange
- Innere Medizin I, Medizinische Universitätsklinik, Tübingen, Germany
| | - Bjoern O Schroeder
- Laboratory for Molecular Infection Medicine Sweden (MIMS) -The Nordic EMBL Partnership for Molecular Medicine, and Department of Molecular Biology, Umeå University, Umeå, Sweden
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Fukunaga M, Suriki K, Kuda T, Shikano A, Toyama A, Takahashi H, Kimura B. Typical indigenous bacteria in the cecum of ddY mice fed a casein-beef tallow diet or whole-egg diet. J Food Biochem 2019; 43:e13064. [PMID: 31573099 DOI: 10.1111/jfbc.13064] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 09/13/2019] [Accepted: 09/13/2019] [Indexed: 02/06/2023]
Abstract
With the aim to prove the existence of food ingredient-susceptible indigenous bacteria (SIBs) in the gut, the gut microbiota of ddY mice fed a diet containing 20% milk casein and 17% beef tallow (CT diet) or 40% whole-egg powder (Egg diet) for 14 days were analyzed by 16S ribosomal RNA gene (V4) amplicon sequencing. At the genus level, abundance levels of Desulfovibrionaceae sp., Oscillospira, and Bacteroides were high in mice fed the CT diet. At the operational taxonomic unit level, Bacteroides acidifaciens- and Bacteroides caecimuris-like bacteria were highly abundant in mice fed the CT diet. Faecalibaculum rodentium- and Allobaculum stercoricanis-like bacteria were highly abundant in the mice fed the Egg diet. These sets of taxa were assumed to be estimates of casein-tallow SIBs and egg SIBs, respectively, in the gut microbiome. Among the SIBs, B. caecimuris and F. rodentium could be isolated using blood and liver agar. PRACTICAL APPLICATIONS: B. caecimuris and F. rodentium are regarded as casein-tallow and/or egg SIBs in mice. It is possible to demonstrate functionality with orally administered food ingredients. Isolation and application of human or livestock SIB is considered promising for the development of new probiotics and functional foods.
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Affiliation(s)
- Mayu Fukunaga
- Department of Food Science and Technology, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Katsunobu Suriki
- Department of Food Science and Technology, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Takashi Kuda
- Department of Food Science and Technology, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Ayane Shikano
- Department of Food Science and Technology, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Ai Toyama
- Department of Food Science and Technology, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Hajime Takahashi
- Department of Food Science and Technology, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Bon Kimura
- Department of Food Science and Technology, Tokyo University of Marine Science and Technology, Tokyo, Japan
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Klaassen MAY, Imhann F, Collij V, Fu J, Wijmenga C, Zhernakova A, Dijkstra G, Festen EAM, Gacesa R, Vich Vila A, Weersma RK. Anti-inflammatory Gut Microbial Pathways Are Decreased During Crohn's Disease Exacerbations. J Crohns Colitis 2019; 13:1439-1449. [PMID: 31066440 PMCID: PMC7142399 DOI: 10.1093/ecco-jcc/jjz077] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND AIMS Crohn's disease [CD] is a chronic inflammatory disorder of the gastrointestinal tract characterised by alternating periods of exacerbation and remission. We hypothesised that changes in the gut microbiome are associated with CD exacerbations, and therefore aimed to correlate multiple gut microbiome features to CD disease activity. METHODS Faecal microbiome data generated using whole-genome metagenomic shotgun sequencing of 196 CD patients were of obtained from the 1000IBD cohort [one sample per patient]. Patient disease activity status at time of sampling was determined by re-assessing clinical records 3 years after faecal sample production. Faecal samples were designated as taken 'in an exacerbation' or 'in remission'. Samples taken 'in remission' were further categorised as 'before the next exacerbation' or 'after the last exacerbation', based on the exacerbation closest in time to the faecal production date. CD activity was correlated with gut microbial composition and predicted functional pathways via logistic regressions using MaAsLin software. RESULTS In total, 105 bacterial pathways were decreased during CD exacerbation (false-discovery rate [FDR] <0.1) in comparison with the gut microbiome of patients both before and after an exacerbation. Most of these decreased pathways exert anti-inflammatory properties facilitating the biosynthesis and fermentation of various amino acids [tryptophan, methionine, and arginine], vitamins [riboflavin and thiamine], and short-chain fatty acids [SCFAs]. CONCLUSIONS CD exacerbations are associated with a decrease in microbial genes involved in the biosynthesis of the anti-inflammatory mediators riboflavin, thiamine, and folate, and SCFAs, suggesting that increasing the intestinal abundances of these mediators might provide new treatment opportunities. These results were generated using bioinformatic analyses of cross-sectional data and need to be replicated using time-series and wet lab experiments.
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Affiliation(s)
- Marjolein A Y Klaassen
- University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands,University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Floris Imhann
- University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands,University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Valerie Collij
- University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands,University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Jingyuan Fu
- University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands,University Medical Center Groningen, Department of Pediatrics, Groningen, The Netherlands
| | - Cisca Wijmenga
- University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Alexandra Zhernakova
- University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands
| | - Gerard Dijkstra
- University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands
| | - Eleonora A M Festen
- University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands,University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Ranko Gacesa
- University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands,University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Arnau Vich Vila
- University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands,University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Rinse K Weersma
- University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands,University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands,Corresponding author: R. K. Weersma, MD, PhD, PO Box 30.001, 9700RB Groningen, The Netherlands. Tel.: +316 41132824; Fax 050 361 9306;
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Vester-Andersen MK, Mirsepasi-Lauridsen HC, Prosberg MV, Mortensen CO, Träger C, Skovsen K, Thorkilgaard T, Nøjgaard C, Vind I, Krogfelt KA, Sørensen N, Bendtsen F, Petersen AM. Increased abundance of proteobacteria in aggressive Crohn's disease seven years after diagnosis. Sci Rep 2019; 9:13473. [PMID: 31530835 PMCID: PMC6748953 DOI: 10.1038/s41598-019-49833-3] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 08/23/2019] [Indexed: 02/07/2023] Open
Abstract
Intestinal dysbiosis in inflammatory bowel disease (IBD) patients depend on disease activity. We aimed to characterize the microbiota after 7 years of follow-up in an unselected cohort of IBD patients according to disease activity and disease severity. Fifty eight Crohn’s disease (CD) and 82 ulcerative colitis (UC) patients were included. Disease activity was assessed by the Harvey-Bradshaw Index for CD and Simple Clinical Colitis Activity Index for UC. Microbiota diversity was assessed by 16S rDNA MiSeq sequencing. In UC patients with active disease and in CD patients with aggressive disease the richness (number of OTUs, p = 0.018 and p = 0.013, respectively) and diversity (Shannons index, p = 0.017 and p = 0.023, respectively) were significantly decreased. In the active UC group there was a significant decrease in abundance of the phylum Firmicutes (p = 0.018). The same was found in CD patients with aggressive disease (p = 0.05) while the abundance of Proteobacteria phylum showed a significant increase (p = 0.03) in CD patients. We found a change in the microbial abundance in UC patients with active disease and in CD patients with aggressive disease. These results suggest that dysbiosis of the gut in IBD patients is not only related to current activity but also to the course of the disease.
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Affiliation(s)
- M K Vester-Andersen
- Gastrounit, Hvidovre Hospital, University of Copenhagen, København, Denmark. .,Department of Internal medicine, Zealand University Hospital, Køge, Denmark.
| | | | - M V Prosberg
- Gastrounit, Hvidovre Hospital, University of Copenhagen, København, Denmark
| | - C O Mortensen
- Department of Gastroenterology, Herlev and Gentofte Hospital, University of Copenhagen, København, Denmark
| | - C Träger
- Department of Gastroenterology, Herlev and Gentofte Hospital, University of Copenhagen, København, Denmark
| | - K Skovsen
- Department of Gastroenterology, Herlev and Gentofte Hospital, University of Copenhagen, København, Denmark
| | - T Thorkilgaard
- Department of Gastroenterology, Herlev and Gentofte Hospital, University of Copenhagen, København, Denmark
| | - C Nøjgaard
- Gastrounit, Hvidovre Hospital, University of Copenhagen, København, Denmark
| | - I Vind
- Gastrounit, Hvidovre Hospital, University of Copenhagen, København, Denmark
| | - K A Krogfelt
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark.,Department of Virus and Microbial Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - N Sørensen
- Clinical-Microbiomics, Ole Maaløesvej 3, Copenhagen, Denmark
| | - F Bendtsen
- Gastrounit, Hvidovre Hospital, University of Copenhagen, København, Denmark
| | - A M Petersen
- Gastrounit, Hvidovre Hospital, University of Copenhagen, København, Denmark.,Department of Clinical Microbiology, Hvidovre Hospital, University of Copenhagen, København, Denmark
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45
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Galazzo G, Tedjo DI, Wintjens DSJ, Savelkoul PHM, Masclee AAM, Bodelier AGL, Pierik MJ, Jonkers DMAE, Penders J. Faecal Microbiota Dynamics and their Relation to Disease Course in Crohn's Disease. J Crohns Colitis 2019; 13:1273-1282. [PMID: 30810207 PMCID: PMC6764104 DOI: 10.1093/ecco-jcc/jjz049] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND Microbial shifts have been associated with disease activity in Crohn's disease [CD], but findings on specific taxa are inconsistent. This may be due to differences in applied methods and cross-sectional study designs. We prospectively examined the faecal microbiota in adult CD patients with changing or stable disease course over time. METHODS Faeces were collected at two time-points from 15 healthy control individuals [HCs], 35 CD patients who were in remission and who maintained remission [RRs], and 22 CD patients during remission and also during subsequent exacerbation [RAs]. The microbial composition was assessed by 16S rRNA [V4] gene sequencing. RESULTS Compared with HCs, patients with CD had a lower microbial richness [p = 0.0002] and diversity [p = 0.005]. Moreover, the microbial community structure of a subset of patients, clustered apart from HCs, was characterized by low microbial diversity and Faecalibacterium abundance. Patients within this cluster did not differ with respect to long-term disease course compared with patients with a 'healthy-appearing' microbiota.Over time, microbial richness and diversity did not change in RR versus RA patients. Although the microbial community structure of both RR and RA patients was less stable over time compared with that of HCs, no differences were observed between the patient groups [p = 0.17]; nor was the stability impacted by Montreal classification, medication use, or surgery. CONCLUSION The altered microbiota composition and stability in CD was neither associated with disease activity nor long-term disease course, questioning its involvement in the development of an exacerbation. The aberrant microbiota composition in a subset of CD patients warrants further exploration of a more microbiota-driven etiology in this group.
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Affiliation(s)
- Gianluca Galazzo
- School of Nutrition and Translational Research in Metabolism [NUTRIM], Department of Medical Microbiology, Maastricht University Medical Center+, Maastricht, The Netherlands,School of Public Health and Primary Care [Caphri], Department of Medical Microbiology, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Danyta I Tedjo
- School of Nutrition and Translational Research in Metabolism [NUTRIM], Department of Medical Microbiology, Maastricht University Medical Center+, Maastricht, The Netherlands,School of Nutrition and Translational Research in Metabolism [NUTRIM], Division Gastroenterology–Hepatology, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Dion S J Wintjens
- School of Nutrition and Translational Research in Metabolism [NUTRIM], Division Gastroenterology–Hepatology, Maastricht University Medical Center+, Maastricht, The Netherlands,Department of Internal Medicine, Division of Gastroenterology and Hepatology, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Paul H M Savelkoul
- School of Nutrition and Translational Research in Metabolism [NUTRIM], Department of Medical Microbiology, Maastricht University Medical Center+, Maastricht, The Netherlands,School of Public Health and Primary Care [Caphri], Department of Medical Microbiology, Maastricht University Medical Center+, Maastricht, The Netherlands,Department of Medical Microbiology & Infection control, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | - Ad A M Masclee
- School of Nutrition and Translational Research in Metabolism [NUTRIM], Division Gastroenterology–Hepatology, Maastricht University Medical Center+, Maastricht, The Netherlands,Department of Internal Medicine, Division of Gastroenterology and Hepatology, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | | | - Marie J Pierik
- School of Nutrition and Translational Research in Metabolism [NUTRIM], Division Gastroenterology–Hepatology, Maastricht University Medical Center+, Maastricht, The Netherlands,Department of Internal Medicine, Division of Gastroenterology and Hepatology, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Daisy M A E Jonkers
- School of Nutrition and Translational Research in Metabolism [NUTRIM], Division Gastroenterology–Hepatology, Maastricht University Medical Center+, Maastricht, The Netherlands,Department of Internal Medicine, Division of Gastroenterology and Hepatology, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - John Penders
- School of Nutrition and Translational Research in Metabolism [NUTRIM], Department of Medical Microbiology, Maastricht University Medical Center+, Maastricht, The Netherlands,School of Public Health and Primary Care [Caphri], Department of Medical Microbiology, Maastricht University Medical Center+, Maastricht, The Netherlands,Corresponding authors: J. Penders, Department of Medical Microbiology, Maastricht University Medical Center+, PO 5800, 6202 AZ, Maastricht, The Netherlands. Tel: +31-(0)433875134; Fax: +31-(0)433676643;
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46
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Altomare A, Putignani L, Del Chierico F, Cocca S, Angeletti S, Ciccozzi M, Tripiciano C, Dalla Piccola B, Cicala M, Guarino MPL. Gut mucosal-associated microbiota better discloses inflammatory bowel disease differential patterns than faecal microbiota. Dig Liver Dis 2019; 51:648-656. [PMID: 30573380 DOI: 10.1016/j.dld.2018.11.021] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 08/07/2018] [Accepted: 11/22/2018] [Indexed: 02/08/2023]
Abstract
BACKGROUND Growing evidence supports the potential role of intestinal microbiota in the pathophysiology of inflammatory bowel diseases (IBD) even if the literature does not reveal uniform alterations. The aim of the study was to evaluate the mucosal (MM) and faecal microbiota (FM) composition in a cohort of IBD patients compared to healthy controls (CTRLs). METHODS Faecal and mucosal samples were collected from 14 IBD patients and 11 CTRLs. The V1-V3 region of 16S rRNA locus was amplified on a 454-Junior Genome Sequencer. Reads were grouped into operational taxonomic units (OTUs) at a sequence similarity level of 97% for taxonomic assignment, and aligned for OTUs matching against Greengenes database. RESULTS Irrespective of disease localization and activity, in the MM of IBD patients a statistically significant increase of Proteobacteria (especially Enterobacteriaceae, Acidaminococcus, Veillonella dispar) and decrease of Firmicutes (especially Roseburia and Faecalibacterium prausnitzii) and Actinobacteria was found compared to CTRLs. In the colon district some specific bacterial biomarkers were identified: Enterobacteriaceae for IBD stools, Bacteroides for IBD biopsies, Mogibacteriaceae, Ruminococcaceae and Prevotella for CTRL stools, Ruminococcaceae for CTRL biopsies. CONCLUSIONS The profiles of FM were more similar to CTRLs, suggesting that microbiota adhering to the gut mucosa better discriminates patients from controls, with the identification of some interesting biomarkers.
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Affiliation(s)
- Annamaria Altomare
- Gastroenterology Unit, University Campus Bio-Medico of Rome, Rome, Italy.
| | - Lorenza Putignani
- Human Microbiome Unit, Bambino Gesù Children's Hospital and Research Institute, Rome, Italy; Parasitology Unit, Bambino Gesù Children's Hospital and Research Institute, Rome, Italy
| | - Federica Del Chierico
- Human Microbiome Unit, Bambino Gesù Children's Hospital and Research Institute, Rome, Italy
| | - Silvia Cocca
- Gastroenterology Unit, University Campus Bio-Medico of Rome, Rome, Italy
| | - Silvia Angeletti
- Clinical Pathology and Microbiology Unit, University Campus Bio-Medico of Rome, Rome, Italy
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy
| | | | - Bruno Dalla Piccola
- Scientific Directorate, Bambino Gesù Children's Hospital and Research Institute, Rome, Italy
| | - Michele Cicala
- Gastroenterology Unit, University Campus Bio-Medico of Rome, Rome, Italy
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47
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Burge K, Gunasekaran A, Eckert J, Chaaban H. Curcumin and Intestinal Inflammatory Diseases: Molecular Mechanisms of Protection. Int J Mol Sci 2019; 20:ijms20081912. [PMID: 31003422 PMCID: PMC6514688 DOI: 10.3390/ijms20081912] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 04/15/2019] [Accepted: 04/17/2019] [Indexed: 02/07/2023] Open
Abstract
Intestinal inflammatory diseases, such as Crohn’s disease, ulcerative colitis, and necrotizing enterocolitis, are becoming increasingly prevalent. While knowledge of the pathogenesis of these related diseases is currently incomplete, each of these conditions is thought to involve a dysfunctional, or overstated, host immunological response to both bacteria and dietary antigens, resulting in unchecked intestinal inflammation and, often, alterations in the intestinal microbiome. This inflammation can result in an impaired intestinal barrier allowing for bacterial translocation, potentially resulting in systemic inflammation and, in severe cases, sepsis. Chronic inflammation of this nature, in the case of inflammatory bowel disease, can even spur cancer growth in the longer-term. Recent research has indicated certain natural products with anti-inflammatory properties, such as curcumin, can help tame the inflammation involved in intestinal inflammatory diseases, thus improving intestinal barrier function, and potentially, clinical outcomes. In this review, we explore the potential therapeutic properties of curcumin on intestinal inflammatory diseases, including its antimicrobial and immunomodulatory properties, as well as its potential to alter the intestinal microbiome. Curcumin may play a significant role in intestinal inflammatory disease treatment in the future, particularly as an adjuvant therapy.
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Affiliation(s)
- Kathryn Burge
- Department of Pediatrics, Division of Neonatology, University of Oklahoma Health Sciences Center, 1200 North Everett Drive, ETNP7504, Oklahoma City, OK 73104, USA.
| | - Aarthi Gunasekaran
- Department of Pediatrics, Division of Neonatology, University of Oklahoma Health Sciences Center, 1200 North Everett Drive, ETNP7504, Oklahoma City, OK 73104, USA.
| | - Jeffrey Eckert
- Department of Pediatrics, Division of Neonatology, University of Oklahoma Health Sciences Center, 1200 North Everett Drive, ETNP7504, Oklahoma City, OK 73104, USA.
| | - Hala Chaaban
- Department of Pediatrics, Division of Neonatology, University of Oklahoma Health Sciences Center, 1200 North Everett Drive, ETNP7504, Oklahoma City, OK 73104, USA.
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48
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Duarte-Silva M, Afonso PC, de Souza PR, Peghini BC, Rodrigues-Júnior V, de Barros Cardoso CR. Reappraisal of antibodies against Saccharomyces cerevisiae (ASCA) as persistent biomarkers in quiescent Crohn's disease. Autoimmunity 2019; 52:37-47. [PMID: 30884988 DOI: 10.1080/08916934.2019.1588889] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A clear correlation exists between microbiota and the dysregulation of the immune response in Inflammatory Bowel Diseases (IBD), which comprise Crohn's disease (CD) and ulcerative colitis (UC). These unbalanced reactions also involve humoral responses, with antibodies against Saccharomyces cerevisiae. Thus, here we aimed to quantify IgA and IgG specific to S. cerevisiae (ASCA) in quiescent CD and UC, to correlate the production of these antibodies with patient's inflammatory response and disease clinical presentation. Twenty-nine subjects (16 CD and 13 UC) and 45 healthy controls were enrolled in this study and had plasma samples tested for ASCA and cytokines (IL-2, IL-4, IL-6, IL-10, IFN-γ, TNF-α), besides clinical evaluation. IBD patients had increase IgA and IgG ASCA, especially those with colonic (L2) and fistulizing (B3) CD. Similarly, patients who dropped out the treatment had augmented ASCA, while IgG was reduced in those receiving sulfasalazine treatment. Furthermore, the quiescent CD patients had elevated IL-6 on plasma, especially in the absence of treatment, together with increased counter regulatory response of IL-10. There was a positive correlation between IgA and IgG on CD but not UC, as well as between IgA and TNF in total IBD patients. In addition, the levels of IgG x TNF, IgA x IL-10 and IgG x IL-10 were also correlated in CD, indicating that ASCA production may be influenced by the inflammatory response. Finally, we concluded that ASCA could be pointed as relevant biomarker of CD presentation and residual inflammation, even in clinical remission patients.
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Affiliation(s)
- Murillo Duarte-Silva
- a Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto , Universidade de São Paulo , Ribeirão Preto , São Paulo , Brazil.,b Departamento de Bioquímica e Imunologia, Faculdade de Medicina de Ribeirão Preto , Universidade de São Paulo , Ribeirão Preto , São Paulo , Brazil
| | - Poliana Cristina Afonso
- c Instituto de Ciências Biológicas e Naturais, Universidade Federal do Triângulo Mineiro , Uberaba , Brazil
| | - Patrícia Reis de Souza
- a Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto , Universidade de São Paulo , Ribeirão Preto , São Paulo , Brazil.,c Instituto de Ciências Biológicas e Naturais, Universidade Federal do Triângulo Mineiro , Uberaba , Brazil
| | - Bethânea Crema Peghini
- c Instituto de Ciências Biológicas e Naturais, Universidade Federal do Triângulo Mineiro , Uberaba , Brazil
| | - Virmondes Rodrigues-Júnior
- c Instituto de Ciências Biológicas e Naturais, Universidade Federal do Triângulo Mineiro , Uberaba , Brazil
| | - Cristina Ribeiro de Barros Cardoso
- a Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto , Universidade de São Paulo , Ribeirão Preto , São Paulo , Brazil
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49
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Caro-Gómez E, Sierra JA, Escobar JS, Álvarez-Quintero R, Naranjo M, Medina S, Velásquez-Mejía EP, Tabares-Guevara JH, Jaramillo JC, León-Varela YM, Muñoz-Durango K, Ramírez-Pineda JR. Green Coffee Extract Improves Cardiometabolic Parameters and Modulates Gut Microbiota in High-Fat-Diet-Fed ApoE -/- Mice. Nutrients 2019; 11:E497. [PMID: 30818779 PMCID: PMC6470615 DOI: 10.3390/nu11030497] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 02/15/2019] [Accepted: 02/22/2019] [Indexed: 12/11/2022] Open
Abstract
Chlorogenic acids (CGA) are the most abundant phenolic compounds in green coffee beans and in the human diet and have been suggested to mitigate several cardiometabolic risk factors. Here, we aimed to evaluate the effect of a water-based standardized green coffee extract (GCE) on cardiometabolic parameters in ApoE-/- mice and to explore the potential underlying mechanisms. Mice were fed an atherogenic diet without (vehicle) or with GCE by gavage (equivalent to 220 mg/kg of CGA) for 14 weeks. We assessed several metabolic, pathological, and inflammatory parameters and inferred gut microbiota composition, diversity, and functional potential. Although GCE did not reduce atherosclerotic lesion progression or plasma lipid levels, it induced important favorable changes. Specifically, improved metabolic parameters, including fasting glucose, insulin resistance, serum leptin, urinary catecholamines, and liver triglycerides, were observed. These changes were accompanied by reduced weight gain, decreased adiposity, lower inflammatory infiltrate in adipose tissue, and protection against liver damage. Interestingly, GCE also modulated hepatic IL-6 and total serum IgM and induced shifts in gut microbiota. Altogether, our results reveal the cooccurrence of these beneficial cardiometabolic effects in response to GCE in the same experimental model and suggest potential mediators and pathways involved.
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Affiliation(s)
- Erika Caro-Gómez
- Grupo Inmunomodulación-GIM, Universidad de Antioquia. Calle 70 No. 52-21, 050010 Medellín, Colombia.
| | - Jelver A Sierra
- Vidarium⁻Nutrition, Health and Wellness Research Center, Grupo Empresarial Nutresa. Calle 8 Sur No. 50-67, 050023 Medellín, Colombia.
| | - Juan S Escobar
- Vidarium⁻Nutrition, Health and Wellness Research Center, Grupo Empresarial Nutresa. Calle 8 Sur No. 50-67, 050023 Medellín, Colombia.
| | - Rafael Álvarez-Quintero
- Grupo de Investigación en Sustancias Bioactivas, Facultad de Ciencias Farmacéuticas y Alimentarias, Universidad de Antioquia. Calle 70 No. 52-21, 050010 Medellín, Colombia.
| | - Mauricio Naranjo
- Colcafé Research Coffee Group, Industria Colombiana de Café S.A.S. Calle 8 Sur No. 50-19, 050023 Medellín, Colombia.
| | - Sonia Medina
- Facultad de Ingeniería, Corporación Universitaria Lasallista, Carrera 51 N°118Sur-57, 055440 Caldas, Colombia.
| | - Eliana P Velásquez-Mejía
- Vidarium⁻Nutrition, Health and Wellness Research Center, Grupo Empresarial Nutresa. Calle 8 Sur No. 50-67, 050023 Medellín, Colombia.
| | - Jorge H Tabares-Guevara
- Grupo Inmunomodulación-GIM, Universidad de Antioquia. Calle 70 No. 52-21, 050010 Medellín, Colombia.
| | - Julio C Jaramillo
- Grupo Inmunomodulación-GIM, Universidad de Antioquia. Calle 70 No. 52-21, 050010 Medellín, Colombia.
| | - Yudy M León-Varela
- Grupo Inmunomodulación-GIM, Universidad de Antioquia. Calle 70 No. 52-21, 050010 Medellín, Colombia.
| | - Katalina Muñoz-Durango
- Vidarium⁻Nutrition, Health and Wellness Research Center, Grupo Empresarial Nutresa. Calle 8 Sur No. 50-67, 050023 Medellín, Colombia.
| | - José R Ramírez-Pineda
- Grupo Inmunomodulación-GIM, Universidad de Antioquia. Calle 70 No. 52-21, 050010 Medellín, Colombia.
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50
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Heidarian F, Alebouyeh M, Shahrokh S, Balaii H, Zali MR. Altered fecal bacterial composition correlates with disease activity in inflammatory bowel disease and the extent of IL8 induction. Curr Res Transl Med 2019; 67:41-50. [PMID: 30685379 DOI: 10.1016/j.retram.2019.01.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 01/10/2019] [Accepted: 01/15/2019] [Indexed: 12/26/2022]
Abstract
PURPOSE OF THE STUDY In this study we investigated the presence and relative abundance of important genera of the gut microbiota in IBD patients and their role in induction of IL8 in a cell culture model. PATIENTS AND METHODS Stool samples of IBD patients and healthy controls were collected and relative diversity of thirteen bacterial families was measured using quantitative real-time PCR assay. Moreover, filtrate of the stool samples was used for treatment of HT-29 cell line to analyze involvement of diversity of the fecal bacterial communities in the extent of IL8 induction. RESULTS Bacteroides, Faecalibacterium prausnitzii, Prevotella spp., and Methanobrevibacterium were significantly less abundant in IBD patients (UC, N = 22; CD, N = 7) compared with control group (N = 29). Increase in relative amounts of Haemophilus, Streptococcus spp., and H. pylori were detected in IBD patients, which was not statistically significant. Relative decrease in amount of Bacteroides spp., Faecalibacterium prausnitzii, and Prevotella spp. were found in UC patients with disease activity score greater than 4; however, higher levels of Streptococcus and Haemophilus were detected in the patients who were at flares. A relationship between the reduction of Haemophilus spp. and higher BMI was shown in IBD patients. Expression of IL8 was significantly higher in the treated cells by the fecal inoculates of IBD patients. Increase in relative amounts of Enterobacteriacea showed a correlation with the higher level of IL8 induction in both groups. CONCLUSIONS These results showed that changes in the fecal microbiota composition could affect disease activity, BMI, and IL8 induction.
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Affiliation(s)
- Farnaz Heidarian
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Department of Biology, School of Basic Sciences, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Masoud Alebouyeh
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Shabnam Shahrokh
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Hedieh Balaii
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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