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Wei X, Dai J, Liu R, Wan G, Gu S, Du Y, Yang X, Wang L, Huang Y, Chen P, Chen X, Yang X, Wang Q. S/O/W Emulsion with CAPE Ameliorates DSS-Induced Colitis by Regulating NF-κB Pathway, Gut Microbiota and Fecal Metabolome in C57BL/6 Mice. Nutrients 2024; 16:1145. [PMID: 38674835 PMCID: PMC11054280 DOI: 10.3390/nu16081145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/09/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
Inflammatory bowel disease (IBD) has attracted much attention worldwide due to its prevalence. In this study, the effect of a solid-in-oil-in-water (S/O/W) emulsion with Caffeic acid phenethyl ester (CAPE, a polyphenolic active ingredient in propolis) on dextran sulfate sodium (DSS)-induced colitis in C57BL/6 mice was evaluated. The results showed that CAPE-emulsion could significantly alleviate DSS-induced colitis through its effects on colon length, reduction in the disease activity index (DAI), and colon histopathology. The results of ELISA and Western blot analysis showed that CAPE-emulsion can down-regulate the excessive inflammatory cytokines in colon tissue and inhibit the expression of p65 in the NF-κB pathway. Furthermore, CAPE-emulsion promoted short-chain fatty acids production in DSS-induced colitis mice. High-throughput sequencing results revealed that CAPE-emulsion regulates the imbalance of gut microbiota by enhancing diversity, restoring the abundance of beneficial bacteria (such as Odoribacter), and suppressing the abundance of harmful bacteria (such as Afipia, Sphingomonas). The results of fecal metabolome showed that CAPE-emulsion restored the DSS-induced metabolic disorder by affecting metabolic pathways related to inflammation and cholesterol metabolism. These research results provide a scientific basis for the use of CPAE-emulsions for the development of functional foods for treating IBD.
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Affiliation(s)
- Xuelin Wei
- School of Food and Bioengineering, Xihua University, Chengdu 610039, China; (X.W.); (R.L.); (G.W.); (S.G.); (Y.D.); (X.Y.); (L.W.); (Y.H.); (P.C.); (X.C.)
| | - Juan Dai
- School of Laboratory Medicine, Chengdu Medical College, Chengdu 610500, China;
| | - Ruijia Liu
- School of Food and Bioengineering, Xihua University, Chengdu 610039, China; (X.W.); (R.L.); (G.W.); (S.G.); (Y.D.); (X.Y.); (L.W.); (Y.H.); (P.C.); (X.C.)
| | - Guochao Wan
- School of Food and Bioengineering, Xihua University, Chengdu 610039, China; (X.W.); (R.L.); (G.W.); (S.G.); (Y.D.); (X.Y.); (L.W.); (Y.H.); (P.C.); (X.C.)
| | - Shiyu Gu
- School of Food and Bioengineering, Xihua University, Chengdu 610039, China; (X.W.); (R.L.); (G.W.); (S.G.); (Y.D.); (X.Y.); (L.W.); (Y.H.); (P.C.); (X.C.)
| | - Yuwei Du
- School of Food and Bioengineering, Xihua University, Chengdu 610039, China; (X.W.); (R.L.); (G.W.); (S.G.); (Y.D.); (X.Y.); (L.W.); (Y.H.); (P.C.); (X.C.)
| | - Xinyue Yang
- School of Food and Bioengineering, Xihua University, Chengdu 610039, China; (X.W.); (R.L.); (G.W.); (S.G.); (Y.D.); (X.Y.); (L.W.); (Y.H.); (P.C.); (X.C.)
| | - Lijun Wang
- School of Food and Bioengineering, Xihua University, Chengdu 610039, China; (X.W.); (R.L.); (G.W.); (S.G.); (Y.D.); (X.Y.); (L.W.); (Y.H.); (P.C.); (X.C.)
| | - Yukun Huang
- School of Food and Bioengineering, Xihua University, Chengdu 610039, China; (X.W.); (R.L.); (G.W.); (S.G.); (Y.D.); (X.Y.); (L.W.); (Y.H.); (P.C.); (X.C.)
| | - Pengfei Chen
- School of Food and Bioengineering, Xihua University, Chengdu 610039, China; (X.W.); (R.L.); (G.W.); (S.G.); (Y.D.); (X.Y.); (L.W.); (Y.H.); (P.C.); (X.C.)
| | - Xianggui Chen
- School of Food and Bioengineering, Xihua University, Chengdu 610039, China; (X.W.); (R.L.); (G.W.); (S.G.); (Y.D.); (X.Y.); (L.W.); (Y.H.); (P.C.); (X.C.)
- Chongqing Key Laboratory of Specialty Food Co-Built by Sichuan and Chongqing, Chengdu 610039, China
| | - Xiao Yang
- School of Food and Bioengineering, Xihua University, Chengdu 610039, China; (X.W.); (R.L.); (G.W.); (S.G.); (Y.D.); (X.Y.); (L.W.); (Y.H.); (P.C.); (X.C.)
- Chongqing Key Laboratory of Specialty Food Co-Built by Sichuan and Chongqing, Chengdu 610039, China
| | - Qin Wang
- Department of Nutrition and Food Science, University of Maryland, College Park, MD 20742, USA
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Deng M, Dan L, Ye S, Chen X, Fu T, Wang X, Chen J. Higher dietary fibre intake is associated with lower risk of inflammatory bowel disease: prospective cohort study. Aliment Pharmacol Ther 2023; 58:516-525. [PMID: 37464899 DOI: 10.1111/apt.17649] [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] [Received: 04/11/2023] [Revised: 05/16/2023] [Accepted: 07/10/2023] [Indexed: 07/20/2023]
Abstract
BACKGROUND Limited prospective studies that have examined the association of dietary fibre with IBD have provided inconsistent evidence. AIM To examine any associations between dietary fibre intake and subsequent incidence of IBD, Crohn's disease (CD) and ulcerative colitis (UC) METHODS: We conducted a prospective cohort study of 470,669 participants from the UK Biobank and estimated dietary fibre intake from a valid food frequency questionnaire at baseline. Incident IBD was ascertained from primary care data and inpatient data. Cox proportional hazard models were used to estimate the hazard ratios (HRs) and 95% confidence intervals (CIs) for associations between dietary fibre intake and the risk of IBD, CD and UC. RESULTS During an average follow-up of 12.1 years, we ascertained 1473 incident IBD cases, including 543 cases of CD and 939 cases of UC. Comparing the lowest quintiles, an inverse association was observed between dietary fibre intake and risk of IBD (HR 0.74, 95% CI 0.58-0.93, p = 0.011) and CD (HR 0.48, 95% CI 0.32-0.72, p < 0.001), but not UC (HR 0.92, 95% CI 0.69-1.24, p = 0.595). For specified sources, dietary fibre intake from fruit and bread decreased the risk of CD, while dietary fibre intake from cereal decreased the risk of UC. CONCLUSIONS Higher consumption of dietary fibre was associated with a lower risk of IBD and CD, but not UC. Our findings support current recommendations to increase the intake of dietary fibre.
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Affiliation(s)
- Minzi Deng
- Department of Gastroenterology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Lintao Dan
- Center for Global Health, Zhejiang University School of Medicine, Hangzhou, China
| | - Shuyu Ye
- Department of Gastroenterology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Xuejie Chen
- Department of Gastroenterology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Tian Fu
- Department of Gastroenterology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Xiaoyan Wang
- Department of Gastroenterology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Jie Chen
- Center for Global Health, Zhejiang University School of Medicine, Hangzhou, China
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Palandurkar GS, Kumar S. Biofilm's Impact on Inflammatory Bowel Diseases. Cureus 2023; 15:e45510. [PMID: 37868553 PMCID: PMC10585119 DOI: 10.7759/cureus.45510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 09/18/2023] [Indexed: 10/24/2023] Open
Abstract
The colon has a large surface area covered with a thick mucus coating. Colon's biomass consists of about 1,012 colony-forming units per gram of feces and 500-1,000 distinct bacterial species. The term inflammatory bowel disease (IBD) indicates the collection of intestinal illnesses in which the digestive system (esophagus, large intestine, mouth, stomach, and small intestine) experiences persistent inflammation. IBD development is influenced by environmental (infections, stress, and nutrition) and genetic factors. The microbes present in gut microbiota help maintain intestinal homeostasis and support immune and epithelial cell growth, differentiation, as well as proliferation. It has been discovered that a variety of variables and microorganisms are crucial for the development of biofilms and mucosal colonization during IBD. An extracellular matrix formed by bacteria supports biofilm production in our digestive system and harms the host's immunological response. Irritable bowel syndrome (IBS) and IBD considerably affect human socioeconomic well-being and the standard of living. IBD is a serious public health issue, affecting millions of people across the globe. The gut microbiome may significantly influence IBS pathogenesis, even though few diagnostic and treatment options are available. As a result, current research focuses more on disrupting biofilm in IBD patients and stresses primarily on drugs that help improve the quality of life for human well-being. We evaluate studies on IBD and bacterial biofilm to add fresh insights into the existing state of knowledge of biofilm formation in IBD, incidence of IBD patients, molecular level of investigations, bacteria that are involved in the formation of biofilm, and present and down the line regimens and probiotics. Planning advanced ways to control and eradicate bacteria in biofilms should be the primary goal to add fresh insights into generating innovative diagnostic and alternative therapy options for IBD.
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Affiliation(s)
- Gopal S Palandurkar
- Department of Medicine, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| | - Sunil Kumar
- Department of Medicine, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
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Shirley DA, Tornel W, Warren CA, Moonah S. Clostridioides difficile Infection in Children: Recent Updates on Epidemiology, Diagnosis, Therapy. Pediatrics 2023; 152:e2023062307. [PMID: 37560802 PMCID: PMC10471512 DOI: 10.1542/peds.2023-062307] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/31/2023] [Indexed: 08/11/2023] Open
Abstract
Clostridioides (formerly Clostridium) difficile is the most important infectious cause of antibiotic-associated diarrhea worldwide and a leading cause of healthcare-associated infection in the United States. The incidence of C. difficile infection (CDI) in children has increased, with 20 000 cases now reported annually, also posing indirect educational and economic consequences. In contrast to infection in adults, CDI in children is more commonly community-associated, accounting for three-quarters of all cases. A wide spectrum of disease severity ranging from asymptomatic carriage to severe diarrhea can occur, varying by age. Fulminant disease, although rare in children, is associated with high morbidity and even fatality. Diagnosis of CDI can be challenging as currently available tests detect either the presence of organism or disease-causing toxin but cannot distinguish colonization from infection. Since colonization can be high in specific pediatric groups, such as infants and young children, biomarkers to aid in accurate diagnosis are urgently needed. Similar to disease in adults, recurrence of CDI in children is common, affecting 20% to 30% of incident cases. Metronidazole has long been considered the mainstay therapy for CDI in children. However, new evidence supports the safety and efficacy of oral vancomycin and fidaxomicin as additional treatment options, whereas fecal microbiota transplantation is gaining popularity for recurrent infection. Recent advancements in our understanding of emerging epidemiologic trends and management of CDI unique to children are highlighted in this review. Despite encouraging therapeutic advancements, there remains a pressing need to optimize CDI therapy in children, particularly as it pertains to severe and recurrent disease.
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Affiliation(s)
| | | | - Cirle A. Warren
- Infectious Diseases and International Health, Department of Medicine
- Complicated C. difficile Clinic, UVA Health, University of Virginia, Charlottesville, Virginia
| | - Shannon Moonah
- Infectious Diseases and International Health, Department of Medicine
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Li FR, Wu KY, Fan WD, Chen GC, Tian H, Wu XB. Long-term exposure to air pollution and risk of incident inflammatory bowel disease among middle and old aged adults. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 242:113835. [PMID: 35816845 DOI: 10.1016/j.ecoenv.2022.113835] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 06/28/2022] [Accepted: 06/29/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Epidemiological evidence regarding the associations between long-term exposure to air pollution and risk of incident inflammatory bowel disease (IBD) is scant. OBJECTIVES We examined the associations of various specific air pollutants with the risk of incident ulcerative colitis and Crohn's disease, two subtypes of IBD, among middle and old aged adults in the UK. We also explored potential susceptible subgroups. METHODS We used data from the UK Biobank study. Information on air pollution, including PM2.5, PM2.5-10, PM10 as well as NO2 and NOx were estimated using the Land Use Regression model. Multivariable Cox proportional hazards models were used to calculate hazard ratios (HRs) and 95% confidence intervals (CIs). RESULTS After a median follow-up of 11.7 years, 1872 incident ulcerative colitis and 865 incident Crohn's disease cases were identified among 455,210 IBD-free participants. HRs (95% CIs) of ulcerative colitis associated with each 1 interquartile range (IQR) increase in PM2.5, PM2.5-10, PM10, NO2, and NOx were 1.06 (1.01, 1.12), 1.03 (0.99, 1.08), 1.09 (1.03, 1.16), 1.12 (1.07, 1.19), and 1.07 (1.02, 1.12), respectively. The associations between all the air pollutants and risk of Crohn's disease were null. Smoking status and sex appeared to respectively modify the associations between some air pollutants and risk of ulcerative colitis and Crohn's disease. CONCLUSION Long-term exposure to various air pollutants was associated with the risk of incident ulcerative colitis but not Crohn's disease, highlighting the importance of developing environmental health strategy to reduce the burden of ulcerative colitis.
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Affiliation(s)
- Fu-Rong Li
- School of Public Health and Emergency Management, Southern University of Science and Technology, Shenzhen, China; Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Ke-Yi Wu
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Wei-Dong Fan
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Guo-Chong Chen
- Department of Nutrition and Food Hygiene, School of Public Health, Soochow University, Suzhou, China; Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Haili Tian
- School of Kinesiology, Shanghai University of Sport, Shanghai, China.
| | - Xian-Bo Wu
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China.
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The Relationship Between Mucosal Microbiota, Colitis, and Systemic Inflammation in Chronic Granulomatous Disorder. J Clin Immunol 2021; 42:312-324. [PMID: 34731398 DOI: 10.1007/s10875-021-01165-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 10/22/2021] [Indexed: 12/31/2022]
Abstract
PURPOSE Chronic granulomatous disorder (CGD) is a primary immunodeficiency which is frequently complicated by inflammatory colitis and is associated with systemic inflammation. Herein, we aimed to investigate the role of the microbiome in the pathogenesis of colitis and systemic inflammation. METHODS We performed 16S rDNA sequencing on mucosal biopsy samples from each segment of 10 CGD patients' colons and conducted compositional and functional pathway prediction analyses. RESULTS The microbiota in samples from colitis patients demonstrated reduced taxonomic alpha-diversity compared to unaffected patients, even in apparently normal bowel segments. Functional pathway richness was similar between the colitic and non-colitic mucosa, although metabolic pathways involved in butyrate biosynthesis or utilization were enriched in patients with colitis and correlated positively with fecal calprotectin levels. One patient with very severe colitis was dominated by Enterococcus spp., while among other patients Bacteroides spp. abundance correlated with colitis severity measured by fecal calprotectin and an endoscopic severity score. In contrast, Blautia abundance is associated with low severity scores and mucosal health. Several taxa and functional pathways correlated with concentrations of inflammatory cytokines in blood but not with colitis severity. Notably, dividing patients into "high" and "low" systemic inflammation groups demonstrated clearer separation than on the basis of colitis status in beta-diversity analyses. CONCLUSION The microbiome is abnormal in CGD-associated colitis and altered functional characteristics probably contribute to pathogenesis. Furthermore, the relationship between the mucosal microbiome and systemic inflammation, independent of colitis status, implies that the microbiome in CGD can influence the inflammatory phenotype of the condition.
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7
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Putignani L, Oliva S, Isoldi S, Del Chierico F, Carissimi C, Laudadio I, Cucchiara S, Stronati L. Fecal and mucosal microbiota profiling in pediatric inflammatory bowel diseases. Eur J Gastroenterol Hepatol 2021; 33:1376-1386. [PMID: 33470709 DOI: 10.1097/meg.0000000000002050] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
BACKGROUND An altered gut microbiota profile has been widely documented in inflammatory bowel diseases (IBD). The intestinal microbial community has been more frequently investigated in the stools than at the level of the mucosa, while most of the studies have been performed in adults. We aimed to define the gut microbiota profile either by assessing fecal and colonic mucosa samples (inflamed or not) from pediatric IBD patients. PATIENTS AND METHODS Fecal and colonic samples from pediatric IBD (Crohn's disease or ulcerative colitis) and controls were analyzed. The relative abundance of bacteria at phylum and genus/species levels and bacterial diversity were determined through 16S rRNA sequence-based of fecal and mucosal microbiota analysis. RESULTS A total of 59 children with IBD (26 Crohn's disease, 33 ulcerative colitis) and 39 controls were analyzed. A clear separation between IBD and controls in the overall composition of fecal and mucosal microbiota was found, as well as a reduced bacterial richness in the fecal microbiota of IBD. At the phylum level, abundance of Proteobacteria and Actinobacteria occurred in fecal microbiota of IBD, while species with anti-inflammatory properties (i.e., Ruminococcus) were reduced. Fusobacterium prevailed in inflamed IBD areas in comparison to noninflamed and controls samples. CONCLUSION Significant alterations in gut microbiota profile were shown in our IBD pediatric patients, in whom an abundance of species with a proinflammatory mucosal activity was clearly detected. An analysis of gut microbiota could be incorporated in designing personalized IBD treatment scenarios in future.
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Affiliation(s)
| | - Salvatore Oliva
- Department of Women's and Children's Health, Sapienza University of Rome
| | - Sara Isoldi
- Department of Women's and Children's Health, Sapienza University of Rome
| | | | - Claudia Carissimi
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Ilaria Laudadio
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | | | - Laura Stronati
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
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8
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Bregaint S, Boyer E, Fong SB, Meuric V, Bonnaure-Mallet M, Jolivet-Gougeon A. Porphyromonas gingivalis outside the oral cavity. Odontology 2021; 110:1-19. [PMID: 34410562 DOI: 10.1007/s10266-021-00647-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 07/31/2021] [Indexed: 12/14/2022]
Abstract
Porphyromonas gingivalis, a Gram-negative anaerobic bacillus present in periodontal disease, is considered one of the major pathogens in periodontitis. A literature search for English original studies, case series and review articles published up to December 2019 was performed using the MEDLINE, PubMed and GoogleScholar databases, with the search terms "Porphyromonas gingivalis" AND the potentially associated condition or systemic disease Abstracts and full text articles were used to make a review of published research literature on P. gingivalis outside the oral cavity. The main points of interest of this narrative review were: (i) a potential direct action of the bacterium and not the systemic effects of the inflammatory acute-phase response induced by the periodontitis, (ii) the presence of the bacterium (viable or not) in the organ, or (iii) the presence of its virulence factors. Virulence factors (gingipains, capsule, fimbriae, hemagglutinins, lipopolysaccharide, hemolysin, iron uptake transporters, toxic outer membrane blebs/vesicles, and DNA) associated with P. gingivalis can deregulate certain functions in humans, particularly host immune systems, and cause various local and systemic pathologies. The most recent studies linking P. gingivalis to systemic diseases were discussed, remembering particularly the molecular mechanisms involved in different infections, including cerebral, cardiovascular, pulmonary, bone, digestive and peri-natal infections. Recent involvement of P. gingivalis in neurological diseases has been demonstrated. P. gingivalis modulates cellular homeostasis and increases markers of inflammation. It is also a factor in the oxidative stress involved in beta-amyloid production.
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Affiliation(s)
- Steeve Bregaint
- Microbiology, INSERM, INRAE, CHU Rennes, Institut NUMECAN (Nutrition Metabolisms and Cancer), Université de Rennes, U1241, 2, avenue du Professeur Léon Bernard, 35043, Rennes, France
| | - Emile Boyer
- Microbiology, INSERM, INRAE, CHU Rennes, Institut NUMECAN (Nutrition Metabolisms and Cancer), Université de Rennes, U1241, 2, avenue du Professeur Léon Bernard, 35043, Rennes, France.,Teaching Hospital Pontchaillou, 2 rue Henri Le Guilloux, 35033, Rennes, France
| | - Shao Bing Fong
- Microbiology, INSERM, INRAE, CHU Rennes, Institut NUMECAN (Nutrition Metabolisms and Cancer), Université de Rennes, U1241, 2, avenue du Professeur Léon Bernard, 35043, Rennes, France
| | - Vincent Meuric
- Microbiology, INSERM, INRAE, CHU Rennes, Institut NUMECAN (Nutrition Metabolisms and Cancer), Université de Rennes, U1241, 2, avenue du Professeur Léon Bernard, 35043, Rennes, France.,Teaching Hospital Pontchaillou, 2 rue Henri Le Guilloux, 35033, Rennes, France
| | - Martine Bonnaure-Mallet
- Microbiology, INSERM, INRAE, CHU Rennes, Institut NUMECAN (Nutrition Metabolisms and Cancer), Université de Rennes, U1241, 2, avenue du Professeur Léon Bernard, 35043, Rennes, France.,Teaching Hospital Pontchaillou, 2 rue Henri Le Guilloux, 35033, Rennes, France
| | - Anne Jolivet-Gougeon
- Microbiology, INSERM, INRAE, CHU Rennes, Institut NUMECAN (Nutrition Metabolisms and Cancer), Université de Rennes, U1241, 2, avenue du Professeur Léon Bernard, 35043, Rennes, France. .,Teaching Hospital Pontchaillou, 2 rue Henri Le Guilloux, 35033, Rennes, France.
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Battey JND, Szostak J, Phillips B, Teng C, Tung CK, Lim WT, Yeo YS, Ouadi S, Baumer K, Thomas J, Martinis J, Sierro N, Ivanov NV, Vanscheeuwijck P, Peitsch MC, Hoeng J. Impact of 6-Month Exposure to Aerosols From Potential Modified Risk Tobacco Products Relative to Cigarette Smoke on the Rodent Gastrointestinal Tract. Front Microbiol 2021; 12:587745. [PMID: 34276574 PMCID: PMC8283309 DOI: 10.3389/fmicb.2021.587745] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 06/10/2021] [Indexed: 01/14/2023] Open
Abstract
Cigarette smoking causes adverse health effects that might occur shortly after smoking initiation and lead to the development of inflammation and cardiorespiratory disease. Emerging studies have demonstrated the role of the intestinal microbiome in disease pathogenesis. The intestinal microbiome is susceptible to the influence of environmental factors such as smoking, and recent studies have indicated microbiome changes in smokers. Candidate modified risk tobacco products (CMRTP) are being developed to provide substitute products to lower smoking-related health risks in smokers who are unable or unwilling to quit. In this study, the ApoE–/– mouse model was used to investigate the impact of cigarette smoke (CS) from the reference cigarette 3R4F and aerosols from two CMRTPs based on the heat-not-burn principle [carbon-heated tobacco product 1.2 (CHTP 1.2) and tobacco heating system 2.2 (THS 2.2)] on the intestinal microbiome over a 6-month period. The effect of cessation or switching to CHTP 1.2 after 3 months of CS exposure was also assessed. Next-generation sequencing was used to evaluate the impact of CMRTP aerosols in comparison to CS on microbiome composition and gene expression in the digestive tract of mice. Our analyses highlighted significant gene dysregulation in response to 3R4F exposure at 4 and 6 months. The findings showed an increase in the abundance of Akkermansiaceae upon CS exposure, which was reversed upon cessation. Cessation resulted in a significant decrease in Akkemansiaceae abundance, whereas switching to CHTP 1.2 resulted in an increase in Lactobacillaceae abundance. These microbial changes could be important for understanding the effect of CS on gut function and its relevance to disease pathogenesis via the microbiome.
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Affiliation(s)
| | - Justyna Szostak
- PMI R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Blaine Phillips
- PMI R&D, Philip Morris International Research Laboratories Pte. Ltd., Science Park II, Singapore, Singapore
| | - Charles Teng
- PMI R&D, Philip Morris International Research Laboratories Pte. Ltd., Science Park II, Singapore, Singapore
| | - Ching Keong Tung
- PMI R&D, Philip Morris International Research Laboratories Pte. Ltd., Science Park II, Singapore, Singapore
| | - Wei Ting Lim
- PMI R&D, Philip Morris International Research Laboratories Pte. Ltd., Science Park II, Singapore, Singapore
| | - Ying Shan Yeo
- PMI R&D, Philip Morris International Research Laboratories Pte. Ltd., Science Park II, Singapore, Singapore
| | - Sonia Ouadi
- PMI R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Karine Baumer
- PMI R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Jerome Thomas
- PMI R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Jacopo Martinis
- PMI R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Nicolas Sierro
- PMI R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | | | | | | | - Julia Hoeng
- PMI R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
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Ashaolu TJ, Fernández-Tomé S. Gut mucosal and adipose tissues as health targets of the immunomodulatory mechanisms of probiotics. Trends Food Sci Technol 2021. [DOI: 10.1016/j.tifs.2021.04.040] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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11
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Li W, Sun Y, Dai L, Chen H, Yi B, Niu J, Wang L, Zhang F, Luo J, Wang K, Guo R, Li L, Zou Q, Ma ZS, Miao Y. Ecological and network analyses identify four microbial species with potential significance for the diagnosis/treatment of ulcerative colitis (UC). BMC Microbiol 2021; 21:138. [PMID: 33947329 PMCID: PMC8097971 DOI: 10.1186/s12866-021-02201-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 04/05/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Ulcerative colitis (UC) is one of the primary types of inflammatory bowel disease (IBD), the occurrence of which has been increasing worldwide. Although IBD is an intensively studied human microbiome-associated disease, research on Chinese populations remains relatively limited, particularly on the mucosal microbiome. The present study aimed to analyze the changes in the mucosal microbiome associated with UC from the perspectives of medical ecology and complex network analysis. RESULTS In total, 56 mucosal microbiome samples were collected from 28 Chinese UC patients and their healthy family partners, followed by amplicon sequencing. Based on sequencing data, we analyzed species diversity, shared species, and inter-species interactions at the whole community, main phyla, and core/periphery species levels. We identified four opportunistic "pathogens" (i.e., Clostridium tertium, Odoribacter splanchnicus, Ruminococcus gnavus, and Flavonifractor plautii) with potential significance for the diagnosis and treatment of UC, which were inhibited in healthy individuals, but unrestricted in the UC patients. In addition, we also discovered in this study: (i) The positive-to-negative links (P/N) ratio, which measures the balance of species interactions or inhibition effects in microbiome networks, was significantly higher in UC patients, indicating loss of inhibition against potentially opportunistic "pathogens" associated with dysbiosis. (ii) Previous studies have reported conflicting evidence regarding species diversity and composition between UC patients and healthy controls. Here, significant differences were found at the major phylum and core/periphery scales, but not at the whole community level. Thus, we argue that the paradoxical results found in existing studies are due to the scale effect. CONCLUSIONS Our results reveal changes in the ecology and network structure of the gut mucosal microbiome that might be associated with UC, and these changes might provide potential therapeutic mechanisms of UC. The four opportunistic pathogens that were identified in the present study deserve further investigation in future studies.
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Affiliation(s)
- Wendy Li
- Computational Biology and Medical Ecology Lab, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, China
| | - Yang Sun
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Digestive Disease, Kunming, Yunnan, China
| | - Lin Dai
- Faculty of Science, Kunming University of Science and Technology, Kunming, China
| | - Hongju Chen
- Computational Biology and Medical Ecology Lab, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, China.,College of Mathematics, Honghe University, Mengzi, Yunnan Province, China
| | - Bin Yi
- College of Mathematics, Honghe University, Mengzi, Yunnan Province, China
| | - Junkun Niu
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Digestive Disease, Kunming, Yunnan, China
| | - Lan Wang
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Digestive Disease, Kunming, Yunnan, China
| | - Fengrui Zhang
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Digestive Disease, Kunming, Yunnan, China
| | - Juan Luo
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Digestive Disease, Kunming, Yunnan, China
| | - Kunhua Wang
- Department of General Surgery, The First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Digestive Disease, Kunming, Yunnan, China
| | - Rui Guo
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Digestive Disease, Kunming, Yunnan, China
| | - Lianwei Li
- Computational Biology and Medical Ecology Lab, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, China
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
| | - Zhanshan Sam Ma
- Computational Biology and Medical Ecology Lab, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China. .,Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
| | - Yinglei Miao
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Digestive Disease, Kunming, Yunnan, China.
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12
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Aldars-García L, Chaparro M, Gisbert JP. Systematic Review: The Gut Microbiome and Its Potential Clinical Application in Inflammatory Bowel Disease. Microorganisms 2021; 9:microorganisms9050977. [PMID: 33946482 PMCID: PMC8147118 DOI: 10.3390/microorganisms9050977] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 04/22/2021] [Accepted: 04/29/2021] [Indexed: 02/07/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic relapsing-remitting systemic disease of the gastrointestinal tract. It is well established that the gut microbiome has a profound impact on IBD pathogenesis. Our aim was to systematically review the literature on the IBD gut microbiome and its usefulness to provide microbiome-based biomarkers. A systematic search of the online bibliographic database PubMed from inception to August 2020 with screening in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines was conducted. One-hundred and forty-four papers were eligible for inclusion. There was a wide heterogeneity in microbiome analysis methods or experimental design. The IBD intestinal microbiome was generally characterized by reduced species richness and diversity, and lower temporal stability, while changes in the gut microbiome seemed to play a pivotal role in determining the onset of IBD. Multiple studies have identified certain microbial taxa that are enriched or depleted in IBD, including bacteria, fungi, viruses, and archaea. The two main features in this sense are the decrease in beneficial bacteria and the increase in pathogenic bacteria. Significant differences were also present between remission and relapse IBD status. Shifts in gut microbial community composition and abundance have proven to be valuable as diagnostic biomarkers. The gut microbiome plays a major role in IBD, yet studies need to go from casualty to causality. Longitudinal designs including newly diagnosed treatment-naïve patients are needed to provide insights into the role of microbes in the onset of intestinal inflammation. A better understanding of the human gut microbiome could provide innovative targets for diagnosis, prognosis, treatment and even cure of this relevant disease.
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Affiliation(s)
- Laila Aldars-García
- Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-IP), Universidad Autónoma de Madrid, 28006 Madrid, Spain; (L.A.-G.); (M.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), 28006 Madrid, Spain
| | - María Chaparro
- Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-IP), Universidad Autónoma de Madrid, 28006 Madrid, Spain; (L.A.-G.); (M.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), 28006 Madrid, Spain
| | - Javier P. Gisbert
- Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-IP), Universidad Autónoma de Madrid, 28006 Madrid, Spain; (L.A.-G.); (M.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), 28006 Madrid, Spain
- Correspondence: ; Tel.: +34-913-093-911; Fax: +34-915-204-013
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13
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Minakshi P, Kumar R, Ghosh M, Brar B, Barnela M, Lakhani P. Application of Polymeric Nano-Materials in Management of Inflammatory Bowel Disease. Curr Top Med Chem 2021; 20:982-1008. [PMID: 32196449 DOI: 10.2174/1568026620666200320113322] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 01/25/2020] [Accepted: 02/24/2020] [Indexed: 02/06/2023]
Abstract
Inflammatory Bowel Disease (IBD) is an umbrella term used to describe disorders that involve Crohn's disease (CD), ulcerative colitis (UC) and pouchitis. The disease occurrence is more prevalent in the working group population which not only hampers the well being of an individual but also has negative economical impact on society. The current drug regime used therapy is very costly owing to the chronic nature of the disease leading to several side effects. The condition gets more aggravated due to the lower concentration of drug at the desired site. Therefore, in the present scenario, a therapy is needed which can maximize efficacy, adhere to quality of life, minimize toxicity and doses, be helpful in maintaining and stimulating physical growth of mucosa with minimum disease complications. In this aspect, nanotechnology intervention is one promising field as it can act as a carrier to reduce toxicity, doses and frequency which in turn help in faster recovery. Moreover, nanomedicine and nanodiagnostic techniques will further open a new window for treatment in understanding pathogenesis along with better diagnosis which is poorly understood till now. Therefore the present review is more focused on recent advancements in IBD in the application of nanotechnology.
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Affiliation(s)
- Prasad Minakshi
- Department of Animal Biotechnology, LLR University of Veterinary and Animal Sciences, Hisar-125001, Haryana, India
| | - Rajesh Kumar
- Department of Veterinary Physiology & Biochemistry, LUVAS, Hisar-125 004, India
| | - Mayukh Ghosh
- Department of Veterinary Physiology and Biochemistry, RGSC, Banaras Hindu University, Mirzapur (UP) - 231001, India
| | - Basanti Brar
- Department of Animal Biotechnology, LLR University of Veterinary and Animal Sciences, Hisar-125001, Haryana, India
| | - Manju Barnela
- Department of Nano & Biotechnology, Guru Jambheshwar University, Hisar-125001, Haryana, India
| | - Preeti Lakhani
- Department of Veterinary Physiology & Biochemistry, LUVAS, Hisar-125 004, India
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14
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Nicholson MR, Mitchell PD, Alexander E, Ballal S, Bartlett M, Becker P, Davidovics Z, Docktor M, Dole M, Felix G, Gisser J, Hourigan SK, Jensen MK, Kaplan JL, Kelsen J, Kennedy M, Khanna S, Knackstedt E, Leier M, Lewis J, Lodarek A, Michail S, Oliva-Hemker M, Patton T, Queliza K, Russell GH, Singh N, Solomon A, Suskind DL, Werlin S, Kellermayer R, Kahn SA. Efficacy of Fecal Microbiota Transplantation for Clostridium difficile Infection in Children. Clin Gastroenterol Hepatol 2020; 18:612-619.e1. [PMID: 31009795 PMCID: PMC7549313 DOI: 10.1016/j.cgh.2019.04.037] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 04/02/2019] [Accepted: 04/05/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND & AIMS Fecal microbiota transplantation (FMT) is commonly used to treat Clostridium difficile infection (CDI). CDI is an increasing cause of diarrheal illness in pediatric patients, but the effects of FMT have not been well studied in children. We performed a multi-center retrospective cohort study of pediatric and young adult patients to evaluate the efficacy, safety, and factors associated with a successful FMT for the treatment of CDI. METHODS We performed a retrospective study of 372 patients, 11 months to 23 years old, who underwent FMT at 18 pediatric centers, from February 1, 2004, to February 28, 2017; 2-month outcome data were available from 335 patients. Successful FMT was defined as no recurrence of CDI in the 2 months following FMT. We performed stepwise logistic regression to identify factors associated with successful FMT. RESULTS Of 335 patients who underwent FMT and were followed for 2 months or more, 271 (81%) had a successful outcome following a single FMT and 86.6% had a successful outcome following a first or repeated FMT. Patients who received FMT with fresh donor stool (odds ratio [OR], 2.66; 95% CI, 1.39-5.08), underwent FMT via colonoscopy (OR, 2.41; 95% CI, 1.26-4.61), did not have a feeding tube (OR, 2.08; 95% CI, 1.05-4.11), or had 1 less episode of CDI before FMT (OR, 1.20; 95% CI, 1.04-1.39) had increased odds for successful FMT. Seventeen patients (4.7%) had a severe adverse event during the 3-month follow-up period, including 10 hospitalizations. CONCLUSIONS Based on the findings from a large multi-center retrospective cohort, FMT is effective and safe for the treatment of CDI in children and young adults. Further studies are required to optimize the timing and method of FMT for pediatric patients-factors associated with success differ from those of adult patients.
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Affiliation(s)
| | | | | | - Sonia Ballal
- Boston Children’s Hospital, Boston, Massachusetts
| | | | - Penny Becker
- Connecticut Children’s Medical Center, Hartford, Connecticut
| | - Zev Davidovics
- Connecticut Children’s Medical Center, Hartford, Connecticut
| | | | - Michael Dole
- Vanderbilt University Medical Center, Nashville, Tennessee
| | - Grace Felix
- Johns Hopkins Children’s Center, Baltimore, Maryland
| | | | - Suchitra K. Hourigan
- Johns Hopkins Children’s Center, Baltimore, Maryland;,Pediatric Specialists of Virginia, Fairfax, Virginia
| | - M. Kyle Jensen
- Primary Children’s Hospital at University of Utah, Salt Lake City, Utah
| | - Jess L. Kaplan
- MassGeneral Hospital for Children, Boston, Massachusetts
| | - Judith Kelsen
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Melissa Kennedy
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | | | | | | | - Jeffery Lewis
- Children’s Center for Digestive Healthcare at Children’s Healthcare of Atlanta, Atlanta, Georgia
| | | | - Sonia Michail
- University of Southern California Children’s Hospital of Los Angeles, Los Angeles, California
| | | | | | - Karen Queliza
- Baylor College of Medicine, Texas Children’s Hospital, Children’s Nutrition and Research Center, Houston, Texas
| | | | - Namita Singh
- Cedars Sinai Medical Center, Los Angeles, California
| | | | - David L. Suskind
- Seattle Children’s Hospital and the University of Washington, Seattle, Washington
| | | | - Richard Kellermayer
- Baylor College of Medicine, Texas Children’s Hospital, Children’s Nutrition and Research Center, Houston, Texas
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15
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Masoodi I, Alshanqeeti AS, Alyamani EJ, AlLehibi AA, Alqutub AN, Alsayari KN, Alomair AO. Microbial dysbiosis in irritable bowel syndrome: A single-center metagenomic study in Saudi Arabia. JGH OPEN 2020; 4:649-655. [PMID: 32782952 PMCID: PMC7411548 DOI: 10.1002/jgh3.12313] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 12/18/2019] [Accepted: 01/23/2020] [Indexed: 12/13/2022]
Abstract
Background The focus of this study was to explore potential differences in colonic mucosal microbiota in irritable bowel syndrome (IBS) patients compared to a control group utilizing a metagenomic study. Methods Mucosal microbiota samples were collected from each IBS patient utilizing jet‐flushing colonic mucosa in unified segments of the colon with distilled water, followed by aspiration, during colonoscopy. All the purified dsDNA was extracted and quantified before metagenomic sequencing using an Illumina platform. An equal number of healthy age‐matched controls were also examined for colonic mucosal microbiota, which were obtained during screening colonoscopies. Results The microbiota data on 50 IBS patients (31 females), with a mean age 43.94 ± 14.50 (range19–65), were analyzed in comparison to 50 controls. Satisfactory DNA samples were subjected to metagenomics study, followed by comprehensive comparative phylogenetic analysis. Metagenomics analysis was carried out, and 3.58G reads were sequenced. Community richness (Chao) and microbial structure in IBS patients were shown to be significantly different from those in the control group. Enrichment of Oxalobacter formigenes, Sutterella wadsworthensis, and Bacteroides pectinophilus was significantly observed in controls, whereas enrichment of Collinsella aerofaciens, Gemella morbillorum, and Veillonella parvula Actinobacteria was observed significantly in the IBS cohort. Conclusion The current study has demonstrated significant differences in the microbiota of IBS patients compared to controls.
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Affiliation(s)
| | - Ali S Alshanqeeti
- National Blood & Cancer Center, Riyadh, Saudi Arabia Riyadh Saudi Arabia
| | - Essam J Alyamani
- National Center for Biotechnology King Abdulaziz City for Science and Technology (KACST) Riyadh Saudi Arabia
| | - Abed A AlLehibi
- Gastroenterology and Hepatology Department King Fahad Medical City Riyadh Saudi Arabia
| | - Adel N Alqutub
- Gastroenterology and Hepatology Department King Fahad Medical City Riyadh Saudi Arabia
| | - Khalid N Alsayari
- Gastroenterology and Hepatology Department King Fahad Medical City Riyadh Saudi Arabia
| | - Ahmed O Alomair
- Gastroenterology and Hepatology Department King Fahad Medical City Riyadh Saudi Arabia
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16
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Dheer R, Davies JM, Quintero MA, Damas OM, Deshpande AR, Kerman DH, Sawyer WP, Pignac-Kobinger J, Ban Y, Fernandez I, Burgueno JF, Phillips MC, Abreu MT. Microbial Signatures and Innate Immune Gene Expression in Lamina Propria Phagocytes of Inflammatory Bowel Disease Patients. Cell Mol Gastroenterol Hepatol 2019; 9:387-402. [PMID: 31740421 PMCID: PMC7015995 DOI: 10.1016/j.jcmgh.2019.10.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 10/29/2019] [Accepted: 10/30/2019] [Indexed: 12/27/2022]
Abstract
BACKGROUND & AIMS The interaction between intestinal microbiota and the immune system plays a vital role in inflammatory bowel disease (IBD). Although numerous deep-sequencing studies have suggested dysbiosis in IBD, identifying specific bacteria from the stool or mucosa that are responsible for disease susceptibility or severity has remained a challenge. Lamina propria phagocytes ideally are localized to interact with bacteria that are in close proximity to, or have invaded, the tissue. Thus, we examined the microbial populations associated with the lamina propria phagocytes in 20 Crohn's disease and 12 ulcerative colitis patients. Specifically, we aimed to address whether the phagocyte-associated microbiota differed from the mucosa-associated microbiota and whether this varied based on IBD type or the state of inflammation. METHODS 16S ribosomal RNA gene sequencing and innate immune gene expression profiling was done on CD11b+ lamina propria phagocytes isolated from the biopsies obtained from IBD patients. RESULTS Phagocyte-associated microbiota was enriched in bacterial species belonging to phylum Proteobacteria, whereas species belonging to phylum Bacteroidetes were enriched in the mucosal microbiota of IBD patients. Disease type was the most influential factor in driving differences in the microbiota of both the mucosa and the lamina propria phagocytes, irrespective of inflammation state o`r anatomic location. Crohn's disease and ulcerative colitis specimens showed similar patterns of increased inflammatory gene expression in phagocytes isolated from inflamed areas compared with those isolated from uninflamed regions. CONCLUSIONS This pilot study shows the feasibility of using lamina propria phagocytes to characterize the microbiota in IBD patients. The approach used in this study can narrow the spectrum of potentially dysbiotic bacterial populations and clinically relevant gene expression signatures in IBD patients.
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Affiliation(s)
- Rishu Dheer
- Division of Gastroenterology, Department of Medicine, University of Miami Miller School of Medicine, Miami, Florida
| | - Julie M Davies
- Division of Gastroenterology, Department of Medicine, University of Miami Miller School of Medicine, Miami, Florida
| | - Maria A Quintero
- Division of Gastroenterology, Department of Medicine, University of Miami Miller School of Medicine, Miami, Florida
| | - Oriana M Damas
- Division of Gastroenterology, Department of Medicine, University of Miami Miller School of Medicine, Miami, Florida
| | - Amar R Deshpande
- Division of Gastroenterology, Department of Medicine, University of Miami Miller School of Medicine, Miami, Florida
| | - David H Kerman
- Division of Gastroenterology, Department of Medicine, University of Miami Miller School of Medicine, Miami, Florida
| | - William Peter Sawyer
- Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida
| | - Judith Pignac-Kobinger
- Division of Gastroenterology, Department of Medicine, University of Miami Miller School of Medicine, Miami, Florida
| | - Yuguang Ban
- Biostatistics and Bioinformatics Core Shared Resource, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
| | - Irina Fernandez
- Division of Gastroenterology, Department of Medicine, University of Miami Miller School of Medicine, Miami, Florida
| | - Juan F Burgueno
- Division of Gastroenterology, Department of Medicine, University of Miami Miller School of Medicine, Miami, Florida
| | - Matthew C Phillips
- Division of Gastroenterology, Department of Medicine, University of Miami Miller School of Medicine, Miami, Florida
| | - Maria T Abreu
- Division of Gastroenterology, Department of Medicine, University of Miami Miller School of Medicine, Miami, Florida.
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17
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Abstract
The composition of the gut microbiome has been associated with various aspects of human health, but the mechanism of this interaction is still unclear. We utilized a cellular system to characterize the effect of the microbiome on human gene expression. We showed that some of these changes in expression may be mediated by changes in chromatin accessibility. Furthermore, we validate the role of a specific microbe and show that changes in its abundance can modify the host gene expression response. These results show an important role of gut microbiota in regulating host gene expression and suggest that manipulation of microbiome composition could be useful in future therapies. Variation in gut microbiome is associated with wellness and disease in humans, and yet the molecular mechanisms by which this variation affects the host are not well understood. A likely mechanism is that of changing gene regulation in interfacing host epithelial cells. Here, we treated colonic epithelial cells with live microbiota from five healthy individuals and quantified induced changes in transcriptional regulation and chromatin accessibility in host cells. We identified over 5,000 host genes that change expression, including 588 distinct associations between specific taxa and host genes. The taxa with the strongest influence on gene expression alter the response of genes associated with complex traits. Using ATAC-seq, we showed that a subset of these changes in gene expression are associated with changes in host chromatin accessibility and transcription factor binding induced by exposure to gut microbiota. We then created a manipulated microbial community with titrated doses of Collinsella, demonstrating that manipulation of the composition of the microbiome under both natural and controlled conditions leads to distinct and predictable gene expression profiles in host cells. Taken together, our results suggest that specific microbes play an important role in regulating expression of individual host genes involved in human complex traits. The ability to fine-tune the expression of host genes by manipulating the microbiome suggests future therapeutic routes. IMPORTANCE The composition of the gut microbiome has been associated with various aspects of human health, but the mechanism of this interaction is still unclear. We utilized a cellular system to characterize the effect of the microbiome on human gene expression. We showed that some of these changes in expression may be mediated by changes in chromatin accessibility. Furthermore, we validate the role of a specific microbe and show that changes in its abundance can modify the host gene expression response. These results show an important role of gut microbiota in regulating host gene expression and suggest that manipulation of microbiome composition could be useful in future therapies.
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18
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Chandra N, Srivastava A, Kumar S. Bacterial biofilms in human gastrointestinal tract: An intricate balance between health and inflammatory bowel diseases. World J Pharmacol 2019; 8:26-40. [DOI: 10.5497/wjp.v8.i3.26] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 07/05/2019] [Accepted: 07/16/2019] [Indexed: 02/06/2023] Open
Abstract
Inflammatory bowel disease (IBD) has been a worldwide health problem. It is characterized by severe intestinal inflammation due to immune responses against the gut microbes in genetically susceptible individuals. The understanding of gut microbiota for its composition and complex interaction in normal and diseased conditions has been assisted by the use of molecular, metagenomics and meta transcriptomics studies. The alteration of intestinal microbiota is the key determinant in the degree of inflammation caused and the prolonged course of disease. The relationship between luminal gut bacteria and innate immunity is also of prime significance. Such developments have further led to the search of specific (including bacteria and fungi) as a causative agent of IBD. Although detailed research has been done for the role of gut microbiota in IBD, molecular mechanisms and related gene expression are still not well understood in this disease, which hampers the generation of effective therapeutic agents for IBD. This paper assessed various factors contributing to IBD, genetic dysbiosis and pathogenic influence in the gut microbiota, interactions such as microbiome-host immune system interaction and microbe-microbe interactions involved in IBD, currently available IBD therapies, followed by a detailed review on bacterial infections that might be involved in IBD, globally and specifically in India.
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Affiliation(s)
- Niharika Chandra
- Faculty of Biotechnology, Institute of Bio-Sciences and Technology, Shri Ramswaroop Memorial University, Uttar Pradesh 225003, India
| | - Ankita Srivastava
- Faculty of Bio-Sciences, Institute of Bio-Sciences and Technology, Shri Ramswaroop Memorial University, Uttar Pradesh 225003, India
| | - Sunil Kumar
- Faculty of Bio-Sciences, Institute of Bio-Sciences and Technology, Shri Ramswaroop Memorial University, Uttar Pradesh 225003, India
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19
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Khan I, Ullah N, Zha L, Bai Y, Khan A, Zhao T, Che T, Zhang C. Alteration of Gut Microbiota in Inflammatory Bowel Disease (IBD): Cause or Consequence? IBD Treatment Targeting the Gut Microbiome. Pathogens 2019; 8:pathogens8030126. [PMID: 31412603 PMCID: PMC6789542 DOI: 10.3390/pathogens8030126] [Citation(s) in RCA: 397] [Impact Index Per Article: 79.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 08/03/2019] [Accepted: 08/05/2019] [Indexed: 02/06/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic complex inflammatory gut pathological condition, examples of which include Crohn’s disease (CD) and ulcerative colitis (UC), which is associated with significant morbidity. Although the etiology of IBD is unknown, gut microbiota alteration (dysbiosis) is considered a novel factor involved in the pathogenesis of IBD. The gut microbiota acts as a metabolic organ and contributes to human health by performing various physiological functions; deviation in the gut flora composition is involved in various disease pathologies, including IBD. This review aims to summarize the current knowledge of gut microbiota alteration in IBD and how this contributes to intestinal inflammation, as well as explore the potential role of gut microbiota-based treatment approaches for the prevention and treatment of IBD. The current literature has clearly demonstrated a perturbation of the gut microbiota in IBD patients and mice colitis models, but a clear causal link of cause and effect has not yet been presented. In addition, gut microbiota-based therapeutic approaches have also shown good evidence of their effects in the amelioration of colitis in animal models (mice) and IBD patients, which indicates that gut flora might be a new promising therapeutic target for the treatment of IBD. However, insufficient data and confusing results from previous studies have led to a failure to define a core microbiome associated with IBD and the hidden mechanism of pathogenesis, which suggests that well-designed randomized control trials and mouse models are required for further research. In addition, a better understanding of this ecosystem will also determine the role of prebiotics and probiotics as therapeutic agents in the management of IBD.
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Affiliation(s)
- Israr Khan
- School of Life Sciences, Lanzhou University, Lanzhou 730000, China
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, Lanzhou University, Lanzhou 730000, China
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, Lanzhou University, Lanzhou 730000, China
| | - Naeem Ullah
- School of Life Sciences, Lanzhou University, Lanzhou 730000, China
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, Lanzhou University, Lanzhou 730000, China
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, Lanzhou University, Lanzhou 730000, China
| | - Lajia Zha
- School of Life Sciences, Lanzhou University, Lanzhou 730000, China
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, Lanzhou University, Lanzhou 730000, China
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, Lanzhou University, Lanzhou 730000, China
| | - Yanrui Bai
- School of Life Sciences, Lanzhou University, Lanzhou 730000, China
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, Lanzhou University, Lanzhou 730000, China
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, Lanzhou University, Lanzhou 730000, China
| | - Ashiq Khan
- School of Life Sciences, Lanzhou University, Lanzhou 730000, China
- Probiotics and Biological Feed Research Center, Lanzhou University, Lanzhou 730000, China
| | - Tang Zhao
- School of Life Sciences, Lanzhou University, Lanzhou 730000, China
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, Lanzhou University, Lanzhou 730000, China
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, Lanzhou University, Lanzhou 730000, China
| | - Tuanjie Che
- Gansu Key Laboratory of Functional Genomics and Molecular Diagnosis, Lanzhou 730000, China
| | - Chunjiang Zhang
- School of Life Sciences, Lanzhou University, Lanzhou 730000, China.
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, Lanzhou University, Lanzhou 730000, China.
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, Lanzhou University, Lanzhou 730000, China.
- Gansu Key Laboratory of Functional Genomics and Molecular Diagnosis, Lanzhou 730000, China.
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20
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Lo Presti A, Zorzi F, Del Chierico F, Altomare A, Cocca S, Avola A, De Biasio F, Russo A, Cella E, Reddel S, Calabrese E, Biancone L, Monteleone G, Cicala M, Angeletti S, Ciccozzi M, Putignani L, Guarino MPL. Fecal and Mucosal Microbiota Profiling in Irritable Bowel Syndrome and Inflammatory Bowel Disease. Front Microbiol 2019; 10:1655. [PMID: 31379797 PMCID: PMC6650632 DOI: 10.3389/fmicb.2019.01655] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 07/04/2019] [Indexed: 12/12/2022] Open
Abstract
An imbalance in the bacterial species resulting in the loss of intestinal homeostasis has been described in inflammatory bowel diseases (IBD) and irritable bowel syndrome (IBS). In this prospective study, we investigated whether IBD and IBS patients exhibit specific changes in richness and distribution of fecal and mucosal-associated microbiota. Additionally, we assessed potential 16S rRNA gene amplicons biomarkers for IBD, IBS, and controls (CTRLs) by comparison of taxonomic composition. The relative abundance of bacteria, at phylum and genus/species levels, and the bacterial diversity were determined through 16S rRNA sequence-based fecal and mucosal microbiota analysis. Linear discriminant analysis effect size (LEfSe) was used for biomarker discovery associated to IBD and IBS as compared to CTRLs. In fecal and mucosal samples, the microbiota richness was characterized by a microbial diversity reduction, going from CTRLs to IBS to IBD. β-diversity analysis showed a clear separation between IBD and CTRLs and between IBD and IBS with no significant separation between IBS and CTRLs. β-diversity showed a clear separation between mucosa and stool samples in all the groups. In IBD, there was no difference between inflamed and not inflamed mucosa. Based upon the LEfSe data, the Anaerostipes and Ruminococcaceae were identified as the most differentially abundant bacterial taxa in CTRLs. Erysipelotrichi was identified as potential biomarker for IBS, while Gammaproteobacteria, Enterococcus, and Enterococcaceae for IBD. This study provides an overview of the alterations of microbiota and may aid in identifying potential 16S rRNA gene amplicons mucosal biomarkers for IBD and IBS.
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Affiliation(s)
| | - Francesca Zorzi
- Gastrointestinal Unit, Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | | | | | - Silvia Cocca
- Unit of Digestive Disease, Campus Bio-Medico University, Rome, Italy
| | - Alessandra Avola
- Unit of Digestive Disease, Campus Bio-Medico University, Rome, Italy
| | - Fabiola De Biasio
- Unit of Digestive Disease, Campus Bio-Medico University, Rome, Italy
| | - Alessandra Russo
- Human Microbiome Unit, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Eleonora Cella
- Unit of Medical Statistics and Molecular Epidemiology, Campus Bio-Medico University, Rome, Italy
| | - Sofia Reddel
- Human Microbiome Unit, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Emma Calabrese
- Gastrointestinal Unit, Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Livia Biancone
- Gastrointestinal Unit, Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Giovanni Monteleone
- Gastrointestinal Unit, Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Michele Cicala
- Unit of Digestive Disease, Campus Bio-Medico University, Rome, Italy
| | - Silvia Angeletti
- Unit of Clinical Laboratory Science, Campus Bio-Medico University, Rome, Italy
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, Campus Bio-Medico University, Rome, Italy
| | - Lorenza Putignani
- Human Microbiome Unit and Parasitology Unit, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
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21
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Masoodi I, Alshanqeeti AS, Ahmad S, Alyamani EJ, Al-Lehibi AA, Qutub AN, Alsayari KN, Alomair AO. Microbial dysbiosis in inflammatory bowel diseases: results of a metagenomic study in Saudi Arabia. MINERVA GASTROENTERO 2019; 65:177-186. [PMID: 31293117 DOI: 10.23736/s1121-421x.19.02576-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND The intestinal microbiota plays an essential role in the pathogenesis of ulcerative colitis (UC)and Crohn disease (CD). METHODS Metagenomic studies were used to study microbiota in the diagnosed cases of UC and CD at King Fahad Medical City, Riyadh, Saudi Arabia. Each segment of the colon was flushed with distilled water during colonoscopy, and the material was aspirated, immediately frozen for the study. The patients attending for screening colonoscopies were taken as age-matched healthy controls. The UC patients were followed clinically for any signs of exacerbation relapse, and CD patients were followed for any complications. RESULTS The metagenomic data on 46 (24 females) patients with CD were analyzed along with a group of age and gender-matched controls. Their age ranged from 14 to 65 years, mean age 25.19±10.67 years. There were 50 UC patient (28 females) mean age of 34.42±12.58, and their age ranged from 13-58 years. This study identified enrichment of 19 genera in the control group (Abiotrophia, Anaerofustis, Butyrivibrio, Campylobacter, Catenibacterium, Coprococcus, Dorea, Eubacterium, Facklamia, Klebsiella, Lactococcus, Oscillibacter, Paenibacillus, Parabacteroides, Parasutterella, Porphyromonas, Prevotella, Ruminococcus, Treponema). There was a significant enrichment of 14 genera in our CD cohort (Beggiatoa, Burkholderia, Cyanothece, Enterococcus, Escherichia, Fusobacterium, Jonquetella, Mitsuokella, Parvimonas, Peptostreptococcus, Shigella, Succinatimonas, ThermoanaerobacterVerrucomicrobiales, Vibrio). There was a significant enrichment of 7 genera in UC cohort (Beggiatoa, Burkholderia, Parascardovia, Parvimonas, Pseudoflavonifractor, Thermoanaerobacter, Verrucomicrobiales). CONCLUSIONS A significant dysbiosis was found in UC and CD patients compared to controls.
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Affiliation(s)
| | | | - Shameem Ahmad
- Department of Gastroenterology and Hepatology, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Essam J Alyamani
- National Center for Biotechnology, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
| | - Abed A Al-Lehibi
- Department of Gastroenterology and Hepatology, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Adel N Qutub
- Department of Gastroenterology and Hepatology, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Khalid N Alsayari
- Department of Gastroenterology and Hepatology, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Ahmed O Alomair
- Department of Gastroenterology and Hepatology, King Fahad Medical City, Riyadh, Saudi Arabia -
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22
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Zakrzewski M, Simms LA, Brown A, Appleyard M, Irwin J, Waddell N, Radford-Smith GL. IL23R-Protective Coding Variant Promotes Beneficial Bacteria and Diversity in the Ileal Microbiome in Healthy Individuals Without Inflammatory Bowel Disease. J Crohns Colitis 2019; 13:451-461. [PMID: 30445599 DOI: 10.1093/ecco-jcc/jjy188] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
BACKGROUND AND AIMS This study aimed to characterize the mucosa-associated microbiota in ileal Crohn's disease [CD] patients and in healthy controls in terms of host genotype and inflammation status. METHODS The mucosa-associated microbiotas of intestinal pinch biopsies from 15 ileal CD patients with mild and moderate disease and from 58 healthy controls were analysed based on 16S ribosomal sequencing to determine microbial profile differences between [1] IL23R, NOD2 and ATG16L1 genotypes in healthy subjects, [2] ileal CD patients and control subjects, and [3] inflamed and non-inflamed mucosal tissue in CD patients. RESULTS The protective variant of the IL23R gene [rs11209026] significantly impacted the microbial composition in the ileum of healthy subjects and was associated with an increased abundance of phylotypes within the family Christensenellaceae as well as increases in diversity and richness. Comparative analysis of healthy and non-inflamed CD microbiome samples indicated a notable decrease in the abundance of Faecalibacterium prausnitzii as well as Shannon diversity and richness. Inflamed and non-inflamed ileal samples of CD subjects had high intra-individual stability and inter-individual variability, but no significant alterations in diversity, richness or taxa were identified. Calprotectin correlated positively with the abundance of Proteobacteria and negatively with diversity in the samples from healthy subjects. CONCLUSIONS The observation of low diversity and low abundance of beneficial bacteria in healthy control subjects carrying the IL23R [rs11209026] wild-type GG genotype indicates that the gut microbiome is influenced by host genetics and is altered prior to disease diagnosis. Faecal calprotectin may be a potential non-invasive screening tool for dysbiosis in subjects without disorders of intestinal inflammation.
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Affiliation(s)
- Martha Zakrzewski
- Medical Genomics, QIMR Berghofer Medical Research Institute, Herston, Brisbane 4006, Australia
| | - Lisa A Simms
- Gut Health, QIMR Berghofer Medical Research Institute, Herston, Brisbane 4006, Australia
| | - Allison Brown
- Gut Health, QIMR Berghofer Medical Research Institute, Herston, Brisbane 4006, Australia.,Department of Gastroenterology and Hepatology, Royal Brisbane and Women's Hospital, Herston, Brisbane 4029, Australia
| | - Mark Appleyard
- Department of Gastroenterology and Hepatology, Royal Brisbane and Women's Hospital, Herston, Brisbane 4029, Australia
| | - James Irwin
- Gut Health, QIMR Berghofer Medical Research Institute, Herston, Brisbane 4006, Australia.,Department of Gastroenterology, Palmerston North Hospital, Palmerston North, New Zealand
| | - Nicola Waddell
- Medical Genomics, QIMR Berghofer Medical Research Institute, Herston, Brisbane 4006, Australia
| | - Graham L Radford-Smith
- Gut Health, QIMR Berghofer Medical Research Institute, Herston, Brisbane 4006, Australia.,Department of Gastroenterology and Hepatology, Royal Brisbane and Women's Hospital, Herston, Brisbane 4029, Australia.,University of Queensland School of Medicine, Herston, Brisbane 4029, Australia
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23
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Yilmaz B, Juillerat P, Øyås O, Ramon C, Bravo FD, Franc Y, Fournier N, Michetti P, Mueller C, Geuking M, Pittet VEH, Maillard MH, Rogler G, Wiest R, Stelling J, Macpherson AJ. Microbial network disturbances in relapsing refractory Crohn's disease. Nat Med 2019; 25:323-336. [PMID: 30664783 DOI: 10.1038/s41591-018-0308-z] [Citation(s) in RCA: 229] [Impact Index Per Article: 45.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 11/19/2018] [Indexed: 02/06/2023]
Abstract
Inflammatory bowel diseases (IBD) can be broadly divided into Crohn's disease (CD) and ulcerative colitis (UC) from their clinical phenotypes. Over 150 host susceptibility genes have been described, although most overlap between CD, UC and their subtypes, and they do not adequately account for the overall incidence or the highly variable severity of disease. Replicating key findings between two long-term IBD cohorts, we have defined distinct networks of taxa associations within intestinal biopsies of CD and UC patients. Disturbances in an association network containing taxa of the Lachnospiraceae and Ruminococcaceae families, typically producing short chain fatty acids, characterize frequently relapsing disease and poor responses to treatment with anti-TNF-α therapeutic antibodies. Alterations of taxa within this network also characterize risk of later disease recurrence of patients in remission after the active inflamed segment of CD has been surgically removed.
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Affiliation(s)
- Bahtiyar Yilmaz
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, Bern, Switzerland.,Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Pascal Juillerat
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, Bern, Switzerland.,Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Ove Øyås
- Department of Biosystems Science and Engineering and SIB Swiss Institute of Bioinformatics, ETH Zurich, Basel, Switzerland
| | - Charlotte Ramon
- Department of Biosystems Science and Engineering and SIB Swiss Institute of Bioinformatics, ETH Zurich, Basel, Switzerland
| | - Francisco Damian Bravo
- Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Yannick Franc
- Institute of Social and Preventive Medicine (IUMSP), Lausanne University Hospital, Lausanne, Switzerland
| | - Nicolas Fournier
- Institute of Social and Preventive Medicine (IUMSP), Lausanne University Hospital, Lausanne, Switzerland
| | - Pierre Michetti
- Gastroenterology La Source-Beaulieu, Lausanne, Switzerland.,Service of Gastroenterology and Hepatology, Department of Medicine, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland
| | - Christoph Mueller
- Division of Experimental Pathology, Institute of Pathology, University of Bern, Bern, Switzerland
| | - Markus Geuking
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, Bern, Switzerland
| | - Valerie E H Pittet
- Institute of Social and Preventive Medicine (IUMSP), Lausanne University Hospital, Lausanne, Switzerland
| | - Michel H Maillard
- Gastroenterology La Source-Beaulieu, Lausanne, Switzerland.,Service of Gastroenterology and Hepatology, Department of Medicine, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland
| | - Gerhard Rogler
- Department of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | | | - Reiner Wiest
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, Bern, Switzerland.,Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Jörg Stelling
- Department of Biosystems Science and Engineering and SIB Swiss Institute of Bioinformatics, ETH Zurich, Basel, Switzerland
| | - Andrew J Macpherson
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, Bern, Switzerland. .,Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, Bern, Switzerland.
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24
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Dinakaran V, Mandape SN, Shuba K, Pratap S, Sakhare SS, Tabatabai MA, Smoot DT, Farmer-Dixon CM, Kesavalu LN, Adunyah SE, Southerland JH, Gangula PR. Identification of Specific Oral and Gut Pathogens in Full Thickness Colon of Colitis Patients: Implications for Colon Motility. Front Microbiol 2019; 9:3220. [PMID: 30666239 PMCID: PMC6330997 DOI: 10.3389/fmicb.2018.03220] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 12/11/2018] [Indexed: 12/31/2022] Open
Abstract
Impaired colon motility is one of the leading problems associated with inflammatory bowel disease (IBD). An expanding body of evidence supports the role of microbiome in normal gut function and in progression of IBD. The objective of this work is to determine whether diseased full thickness colon specimens, including the neuromuscular region (critical for colon motility function), contain specific oral and gut pathogens. In addition, we compared the differences in colon microbiome between Caucasians (CA) and African Americans (AA). Thirty-nine human full thickness colon (diseased colon and adjacent healthy colon) specimens were collected from Crohn's Colitis (CC) or Ulcerative Colitis (UC) patients while they underwent elective colon surgeries. We isolated and analyzed bacterial ribosomal RNA (rRNA) from colon specimens by amplicon sequencing of the 16S rRNA gene region. The microbiome proportions were quantified into Operational Taxonomic Units (OTUs) by analysis with Quantitative Insights Into Microbial ecology (QIIME) platform. Two hundred twenty-eight different bacterial species were identified by QIIME analysis. However, we could only decipher the species name of fifty-three bacteria. Our results show that proportion of non-detrimental bacteria in CC or UC colon samples were altered compared to adjacent healthy colon specimens. We further show, for the first time in full thickness colon specimens, that microbiome of CC and UC diseased specimens is dominated by putative oral pathogens belonging to the Phyla Firmicutes (Streptococcus, Staphylococcus, Peptostreptococcus), and Fusobacteria (Fusobacterium). In addition, we have identified patterns of differences in microbiome levels between CA and AA specimens with potential implications for health disparities research. Overall, our results suggest a significant association between oral and gut microbes in the modulation of colon motility in colitis patients.
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Affiliation(s)
- Vasudevan Dinakaran
- Department of ODS & Research, School of Dentistry, Meharry Medical College, Nashville, TN, United States
| | - Sammed N Mandape
- Bioinformatics Core, School of Graduate Studies/Research & School of Medicine, Meharry Medical College, Nashville, TN, United States
| | - Kristina Shuba
- Department of ODS & Research, School of Dentistry, Meharry Medical College, Nashville, TN, United States
| | - Siddharth Pratap
- Bioinformatics Core, School of Graduate Studies/Research & School of Medicine, Meharry Medical College, Nashville, TN, United States
| | - Shruti S Sakhare
- Bioinformatics Core, School of Graduate Studies/Research & School of Medicine, Meharry Medical College, Nashville, TN, United States
| | - Mohammad Ali Tabatabai
- Department of Public Health, School of Graduate Studies & Research, Meharry Medical College, Nashville, TN, United States
| | - Duane T Smoot
- Department of Internal Medicine, Division of Gastroenterology & Hepatology, Meharry Medical College, Nashville, TN, United States
| | - Cherae M Farmer-Dixon
- Department of ODS & Research, School of Dentistry, Meharry Medical College, Nashville, TN, United States
| | - Lakshmyya N Kesavalu
- Department of Periodontology, College of Dentistry, University of Florida, Gainesville, FL, United States
| | - Samuel Evans Adunyah
- Department of Biochemistry, Cancer Biology, Neuroscience & Pharmacology, Meharry Medical College, Nashville, TN, United States
| | - Janet Hayes Southerland
- Department of Nutrition Metabolism & Oral Surgery, University of Texas Medical Branch at Galveston, Galveston, TX, United States
| | - Pandu R Gangula
- Department of ODS & Research, School of Dentistry, Meharry Medical College, Nashville, TN, United States
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25
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El Mouzan MI, Winter HS, Assiri AA, Korolev KS, Al Sarkhy AA, Dowd SE, Al Mofarreh MA, Menon R. Microbiota profile in new-onset pediatric Crohn's disease: data from a non-Western population. Gut Pathog 2018; 10:49. [PMID: 30519287 PMCID: PMC6263052 DOI: 10.1186/s13099-018-0276-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 11/23/2018] [Indexed: 02/07/2023] Open
Abstract
Background The role of microbiota in Crohn’s disease (CD) is increasingly recognized. However, most of the reports are from Western populations. Considering the possible variation from other populations, the aim of this study was to describe the microbiota profile in children with CD in Saudi Arabia, a non-Western developing country population. Results Significantly more abundant genera in children with CD included Fusobacterium, Peptostreptococcus, Psychrobacter, and Acinetobacter; whereas the most significantly-depleted genera included Roseburia, Clostridium, Ruminococcus, Ruminoclostridium, Intestinibacter, Mitsuokella, Megasphaera, Streptococcus, Lactobacillus, Turicibacter, and Paludibacter. Alpha diversity was significantly reduced in stool (p = 0.03) but not in mucosa (p = 0.31). Beta diversity showed significant difference in community composition between control and CD samples (p = 0.03). Conclusion In this developing country, we found a pattern of microbiota in children with CD similar to Western literature, suggesting a role of recent dietary lifestyle changes in this population on microbiota structure.
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Affiliation(s)
- Mohammad I El Mouzan
- 1Pediatric IBD Research Group, Gastroenterology Division, Department of Pediatrics, King Saud University, P. O. Box 2925, Riyadh, 11461 Kingdom of Saudi Arabia
| | - Harland S Winter
- Mass General Hospital for Children, Pediatric IBD Program Boston, Boston, USA
| | - Assad A Assiri
- 3Department of Pediatrics, Gastroenterology Division, Prince Abdullah Bin Khalid Celiac Disease Research Chair, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Kirill S Korolev
- 4Physics Department and Bioinformatics Program, Boston University, Boston, USA
| | - Ahmad A Al Sarkhy
- 3Department of Pediatrics, Gastroenterology Division, Prince Abdullah Bin Khalid Celiac Disease Research Chair, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | | | | | - Rajita Menon
- 7Physics Department, Boston University, Boston, USA
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26
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Figliuolo VR, Coutinho-Silva R, Coutinho CMLM. Contribution of sulfate-reducing bacteria to homeostasis disruption during intestinal inflammation. Life Sci 2018; 215:145-151. [PMID: 30414430 DOI: 10.1016/j.lfs.2018.11.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 11/02/2018] [Accepted: 11/05/2018] [Indexed: 12/26/2022]
Abstract
Alteration in microbial populations and metabolism are key events associated with disruption of intestinal homeostasis and immune tolerance during intestinal inflammation. A substantial imbalance in bacterial populations in the intestine and their relationships with the host have been observed in patients with inflammatory bowel disease (IBD), believed to be part of an intricate mechanism of triggering and progression of intestinal inflammation. Because elevated numbers of sulfate-reducing bacteria (SRB) have been found in the intestines of patients with IBD, the study of their interaction with intestinal cells and their potential involvement in IBD has been the focus of investigation to better understand the intestinal pathology during IBD, as well as to find new ways to treat the disease. SRB not only directly interact with intestinal epithelial cells during intestinal inflammation but may also promote intestinal damage through generation of hydrogen sulfide at high levels. Herein we review the literature to discuss the various aspects of SRB interaction with host intestinal tissue, focusing on their interaction with intestinal epithelial and immune cells during intestinal inflammation.
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Affiliation(s)
- Vanessa Ribeiro Figliuolo
- Instituto de Biofísica Carlos Chagas Filho - IBCCF, Universidade Federal do Rio de Janeiro, RJ, Brazil; LITEB, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, RJ, Brazil; Department of Pediatrics, University of Arizona, Tucson, AZ, USA
| | - Robson Coutinho-Silva
- Instituto de Biofísica Carlos Chagas Filho - IBCCF, Universidade Federal do Rio de Janeiro, RJ, Brazil
| | - Claudia Mara Lara Melo Coutinho
- Departamento de Biologia Celular e Molecular, Instituto de Biologia, Universidade Federal Fluminense, Niteroi, RJ, Brazil; LITEB, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, RJ, Brazil.
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27
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Inflammation-independent TL1A-mediated intestinal fibrosis is dependent on the gut microbiome. Mucosal Immunol 2018; 11:1466-1476. [PMID: 29988118 PMCID: PMC6162160 DOI: 10.1038/s41385-018-0055-y] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 05/16/2018] [Accepted: 06/04/2018] [Indexed: 02/08/2023]
Abstract
Tumor necrosis factor-like cytokine 1A (TL1A, TNFSF15) is implicated in inflammatory bowel disease (IBD), modulating the location and severity of intestinal inflammation and fibrosis. TL1A expression is increased in inflamed gut mucosa and associated with fibrostenosing Crohn's disease. Tl1a-overexpression in mice lead to spontaneous ileitis, and exacerbated induced proximal colitis and fibrosis. IBD is associated with shifts in the gut microbiome, but the effect of differing microbial populations and their interaction with TL1A on fibrosis has not been investigated. We demonstrate that the pro-fibrotic and inflammatory phenotype resulting from Tl1a-overexpression is abrogated in the absence of resident microbiota. To evaluate if this is due to the absence of a unique bacterial population, as opposed to any bacteria per se, we gavaged germ-free (GF) wild-type and Tl1a-transgenic (Tl1a-Tg) mice with stool from specific pathogen free (SPF) mice and a healthy human donor (Hu). Reconstitution with SPF, but not Hu microbiota, resulted in increased intestinal collagen deposition and fibroblast activation in Tl1a-Tg mice. Notably, there was reduced fibroblast migration and activation under GF conditions compared to native conditions. We then identified several candidate organisms that correlated directly with increased fibrosis in reconstituted mice and showed that these organisms directly impact fibroblast function in vitro. Thus, Tl1a-mediated intestinal fibrosis and fibroblast activation are dependent on specific microbial populations.
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28
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Virgile C, Hauk P, Wu HC, Shang W, Tsao CY, Payne GF, Bentley WE. Engineering bacterial motility towards hydrogen-peroxide. PLoS One 2018; 13:e0196999. [PMID: 29750783 PMCID: PMC5947916 DOI: 10.1371/journal.pone.0196999] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 04/24/2018] [Indexed: 11/19/2022] Open
Abstract
Synthetic biologists construct innovative genetic/biological systems to treat environmental, energy, and health problems. Many systems employ rewired cells for non-native product synthesis, while a few have employed the rewired cells as 'smart' devices with programmable function. Building on the latter, we developed a genetic construct to control and direct bacterial motility towards hydrogen peroxide, one of the body's immune response signaling molecules. A motivation for this work is the creation of cells that can target and autonomously treat disease, the latter signaled by hydrogen peroxide release. Bacteria naturally move towards a variety of molecular cues (e.g., nutrients) in the process of chemotaxis. In this work, we engineered bacteria to recognize and move towards hydrogen peroxide, a non-native chemoattractant and potential toxin. Our system exploits oxyRS, the native oxidative stress regulon of E. coli. We first demonstrated H2O2-mediated upregulation motility regulator, CheZ. Using transwell assays, we showed a two-fold increase in net motility towards H2O2. Then, using a 2D cell tracking system, we quantified bacterial motility descriptors including velocity, % running (of tumble/run motions), and a dynamic net directionality towards the molecular cue. In CheZ mutants, we found that increased H2O2 concentration (0-200 μM) and induction time resulted in increased running speeds, ultimately reaching the native E. coli wild-type speed of ~22 μm/s with a ~45-65% ratio of running to tumbling. Finally, using a microfluidic device with stable H2O2 gradients, we characterized responses and the potential for "programmed" directionality towards H2O2 in quiescent fluids. Overall, the synthetic biology framework and tracking analysis in this work will provide a framework for investigating controlled motility of E. coli and other 'smart' probiotics for signal-directed treatment.
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Affiliation(s)
- Chelsea Virgile
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland, United States of America
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland, United States of America
| | - Pricila Hauk
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland, United States of America
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland, United States of America
| | - Hsuan-Chen Wu
- Department of Biochemical Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Wu Shang
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland, United States of America
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland, United States of America
| | - Chen-Yu Tsao
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland, United States of America
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland, United States of America
| | - Gregory F. Payne
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland, United States of America
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland, United States of America
| | - William E. Bentley
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland, United States of America
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland, United States of America
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29
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Savin Z, Kivity S, Yonath H, Yehuda S. Smoking and the intestinal microbiome. Arch Microbiol 2018; 200:677-684. [DOI: 10.1007/s00203-018-1506-2] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Revised: 03/07/2018] [Accepted: 03/23/2018] [Indexed: 12/21/2022]
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Hirano A, Umeno J, Okamoto Y, Shibata H, Ogura Y, Moriyama T, Torisu T, Fujioka S, Fuyuno Y, Kawarabayasi Y, Matsumoto T, Kitazono T, Esaki M. Comparison of the microbial community structure between inflamed and non-inflamed sites in patients with ulcerative colitis. J Gastroenterol Hepatol 2018; 33:1590-1597. [PMID: 29462845 DOI: 10.1111/jgh.14129] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 02/13/2018] [Accepted: 02/15/2018] [Indexed: 12/15/2022]
Abstract
BACKGROUND AND AIM The gut microbiota is suggested to play an important role in the pathogenesis of ulcerative colitis (UC). However, interindividual and spatial variations hamper the identification of UC-related changes. We thus investigated paired mucosa-associated microbiota obtained from both inflamed and non-inflamed sites of UC patients and corresponding sites of non-inflammatory bowel disease (IBD) controls. METHODS Mucosal biopsies of both inflamed and non-inflamed sites were obtained from 14 patients with active UC of the left-sided or proctitis type. Paired mucosal biopsies of the corresponding sites were obtained from 14 non-IBD controls. The microbial community structure was investigated using 16S ribosomal RNA gene sequences, followed by data analysis using qiime and LEfSe softwares. RESULTS Microbial alpha diversity in both inflamed and non-inflamed sites was significantly lower in UC patients compared with non-IBD controls. There were more microbes of the genus Cloacibacterium and the Tissierellaceae family, and there were less microbes of the genus Neisseria at the inflamed site when compared with the non-inflamed site in UC patients. Decreased abundance of the genera Prevotella, Eubacterium, Neisseria, Leptotrichia, Bilophila, Desulfovibrio, and Butyricimonas was evident at the inflamed site of UC patients compared with the corresponding site of non-IBD controls. Among these taxa, the genera Prevotella and Butyricimonas were also less abundant at the non-inflamed site of UC patients compared with the corresponding site in non-IBD controls. CONCLUSIONS Mucosal microbial dysbiosis occurs at both inflamed and non-inflamed sites in UC patients. The taxa showing altered abundance in UC patients might mediate colonic inflammation.
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Affiliation(s)
- Atsushi Hirano
- Department of Medicine and Clinical Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Junji Umeno
- Department of Medicine and Clinical Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yasuharu Okamoto
- Department of Medicine and Clinical Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hiroki Shibata
- Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Yoshitoshi Ogura
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tomohiko Moriyama
- Department of Medicine and Clinical Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Takehiro Torisu
- Department of Medicine and Clinical Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Shin Fujioka
- Department of Medicine and Clinical Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yuta Fuyuno
- Department of Medicine and Clinical Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yutaka Kawarabayasi
- National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
| | - Takayuki Matsumoto
- Division of Gastroenterology, Department of Internal Medicine, Iwate Medical University, Iwate, Japan
| | - Takanari Kitazono
- Department of Medicine and Clinical Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Motohiro Esaki
- Department of Medicine and Clinical Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
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31
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Omori M, Maeda S, Igarashi H, Ohno K, Sakai K, Yonezawa T, Horigome A, Odamaki T, Matsuki N. Fecal microbiome in dogs with inflammatory bowel disease and intestinal lymphoma. J Vet Med Sci 2017; 79:1840-1847. [PMID: 28993566 PMCID: PMC5709562 DOI: 10.1292/jvms.17-0045] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Although alteration of commensal microbiota is associated with chronic gastrointestinal (GI) diseases such as inflammatory bowel disease (IBD) in dogs, the microbiota composition in intestinal lymphoma, an important differential
diagnosis of canine IBD, has not been investigated. The objective of this study was to compare the fecal microbiota in dogs with IBD, dogs with intestinal lymphoma, and healthy dogs. Eight dogs with IBD, eight dogs with intestinal
lymphoma, and fifteen healthy dogs were included in the study. Fecal samples were analyzed by 16S rRNA gene next-generation sequencing. Rarefaction analysis failed to reveal any difference in bacterial diversity among healthy dogs
and diseased dogs. Based on PCoA plots of unweighted UniFrac distances, the bacterial composition in dogs with intestinal lymphoma was different from those observed in dogs with IBD and healthy dogs. When compared with healthy
dogs, intestinal lymphoma subjects showed significant increases in organisms belonging to the Eubacteriaceae family. The proportion of the family Paraprevotellaceae and the genus Porphyromonas was significantly
higher in dogs with IBD compared to healthy dogs. These observations suggest that dysbiosis is associated with intestinal lymphoma as well as IBD in dogs.
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Affiliation(s)
- Marie Omori
- Department of Veterinary Clinical Pathobiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Shingo Maeda
- Department of Veterinary Clinical Pathobiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Hirotaka Igarashi
- Department of Veterinary Internal Medicine, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Koichi Ohno
- Department of Veterinary Internal Medicine, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kosei Sakai
- Department of Veterinary Clinical Pathobiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Tomohiro Yonezawa
- Department of Veterinary Clinical Pathobiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Ayako Horigome
- Food Science and Technology Institute, Morinaga Milk Industry Co., Ltd., 5-1-83 Higashihara, Zama, Kanagawa 252-8583, Japan
| | - Toshitaka Odamaki
- Food Science and Technology Institute, Morinaga Milk Industry Co., Ltd., 5-1-83 Higashihara, Zama, Kanagawa 252-8583, Japan
| | - Naoaki Matsuki
- Department of Veterinary Clinical Pathobiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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The gut bacterium and pathobiont Bacteroides vulgatus activates NF-κB in a human gut epithelial cell line in a strain and growth phase dependent manner. Anaerobe 2017; 47:209-217. [DOI: 10.1016/j.anaerobe.2017.06.002] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 05/17/2017] [Accepted: 06/01/2017] [Indexed: 01/06/2023]
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Hart ML, Ericsson AC, Franklin CL. Differing Complex Microbiota Alter Disease Severity of the IL-10 -/- Mouse Model of Inflammatory Bowel Disease. Front Microbiol 2017; 8:792. [PMID: 28553262 PMCID: PMC5425584 DOI: 10.3389/fmicb.2017.00792] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 04/18/2017] [Indexed: 12/30/2022] Open
Abstract
It is estimated that 1.4 million people in the United States suffer from Inflammatory Bowel Disease (IBD), with an overall annual health care cost of more than $1.7 billion. Although the exact etiology of this disease remains unknown, research suggests that it is a multifactorial disease associated with aberrant gastrointestinal microbial populations (dysbiosis). The C57BL/6 and C3H/HeJBir mouse strains with targeted mutations in the IL-10 gene are commonly used models to study IBD. However, anecdotally, disease phenotype can vary in severity from lab to lab. Moreover, studies using germfree and monocolonized mice have suggested that gut microbiota (GM) are critical to disease induction in these models. With recent studies suggesting variation in naturally occurring GM composition and complexity among mouse producers, we hypothesized that differences in these naturally occurring complex GM profiles may modulate disease severity in the IL-10−/− mouse model. To test this hypothesis, we use a technique referred to as complex microbiota targeted rederivation (CMTR) to transfer genetically identical C57BL/6 IL-10−/− and C3H/HeJBir IL-10−/− embryos into surrogate CD-1 or C57BL/6 dams from different commercial producers with varying microbiota complexity and composition. We found that disease severity significantly and reproducibly differed among mice in both IL-10−/− strains, dependent on differing maternally inherited GM. Furthermore, disease severity was associated with alterations in relative abundance of several physiologically relevant bacterial species. These findings suggest that the composition of the resident GM is a primary determinant of disease severity in IBD and provide proof-of-concept that CMTR can be used to investigate the contribution of contemporary complex GM on disease phenotype and reproducibility.
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Affiliation(s)
- Marcia L Hart
- Comparative Medicine Program, Department of Veterinary Pathobiology, University of MissouriColumbia, MO, USA.,Department of Veterinary Pathobiology, University of MissouriColumbia, MO, USA
| | - Aaron C Ericsson
- Department of Veterinary Pathobiology, University of MissouriColumbia, MO, USA.,University of Missouri Metagenomics Center, University of MissouriColumbia, MO, USA.,Mutant Mouse Resource and Research Center, University of MissouriColumbia, MO, USA
| | - Craig L Franklin
- Comparative Medicine Program, Department of Veterinary Pathobiology, University of MissouriColumbia, MO, USA.,Department of Veterinary Pathobiology, University of MissouriColumbia, MO, USA.,University of Missouri Metagenomics Center, University of MissouriColumbia, MO, USA.,Mutant Mouse Resource and Research Center, University of MissouriColumbia, MO, USA
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Chiriac MT, Mahapatro M, Neurath MF, Becker C. The Microbiome in Visceral Medicine: Inflammatory Bowel Disease, Obesity and Beyond. Visc Med 2017; 33:153-162. [PMID: 28560232 DOI: 10.1159/000470892] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
It has become increasingly evident over the past two decades that the microbiota plays a nurturing role in the development of the immune system. This appears to be important since the amplitude of immune responses has a crucial regulatory function in homeostasis and the prevention of unwanted inflammation. Hence, a malfunctioning gut flora has been shown to play a key role in visceral medicine. Strong evidence demonstrates for example that intestinal inflammation can develop as a result of a dysregulated microbiota, deficient antimicrobial responses, and aberrant bacterial translocation into the bowel wall. In healthy individuals, the bacterial translocation is blocked by a single layer of highly specialized intestinal epithelial cells which forms a strong barrier that lines the gut wall. This structure is responsible for an efficient absorption of nutrients while keeping the luminal flora at bay. In susceptible individuals, for yet incompletely understood reasons, either defective epithelial barrier function or dysregulated microbial composition or microbial pathogens drive intestinal inflammation. Many therapeutic strategies focusing on the modulation of the microbiota have been proposed recently but future research including prospective human studies and gnotobiotic mouse models are still needed to evaluate the contribution and potential therapeutic value of individual bacteria to human health.
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Affiliation(s)
- Mircea T Chiriac
- Department of Medicine 1, University Hospital Erlangen, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Mousumi Mahapatro
- Department of Medicine 1, University Hospital Erlangen, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Markus F Neurath
- Department of Medicine 1, University Hospital Erlangen, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Christoph Becker
- Department of Medicine 1, University Hospital Erlangen, University of Erlangen-Nuremberg, Erlangen, Germany
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Mayers MD, Moon C, Stupp GS, Su AI, Wolan DW. Quantitative Metaproteomics and Activity-Based Probe Enrichment Reveals Significant Alterations in Protein Expression from a Mouse Model of Inflammatory Bowel Disease. J Proteome Res 2017; 16:1014-1026. [PMID: 28052195 DOI: 10.1021/acs.jproteome.6b00938] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Tandem mass spectrometry based shotgun proteomics of distal gut microbiomes is exceedingly difficult due to the inherent complexity and taxonomic diversity of the samples. We introduce two new methodologies to improve metaproteomic studies of microbiome samples. These methods include the stable isotope labeling in mammals to permit protein quantitation across two mouse cohorts as well as the application of activity-based probes to enrich and analyze both host and microbial proteins with specific functionalities. We used these technologies to study the microbiota from the adoptive T cell transfer mouse model of inflammatory bowel disease (IBD) and compare these samples to an isogenic control, thereby limiting genetic and environmental variables that influence microbiome composition. The data generated highlight quantitative alterations in both host and microbial proteins due to intestinal inflammation and corroborates the observed phylogenetic changes in bacteria that accompany IBD in humans and mouse models. The combination of isotope labeling with shotgun proteomics resulted in the total identification of 4434 protein clusters expressed in the microbial proteomic environment, 276 of which demonstrated differential abundance between control and IBD mice. Notably, application of a novel cysteine-reactive probe uncovered several microbial proteases and hydrolases overrepresented in the IBD mice. Implementation of these methods demonstrated that substantial insights into the identity and dysregulation of host and microbial proteins altered in IBD can be accomplished and can be used in the interrogation of other microbiome-related diseases.
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Affiliation(s)
- Michael D Mayers
- Department of Molecular and Experimental Medicine, ‡Department of Integrative Structural and Computational Biology, and §Department of Chemical Physiology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Clara Moon
- Department of Molecular and Experimental Medicine, ‡Department of Integrative Structural and Computational Biology, and §Department of Chemical Physiology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Gregory S Stupp
- Department of Molecular and Experimental Medicine, ‡Department of Integrative Structural and Computational Biology, and §Department of Chemical Physiology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Andrew I Su
- Department of Molecular and Experimental Medicine, ‡Department of Integrative Structural and Computational Biology, and §Department of Chemical Physiology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Dennis W Wolan
- Department of Molecular and Experimental Medicine, ‡Department of Integrative Structural and Computational Biology, and §Department of Chemical Physiology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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Vrakas S, Mountzouris KC, Michalopoulos G, Karamanolis G, Papatheodoridis G, Tzathas C, Gazouli M. Intestinal Bacteria Composition and Translocation of Bacteria in Inflammatory Bowel Disease. PLoS One 2017; 12:e0170034. [PMID: 28099495 PMCID: PMC5242456 DOI: 10.1371/journal.pone.0170034] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 12/27/2016] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Live commensal intestinal bacteria are present in the peripheral blood where they can induce inflammation. OBJECTIVE To evaluate the intestinal bacteria composition and translocation of bacteria in IBD. METHODS Both blood and tissue biopsy samples were collected from adult patients with active/inactive Crohn's disease (CD), active/inactive ulcerative colitis (UC) and healthy individuals. Most of the patients were newly diagnosed and none of them received antibiotics. Using a reverse transcription-quantitative real-time PCR (RT-qPCR) method, we determined the composition of microbiota. NOD2/CARD15 genotyping was also studied. RESULTS Total bacterial DNA concentration was increased in tissue and blood samples of IBD patients compared to healthy controls. Furthermore, the active IBD cases had higher total bacterial DNA concentration levels compared to the inactive cases. Three species characterized dysbiosis in IBD, namely an increase of Bacteroides spp in active and inactive IBD samples, and a decrease in Clostridium leptum group (IV), and Faecalibacterium prausnitzi in both active and inactive IBD patients. No significant association between bacterial translocation and NOD2/CARD15 mutations was found. CONCLUSIONS The composition of the microbiota in IBD patients differs from that of healthy controls. The high rate of bacterial DNA in the blood samples indicates translocation in inflammatory bowel disease.
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Affiliation(s)
- Spyros Vrakas
- Gastroenterology Department, Tzaneion General Hospital, Piraeus, Greece
| | | | | | - George Karamanolis
- Gastroenterology Unit, 2nd University Surgical Department Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - George Papatheodoridis
- Department of Gastroenterology, Medical School, National and Kapodistrian University of Athens Laiko Hospital of Athens, Athens, Greece
| | | | - Maria Gazouli
- Department of Basic Medical Sciences, Laboratory of Biology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
- * E-mail:
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Shawki A, McCole DF. Mechanisms of Intestinal Epithelial Barrier Dysfunction by Adherent-Invasive Escherichia coli. Cell Mol Gastroenterol Hepatol 2017; 3:41-50. [PMID: 28174756 PMCID: PMC5247418 DOI: 10.1016/j.jcmgh.2016.10.004] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 10/14/2016] [Indexed: 12/12/2022]
Abstract
Pathobiont expansion, such as that of adherent-invasive Escherichia coli (AIEC), is an emerging factor associated with inflammatory bowel disease. The intestinal epithelial barrier is the first line of defense against these pathogens. Inflammation plays a critical role in altering the epithelial barrier and is a major factor involved in promoting the expansion and pathogenesis of AIEC. AIEC in turn can exacerbate intestinal epithelial barrier dysfunction by targeting multiple elements of the barrier. One critical element of the epithelial barrier is the tight junction. Increasing evidence suggests that AIEC may selectively target protein components of tight junctions, leading to increased barrier permeability. This may represent one mechanism by which AIEC could contribute to the development of inflammatory bowel disease. This review article discusses potential mechanisms by which AIEC can disrupt epithelial tight junction function and intestinal barrier function.
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Key Words
- AIEC, adherent-invasive Escherichia coli
- AJ, adherens junction
- AJC, apical junctional complex
- BP, bacterial peptidoglycans
- CD, Crohn’s disease
- CEACAM6, carcinoembryonic antigen–related cell-adhesion molecule
- IBD, inflammatory bowel disease
- IEC, intestinal epithelial cell
- IFN, interferon
- IL, interleukin
- Inflammatory Bowel Disease
- Intestinal Permeability
- JAM-A, junctional adhesion molecule-A
- LPF, long polar fimbriae
- MLC, myosin light chain
- MLCK, myosin light chain kinase
- NF-κB, nuclear factor-κB
- NOD2, nucleotide-binding oligomerization domain 2
- PDZ, PSD95-DlgA-zonula occludens-1 homology domain
- TJ, tight junction
- TNF, tumor necrosis factor
- Tight Junctions
- UC, ulcerative colitis
- ZO, zonula occludens
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Affiliation(s)
| | - Declan F. McCole
- Division of Biomedical Sciences, University of California Riverside, Riverside, California
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38
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Fecal Microbiota and Metabolome in a Mouse Model of Spontaneous Chronic Colitis: Relevance to Human Inflammatory Bowel Disease. Inflamm Bowel Dis 2016; 22:2767-2787. [PMID: 27824648 DOI: 10.1097/mib.0000000000000970] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND Dysbiosis of the gut microbiota may be involved in the pathogenesis of inflammatory bowel disease (IBD). However, the mechanisms underlying the role of the intestinal microbiome and metabolome in IBD onset and its alteration during active treatment and recovery remain unknown. Animal models of chronic intestinal inflammation with similar microbial and metabolomic profiles would enable investigation of these mechanisms and development of more effective treatments. Recently, the Winnie mouse model of colitis closely representing the clinical symptoms and characteristics of human IBD has been developed. In this study, we have analyzed fecal microbial and metabolomic profiles in Winnie mice and discussed their relevance to human IBD. METHODS The 16S rRNA gene was sequenced from fecal DNA of Winnie and C57BL/6 mice to define operational taxonomic units at ≥97% similarity threshold. Metabolomic profiling of the same fecal samples was performed by gas chromatography-mass spectrometry. RESULTS Composition of the dominant microbiota was disturbed, and prominent differences were evident at all levels of the intestinal microbiome in fecal samples from Winnie mice, similar to observations in patients with IBD. Metabolomic profiling revealed that chronic colitis in Winnie mice upregulated production of metabolites and altered several metabolic pathways, mostly affecting amino acid synthesis and breakdown of monosaccharides to short chain fatty acids. CONCLUSIONS Significant dysbiosis in the Winnie mouse gut replicates many changes observed in patients with IBD. These results provide justification for the suitability of this model to investigate mechanisms underlying the role of intestinal microbiota and metabolome in the pathophysiology of IBD.
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He Y, Wen Q, Yao F, Xu D, Huang Y, Wang J. Gut-lung axis: The microbial contributions and clinical implications. Crit Rev Microbiol 2016; 43:81-95. [PMID: 27781554 DOI: 10.1080/1040841x.2016.1176988] [Citation(s) in RCA: 157] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Gut microbiota interacts with host immune system in ways that influence the development of disease. Advances in respiratory immune system also broaden our knowledge of the interaction between host and microbiome in the lung. Increasing evidence indicated the intimate relationship between the gastrointestinal tract and respiratory tract. Exacerbations of chronic gut and lung disease have been shown to share key conceptual features with the disorder and dysregulation of the microbial ecosystem. In this review, we discuss the impact of gut and lung microbiota on disease exacerbation and progression, and the recent understanding of the immunological link between the gut and the lung, the gut-lung axis.
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Affiliation(s)
- Yang He
- a Department of Cancer Center, Union Hospital , Tongji Medical College, Huazhong University of Science and Technology , Wuhan , China
| | - Qu Wen
- a Department of Cancer Center, Union Hospital , Tongji Medical College, Huazhong University of Science and Technology , Wuhan , China
| | - Fangfang Yao
- a Department of Cancer Center, Union Hospital , Tongji Medical College, Huazhong University of Science and Technology , Wuhan , China
| | - Dong Xu
- b Department of Infectious Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan , China
| | - Yuancheng Huang
- b Department of Infectious Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan , China
| | - Junshuai Wang
- c Department of Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan , China
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Abstract
The relevance of biogeography to the distal gut microbiota has been investigated in both health and inflammatory bowel disease (IBD), however multiple factors, including sample type and methodology, microbiota characterization and interpersonal variability make the construction of a core model of colonic biogeography challenging. In addition, how phylogenetic classification relates to immunogenicity and whether consistent alterations in the microbiota are associated with ulcerative colitis (UC) remain open questions. This addendum seeks to review the human colonic microbiota in health and UC as currently understood, in the broader context of the human microbiome.
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Affiliation(s)
- Aonghus Lavelle
- School of Medicine and Medical Science,
University College Dublin, Dublin, Ireland,Centre for Colorectal Disease, St.
Vincent's University Hospital, Dublin,
Ireland
| | - Grainne Lennon
- School of Medicine and Medical Science,
University College Dublin, Dublin, Ireland,Centre for Colorectal Disease, St.
Vincent's University Hospital, Dublin,
Ireland
| | - Desmond C. Winter
- School of Medicine and Medical Science,
University College Dublin, Dublin, Ireland,Centre for Colorectal Disease, St.
Vincent's University Hospital, Dublin,
Ireland
| | - P. Ronan O'Connell
- School of Medicine and Medical Science,
University College Dublin, Dublin, Ireland,Centre for Colorectal Disease, St.
Vincent's University Hospital, Dublin,
Ireland
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41
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Abegunde AT, Muhammad BH, Bhatti O, Ali T. Environmental risk factors for inflammatory bowel diseases: Evidence based literature review. World J Gastroenterol 2016; 22:6296-6317. [PMID: 27468219 PMCID: PMC4945988 DOI: 10.3748/wjg.v22.i27.6296] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 05/19/2016] [Accepted: 06/28/2016] [Indexed: 02/06/2023] Open
Abstract
AIM: Advances in genetics and immunology have contributed to the current understanding of the pathogenesis of inflammatory bowel diseases (IBD).
METHODS: The current opinion on the pathogenesis of IBD suggests that genetically susceptible individuals develop intolerance to dysregulated gut microflora (dysbiosis) and chronic inflammation develops as a result of environmental insults. Environmental exposures are innumerable with varying effects during the life course of individuals with IBD. Studying the relationship between environmental factors and IBD may provide the missing link to increasing our understanding of the etiology and increased incidence of IBD in recent years with implications for prevention, diagnosis, and treatment. Environmental factors are heterogeneous and genetic predisposition, immune dysregulation, or dysbiosis do not lead to the development of IBD in isolation.
RESULTS: Current challenges in the study of environmental factors and IBD are how to effectively translate promising results from experimental studies to humans in order to develop models that incorporate the complex interactions between the environment, genetics, immunology, and gut microbiota, and limited high quality interventional studies assessing the effect of modifying environmental factors on the natural history and patient outcomes in IBD.
CONCLUSION: This article critically reviews the current evidence on environmental risk factors for IBD and proposes directions for future research.
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Abstract
The intestinal microbiota has important metabolic and host-protective functions. Conversely to these beneficial functions, the intestinal microbiota is thought to play a central role in the etiopathogenesis of inflammatory bowel disease (IBD; Crohn's disease and ulcerative colitis), a chronic inflammation of the gut mucosa. Genetic screens and studies in experimental mouse models have clearly demonstrated that IBD can develop due to excessive translocation of bacteria into the bowel wall or dysregulated handling of bacteria in genetically susceptible hosts. In healthy individuals, the microbiota is efficiently separated from the mucosal immune system of the gut by the gut barrier, a single layer of highly specialized epithelial cells, some of which are equipped with innate immune functions to prevent or control access of bacterial antigens to the mucosal immune cells. It is currently unclear whether the composition of the microbial flora or individual bacterial strains or pathogens induces or supports the pathogenesis of IBD. Further research will be necessary to carefully dissect the contribution of individual bacterial species to this disease and to ascertain whether specific modulation of the intestinal microbiome may represent a valuable further option for future therapeutic strategies.
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Affiliation(s)
- Christoph Becker
- Christoph Becker, PhD, is associated professor, Markus F. Neurath, MD, is director, and Stefan Wirtz, PhD, is senior scientist at the Department of Medicine 1 at the Friedrich-Alexander University Erlangen-Nuremberg in Erlangen, Germany
| | - Markus F Neurath
- Christoph Becker, PhD, is associated professor, Markus F. Neurath, MD, is director, and Stefan Wirtz, PhD, is senior scientist at the Department of Medicine 1 at the Friedrich-Alexander University Erlangen-Nuremberg in Erlangen, Germany
| | - Stefan Wirtz
- Christoph Becker, PhD, is associated professor, Markus F. Neurath, MD, is director, and Stefan Wirtz, PhD, is senior scientist at the Department of Medicine 1 at the Friedrich-Alexander University Erlangen-Nuremberg in Erlangen, Germany
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43
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RETRACTED ARTICLE: Mouse models of intestinal inflammation and cancer. Arch Toxicol 2016; 90:2109-2130. [DOI: 10.1007/s00204-016-1747-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 06/01/2016] [Indexed: 12/19/2022]
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Shah R, Cope JL, Nagy-Szakal D, Dowd S, Versalovic J, Hollister EB, Kellermayer R. Composition and function of the pediatric colonic mucosal microbiome in untreated patients with ulcerative colitis. Gut Microbes 2016; 7:384-96. [PMID: 27217061 PMCID: PMC5046168 DOI: 10.1080/19490976.2016.1190073] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Inflammatory bowel diseases (IBD) are chronic intestinal inflammatory disorders characterized by a complex disruption of the physiologic interaction between the host immune system and intestinal microbes precipitated by environmental factors. Numerous observations indicate the altered composition and function of the intestinal microbiome of patients with ulcerative colitis (UC), a subtype of IBD. The accuracy of these results may be limited by confounding factors, such as concurrent medication use. To address these limitations, we examined the colonic mucosal microbiome of pediatric patients with UC prior to initiating treatment. Based on bacterial 16S rRNA gene sequencing, we identified a significant decrease in the phylum Verrucomicrobia in patients with UC. At the genus level, we observed a significant decrease in the short chain fatty acid producer Roseburia. Despite these compositional changes, we did not identify inferred gene content differences between the UC and control groups. To determine if microbial taxa may be associated with clinical outcomes, we retrospectively assessed the clinical course of the UC patients. Despite similar metrics of OTU richness and diversity, multiple OTU differences were observed between patients who responded to therapy and those who did not. Our observations regarding the mucosal microbiome and the associations with differential clinical outcomes support the contributions of gut microbes to disease onset and modulation.
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Affiliation(s)
- Rajesh Shah
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Julia L. Cope
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA,Texas Children's Microbiome Center, Texas Children's Hospital, Houston, TX, USA
| | - Dorottya Nagy-Szakal
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA,USDA/ARS Children's Nutrition Research Center, Texas Children's Hospital, Houston, TX, USA
| | - Scot Dowd
- Molecular Research (MR DNA), Shallowater, TX, USA
| | - James Versalovic
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA,Texas Children's Microbiome Center, Texas Children's Hospital, Houston, TX, USA
| | - Emily B. Hollister
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA,Texas Children's Microbiome Center, Texas Children's Hospital, Houston, TX, USA
| | - Richard Kellermayer
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA,USDA/ARS Children's Nutrition Research Center, Texas Children's Hospital, Houston, TX, USA
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Munyaka PM, Rabbi MF, Khafipour E, Ghia JE. Acute dextran sulfate sodium (DSS)-induced colitis promotes gut microbial dysbiosis in mice. J Basic Microbiol 2016; 56:986-98. [PMID: 27112251 DOI: 10.1002/jobm.201500726] [Citation(s) in RCA: 171] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 03/18/2016] [Indexed: 12/20/2022]
Abstract
UNLABELLED The most widely used and characterized experimental model of ulcerative colitis (UC) is the epithelial erosion, dextran sulfate sodium (DSS)-induced colitis, which is developed by administration of DSS in drinking water. We investigated fecal and colonic mucosa microbial composition and functional changes in mice treated with DSS. C57Bl/6 mice received 5% DSS in drinking water for 5 days. Inflammation was evaluated clinically and by analysis of colonic tissue cytokine levels and C-reactive protein (CRP) in the serum. Colonic mucosa and fecal samples were used for DNA extraction and the V4 region of bacterial 16S rRNA gene was subjected to MiSeq Illumina sequencing. Alpha- and beta-diversities, and compositional differences at phylum and genus levels were determined, and bacterial functional pathways were predicted. DSS increased disease severity, serum CRP and cytokines IL-1β and IL-6, but decreased bacterial species richness, and shifted bacterial community composition. Bacteroides, Turicibacter, Escherichia, Clostridium, Enterobacteriaceae, Clostridiaceae, Bacteroidaceae, Bacteroidales, among other taxa were associated with DSS treatment in fecal and colonic samples. Also, DSS altered microbial functional pathways in both colonic mucosa and fecal samples. CONCLUSIONS The development of colitis in DSS model was accompanied with reduced microbial diversity and dysbiosis of gut microbiota at lower taxonomical levels.
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Affiliation(s)
- Peris Mumbi Munyaka
- Department of Immunology, University of Manitoba, Winnipeg, Manitoba, Canada.,Department of Animal Science, University of Manitoba, Winnipeg, Manitoba, Canada
| | | | - Ehsan Khafipour
- Department of Animal Science, University of Manitoba, Winnipeg, Manitoba, Canada. .,Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada.
| | - Jean-Eric Ghia
- Department of Immunology, University of Manitoba, Winnipeg, Manitoba, Canada. .,Department of Internal Medicine, Section of Gastroenterology, University of Manitoba, Winnipeg, Manitoba, Canada. .,Inflammatory Bowel Disease Clinical & Research Centre, University of Manitoba, Winnipeg, Manitoba, Canada.
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The Roles of Inflammation, Nutrient Availability and the Commensal Microbiota in Enteric Pathogen Infection. Microbiol Spectr 2016; 3. [PMID: 26185088 DOI: 10.1128/microbiolspec.mbp-0008-2014] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The healthy human intestine is colonized by as many as 1014 bacteria belonging to more than 500 different species forming a microbial ecosystem of unsurpassed diversity, termed the microbiota. The microbiota's various bacterial members engage in a physiological network of cooperation and competition within several layers of complexity. Within the last 10 years, technological progress in the field of next-generation sequencing technologies has tremendously advanced our understanding of the wide variety of physiological and pathological processes that are influenced by the commensal microbiota (1, 2). An increasing number of human disease conditions, such as inflammatory bowel diseases (IBD), type 2 diabetes, obesity, allergies and colorectal cancer are linked with altered microbiota composition (3). Moreover, a clearer picture is emerging of the composition of the human microbiota in healthy individuals, its variability over time and between different persons and how the microbiota is shaped by environmental factors (i.e., diet) and the host's genetic background (4). A general feature of a normal, healthy gut microbiota can generate conditions in the gut that disfavor colonization of enteric pathogens. This is termed colonization-resistance (CR). Upon disturbance of the microbiota, CR can be transiently disrupted, and pathogens can gain the opportunity to grow to high levels. This disruption can be caused by exposure to antibiotics (5, 6), changes in diet (7, 8), application of probiotics and drugs (9), and a variety of diseases (3). Breakdown of CR can boost colonization by intrinsic pathogens or increase susceptibility to infections (10). One consequence of pathogen expansion is the triggering of inflammatory host responses and pathogen-mediated disease. Interestingly, human enteric pathogens are part of a small group of bacterial families that belong to the Proteobacteria: the Enterobacteriaceae (E. coli, Yersinia spp., Salmonella spp., Shigella spp.), the Vibrionaceae (Vibrio cholerae) and the Campylobacteriaceae (Campylobacter spp.). In general, members of these families (be it commensals or pathogens) only constitute a minority of the intestinal microbiota. However, proteobacterial "blooms" are a characteristic trait of an abnormal microbiota such as in the course of antibiotic therapy, dietary changes or inflammation (11). It has become clear that the gut microbiota not only plays a major role in priming and regulating mucosal and systemic immunity, but that the immune system also contributes to host control over microbiota composition. These two ways of mutual communication between the microbiota and the immune system were coined as "outside-in" and "inside-out," respectively (12). The significance of those interactions for human health is particularly evident in Crohn's disease (CD) and Ulcerative Colitis (UC). The symptoms of these recurrent, chronic types of gut inflammation are caused by an excessive immune response against one's own commensal microbiota (13). It is assumed that deregulated immune responses can be caused by a genetic predisposition, leading to, for example, the impairment of intestinal barrier function or disruption of mucosal T-cell homeostasis. In CD or UC patients, an abnormally composed microbiota, referred to as "dysbiosis," is commonly observed (discussed later). This is often characterized by an increased relative abundance of facultative anaerobic bacteria (e.g., Enterobacteriaeceae, Bacilli) and, at the same time, depletion of obligate anaerobic bacteria of the classes Bacteroidia and Clostridia. So far, it is unclear whether dysbiosis is a cause or a consequence of inflammatory bowel disease (IBD). In fact, both scenarios are equally conceivable. Recent work suggests that inflammatory immune responses in the gut (both IBD and pathogen-induced) can alter the gut luminal milieu in a way that favors dysbiosis (14). In this chapter, I present a survey on our current state of understanding of the characteristics and mechanisms underlying gut inflammation-associated dysbiosis. The role of dysbiosis in enteric infections and human IBD is discussed. In addition, I will focus on competition of enteric pathogens and the gut microbiota in the inflamed gut and the role of dysbiotic microbiota alterations (e.g., "Enterobacterial blooms" (11)) for the evolution of pathogenicity.
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Intestinal barrier dysfunction: implications for chronic inflammatory conditions of the bowel. Nutr Res Rev 2016; 29:40-59. [DOI: 10.1017/s0954422416000019] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
AbstractThe intestinal epithelium of adult humans acts as a differentially permeable barrier that separates the potentially harmful contents of the lumen from the underlying tissues. Any dysfunction of this boundary layer that disturbs the homeostatic equilibrium between the internal and external environments may initiate and sustain a biochemical cascade that results in inflammation of the intestine. Key to such dysfunction are genetic, microbial and other environmental factors that, singularly or in combination, result in chronic inflammation that is symptomatic of inflammatory bowel disease (IBD). The aim of the present review is to assess the scientific evidence to support the hypothesis that defective transepithelial transport mechanisms and the heightened absorption of intact antigenic proinflammatory oligopeptides are important contributing factors in the pathogenesis of IBD.
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Kabeerdoss J, Jayakanthan P, Pugazhendhi S, Ramakrishna BS. Alterations of mucosal microbiota in the colon of patients with inflammatory bowel disease revealed by real time polymerase chain reaction amplification of 16S ribosomal ribonucleic acid. Indian J Med Res 2016; 142:23-32. [PMID: 26261163 PMCID: PMC4557246 DOI: 10.4103/0971-5916.162091] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Background & objectives: Alterations in microbial communities closely associated with the intestinal mucosa are likely to be important in the pathogenesis of inflammatory bowel disease (IBD). We examined the abundance of specific microbial populations in colonic mucosa of patients with ulcerative colitis (UC), Crohn's disease (CD) and controls using reverse transcription quantitative polymerase chain reaction (RT-qPCR) amplification of 16S ribosomal ribonucleic acid (16S rRNA). Methods: RNA was extracted from colonic mucosal biopsies of patients with UC (32), CD (28) and patients undergoing screening colonoscopy (controls), and subjected to RT-qPCR using primers targeted at 16S rRNA sequences specific to selected microbial populations. Results: Bacteroides-Prevotella-Porphyromonas group and Enterobacteriaceae were the most abundant mucosal microbiota. Bacteroides and Lactobacillus abundance was greater in UC patients compared with controls or CD. Escherichia coli abundance was increased in UC compared with controls. Clostridium coccoides group and C. leptum group abundances were reduced in CD compared with controls. Microbial population did not differ between diseased and adjacent normal mucosa, or between untreated patients and those already on medical treatment. The Firmicutes to Bacteroidetes ratio was significantly decreased in both UC and CD compared with controls, indicative of a dysbiosis in both conditions. Interpretation & conclusions: Dysbiosis appears to be a primary feature in both CD and UC. Microbiome-directed interventions are likely to be appropriate in therapy of IBD.
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Identification of Commensal Species Positively Correlated with Early Stress Responses to a Compromised Mucus Barrier. Inflamm Bowel Dis 2016; 22:826-40. [PMID: 26926038 DOI: 10.1097/mib.0000000000000688] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Our aims were (1) to correlate changes in the microbiota to intestinal gene expression before and during the development of colitis in Muc2 mice and (2) to investigate whether the heterozygote Muc2 mouse would reveal host markers of gut barrier stress. METHODS Colon histology, transcriptomics, and microbiota profiling of faecal samples was performed on wild type, Muc2, and Muc2 mice at 2, 4, and 8 weeks of age. RESULTS Muc2 mice develop colitis in proximal colon after weaning, resulting in inflammatory and adaptive immune responses, and expression of genes associated with human inflammatory bowel disease. Muc2 mice do not develop colitis, but produce a thinner mucus layer. The transcriptome of Muc2 mice revealed differential expression of genes participating in mucosal stress responses and exacerbation of a transient inflammatory state around the time of weaning. Young wild type and Muc2 mice have a more constrained group of bacteria as compared with the Muc2 mice, but at 8 weeks the microbiota composition is more similar in all mice. At all ages, microbiota composition discriminated the groups of mice according to their genotype. Specific bacterial clusters correlated with altered gene expression responses to stress and bacteria, before colitis development, including colitogenic members of the genus Bacteroides. CONCLUSIONS The abundance of Bacteroides pathobionts increased before histological signs of pathology suggesting they may play a role in triggering the development of colitis. The Muc2 mouse produces a thinner mucus layer and can be used to study mucus barrier stress in the absence of colitis.
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Forbes JD, Van Domselaar G, Bernstein CN. Microbiome Survey of the Inflamed and Noninflamed Gut at Different Compartments Within the Gastrointestinal Tract of Inflammatory Bowel Disease Patients. Inflamm Bowel Dis 2016; 22:817-25. [PMID: 26937623 DOI: 10.1097/mib.0000000000000684] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BACKGROUND We aimed to contrast the mucosal microbiota in Crohn's disease (CD) and ulcerative colitis (UC). METHODS We assessed the concept of localized dysbiosis by comparing the bacterial communities of inflamed and noninflamed mucosa of patients with inflammatory bowel disease (IBD) and by analysis of the microbiota composition at distinct gut compartments (ileum, cecum, mid-colon, and rectum). We performed 16S rDNA sequencing to analyze population structures. Quality control and operational taxonomic unit classification of reads were performed using mothur with statistical analyses executed in the R package, phyloseq. RESULTS There was no variation in any phyla or genera comparing inflamed to noninflamed mucosa within CD (or UC) or when comparing different gut compartments within CD (or UC). There were differences between the inflamed and noninflamed mucosa between CD and UC: analysis of the inflamed IBD gut at the phylum level indicated that Bacteroidetes (P = 0.002) and Fusobacteria (P < 0.05) were detected more frequently in inflamed CD mucosa than in inflamed UC mucosa. Conversely, Proteobacteria and Firmicutes (P < 0.05) were more frequently observed in the inflamed UC mucosa. At the genus level, the abundance of Faecalibacterium (P ≤ 0.05), Bacteroides (P = 0.003), and Pseudomonas (P < 0.001) were significantly different between the inflamed CD and UC and the abundance of 13 genera were significantly different within the noninflamed mucosa. The noninflamed UC mucosa was the most different from non-IBD mucosa. CONCLUSIONS Dramatic shifts of microbial communities were not observed between the noninflamed and inflamed mucosa within CD (or UC) although both the inflamed (and noninflamed) mucosa was different between CD and UC.
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Affiliation(s)
- Jessica D Forbes
- *Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Canada; †Bioinformatics Core, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada; and ‡Department of Internal Medicine, IBD Clinical and Research Centre, University of Manitoba, Canada
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