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Estevinho MM, Cabeda J, Santiago M, Machado E, Silva R, Duro M, Pita I, Morais R, Macedo G, Bull TJ, Magro F, Sarmento A. Viable Mycobacterium avium subsp. paratuberculosis Colonizes Peripheral Blood of Inflammatory Bowel Disease Patients. Microorganisms 2023; 11:1520. [PMID: 37375022 DOI: 10.3390/microorganisms11061520] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/31/2023] [Accepted: 06/04/2023] [Indexed: 06/29/2023] Open
Abstract
Pathobionts, particularly Mycobacterium avium subsp. paratuberculosis (MAP) and Escherichia coli isolates with adherence/invasive ability (AIEC) have been associated with inflammatory bowel disease (IBD), particularly Crohn's disease (CD). This study aimed to evaluate the frequency of viable MAP and AIEC in a cohort of IBD patients. As such, MAP and E. coli cultures were established from faecal and blood samples (with a total n = 62 for each) of patients with CD (n = 18), ulcerative colitis (UC, n = 15), or liver cirrhosis (n = 7), as well as from healthy controls (HC, n = 22). Presumptive positive cultures were tested by polymerase chain reaction (PCR), for a positive confirmation of MAP or E. coli identity. E. coli-confirmed isolates were then tested for AIEC identity using adherence and invasion assays in the epithelial cell line of Caco-2 and survival and replication assays in the macrophage cell line of J774. MAP sub-culture and genome sequencing were also performed. MAP was more frequently cultured from the blood and faecal samples of patients with CD and cirrhosis. E. coli presumptive colonies were isolated from the faecal samples of most individuals, in contrast to what was registered for the blood samples. Additionally, from the confirmed E. coli isolates, only three had an AIEC-like phenotype (i.e., one CD patient and two UC patients). This study confirmed the association between MAP and CD; however, it did not find a strong association between the presence of AIEC and CD. It may be hypothesized that the presence of viable MAP in the bloodstream of CD patients contributes to disease reactivation.
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Affiliation(s)
- Maria Manuela Estevinho
- Department of Gastroenterology, Vila Nova de Gaia/Espinho Hospital Center, 4434-502 Vila Nova de Gaia, Portugal
- Department of Biomedicine, Unit of Pharmacology and Therapeutics, Faculty of Medicine, University of Porto, 4050-313 Porto, Portugal
| | - José Cabeda
- FP-I3ID, Universidade Fernando Pessoa, 4200-150 Porto, Portugal
- Escola Superior de Saúde Fernando Pessoa, 4200-253 Porto, Portugal
- Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR, CIMAR), 4450-208 Matosinhos, Portugal
| | - Mafalda Santiago
- Department of Biomedicine, Unit of Pharmacology and Therapeutics, Faculty of Medicine, University of Porto, 4050-313 Porto, Portugal
| | - Elisabete Machado
- FP-I3ID, Universidade Fernando Pessoa, 4200-150 Porto, Portugal
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, REQUIMTE, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- Faculdade de Ciências da Saúde, Universidade Fernando Pessoa, 4200-150 Porto, Portugal
| | - Ricardo Silva
- FP-I3ID, Universidade Fernando Pessoa, 4200-150 Porto, Portugal
- Escola Superior de Saúde Fernando Pessoa, 4200-253 Porto, Portugal
| | - Mary Duro
- FP-I3ID, Universidade Fernando Pessoa, 4200-150 Porto, Portugal
- Escola Superior de Saúde Fernando Pessoa, 4200-253 Porto, Portugal
- LAQV@REQUIMTE, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Inês Pita
- Department of Gastroenterology, Entre Douro e Vouga Hospital Center, 4520-211 Santa Maria da Feira, Portugal
| | - Rui Morais
- Department of Gastroenterology, São João University Hospital Center, 4200-319 Porto, Portugal
| | - Guilherme Macedo
- Department of Gastroenterology, São João University Hospital Center, 4200-319 Porto, Portugal
| | - Tim J Bull
- Institute of Infection and Immunity, St George's University of London, London SW17 ORE, UK
| | - Fernando Magro
- Department of Biomedicine, Unit of Pharmacology and Therapeutics, Faculty of Medicine, University of Porto, 4050-313 Porto, Portugal
- Department of Gastroenterology, São João University Hospital Center, 4200-319 Porto, Portugal
| | - Amélia Sarmento
- FP-I3ID, Universidade Fernando Pessoa, 4200-150 Porto, Portugal
- Faculdade de Ciências da Saúde, Universidade Fernando Pessoa, 4200-150 Porto, Portugal
- I3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-150 Porto, Portugal
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2
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Jiang W, Liu J, Zhao X, Yang W. Melatonin ameliorates lung cell inflammation and apoptosis caused by Klebsiella pneumoniae via AMP-activated protein kinase. Inflammopharmacology 2022; 30:2345-2357. [PMID: 36131109 PMCID: PMC9491669 DOI: 10.1007/s10787-022-01073-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 09/07/2022] [Indexed: 12/04/2022]
Abstract
Klebsiella pneumoniae is a Gram-negative bacterium and the causative agent of several life-threatening nosocomial infections, including pneumonia. K. pneumoniae induces acute lung injury and inflammation in humans that require immediate hospitalization and treatment. Therefore, attenuation of K. pneumoniae-induced inflammation is necessary for the survival of patients. This study investigated the mechanisms by which melatonin abrogated K. pneumoniae-induced inflammation and apoptosis of lung cell lines, HLF-1 and BEAS-2B. Our results showed that in vitro infection of HLF-1 and BEAS-2B cells by K. pneumoniae significantly induced inflammation and apoptosis increased elevated levels of IL-6, CXCL1, CXCL2, and caspase-9 mRNA. However, these effects were abrogated by melatonin treatment. Infection with K. pneumoniae significantly increased the expression of AMP-induced protein kinase (AMPK). Furthermore, AMPK silencing significantly abrogated the suppression of inflammation and apoptosis in melatonin-infected K. pneumoniae lung cells. Melatonin could alleviate K. pneumoniae infection-induced inflammation in three-dimensional lung spheroids. In conclusion, our study demonstrated that melatonin abrogated K. pneumoniae-induced inflammation and apoptosis in lung cells through AMPK. Our study demonstrated the potential of melatonin for therapy against K. pneumoniae infections including pneumonia.
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Affiliation(s)
- Wei Jiang
- Department of Infectious Diseases, Tianjin First Central Hospital, Tianjin, 300192, China
| | - Jun Liu
- Department of Infectious Diseases, Tianjin First Central Hospital, Tianjin, 300192, China
| | - Xuequn Zhao
- Department of Infectious Diseases, Tianjin First Central Hospital, Tianjin, 300192, China
| | - Wenjie Yang
- Department of Infectious Diseases, Tianjin First Central Hospital, Tianjin, 300192, China.
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3
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Kamali Dolatabadi R, Feizi A, Halaji M, Fazeli H, Adibi P. The Prevalence of Adherent-Invasive Escherichia coli and Its Association With Inflammatory Bowel Diseases: A Systematic Review and Meta-Analysis. Front Med (Lausanne) 2021; 8:730243. [PMID: 34926490 PMCID: PMC8678049 DOI: 10.3389/fmed.2021.730243] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 10/22/2021] [Indexed: 12/12/2022] Open
Abstract
Inflammatory bowel diseases (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), are known as chronic gastrointestinal inflammatory disorders. The present systematic review and meta analysis was conducted to estimate the prevalence of adherent-invasive Escherichia coli (AIEC) isolates and their phylogenetic grouping among IBD patients compared with the controls. A systematic literature search was conducted among published papers by international authors until April 30, 2020 in Web of Science, Scopus, EMBASE, and PubMed databases. The pooled prevalence of AIEC isolates and their phylogenetic grouping among IBD patients as well as in controls was estimated using fixed or random effects models. Furthermore, for estimating the association of colonization by AIEC with IBD, odds ratio along with 95% confidence interval was reported. A total of 205 articles retrieved by the initial search of databases, 13 case–control studies met the eligibility criteria for inclusion in the meta analysis. There were 465 IBD cases (348 CD and 117 UC) and 307 controls. The pooled prevalence of AIEC isolates were 28% (95% CI: 18–39%), 29% (95% CI: 20–40%), 13% (95% CI: 1–30%), and 9% (95% CI: 3–19%), respectively among IBD, CD, UC, and control group, respectively. Our results revealed that the most frequent AIEC phylogroup in the IBD, CD, and control groups was B2. Fixed-effects meta analysis showed that colonization of AIEC is significantly associated with IBD (OR: 2.93; 95% CI: 1.90–4.52; P < 0.001) and CD (OR: 3.07; 95% CI: 1.99–4.74; P < 0.001), but not with UC (OR: 2.29; 95% CI: 0.81–6.51; P = 0.11). In summary, this meta analysis revealed that colonization by AIEC is more frequent in IBD and is associated with IBD (CD and UC). Our results suggested that the affects of IBD in patients colonized with the AIEC pathovar is not random, it is in fact a specific disease-related pathovar.
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Affiliation(s)
- Razie Kamali Dolatabadi
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Awat Feizi
- Department of Biostatistics and Epidemiology, School of Health, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mehrdad Halaji
- Infectious Diseases and Tropical Medicine Research Center, Babol University of Medical Sciences, Babol, Iran.,Department of Microbiology, School of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Hossein Fazeli
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Peyman Adibi
- Gastroenterology and Hepatology Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
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4
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Torres J, Halfvarson J, Rodríguez-Lago I, Hedin CRH, Jess T, Dubinsky M, Croitoru K, Colombel JF. Results of the Seventh Scientific Workshop of ECCO: Precision Medicine in IBD-Prediction and Prevention of Inflammatory Bowel Disease. J Crohns Colitis 2021; 15:1443-1454. [PMID: 33730755 DOI: 10.1093/ecco-jcc/jjab048] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Inflammatory bowel disease [IBD] is a complex chronic disorder with no clear aetiology and no known cure. Despite recent advances in overall disease management and improved therapeutics, patients with IBD still experience a substantial burden. Furthermore, as the incidence continues to increase in developing areas of the world, it is expected that the burden of IBD to society will increase and exert tremendous pressure on health care systems worldwide. Therefore, new strategies to prevent the global increase of IBD are urgently required. Data are being progressively acquired on the period preceding disease diagnosis, which support the concept that IBD has a preclinical period that may reveal the triggers of disease and may be amenable to early intervention. Having a better knowledge of this preclinical period will increase the potential not only for improved understanding of disease pathogenesis and improved therapeutics, but also for disease prediction and prevention.
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Affiliation(s)
- Joana Torres
- Division of Gastroenterology, Hospital Beatriz Ângelo, Loures, Portugal.,Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Jonas Halfvarson
- Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Iago Rodríguez-Lago
- Department of Gastroenterology, Hospital de Galdakao, and Biocruces Bizkaia Health Research Institute, Bilbao, Spain
| | - Charlotte R H Hedin
- Karolinska Institutet, Department of Medicine Solna, Stockholm, Sweden.,Karolinska University Hospital, Gastroenterology unit, Department of Gastroenterology, Dermatovenereology and Rheumatology, Stockholm, Sweden
| | - Tine Jess
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen S, Denmark.,PREDICT, Institute of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Marla Dubinsky
- Division of Pediatric Gastroenterology and Nutrition, Susan and Leonard Feinstein Inflammatory Bowel Disease Clinical Center, Icahn School of Medicine Mount Sinai, New York, NY, USA
| | - Kenneth Croitoru
- Center for Inflammatory Bowel Disease, Mount Sinai Hospital, Toronto, ON, Canada.,Division of Gastroenterology and Hepatology, University of Toronto, Toronto, ON, Canada
| | - Jean-Frédéric Colombel
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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5
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Nadalian B, Yadegar A, Houri H, Olfatifar M, Shahrokh S, Asadzadeh Aghdaei H, Suzuki H, Zali MR. Prevalence of the pathobiont adherent-invasive Escherichia coli and inflammatory bowel disease: a systematic review and meta-analysis. J Gastroenterol Hepatol 2021; 36:852-863. [PMID: 32929762 DOI: 10.1111/jgh.15260] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/08/2020] [Accepted: 09/07/2020] [Indexed: 12/21/2022]
Abstract
BACKGROUND AND AIM Escherichia coli pathobionts and particularly the adherent-invasive E. coli (AIEC) may play a putative role in initiating and maintaining the inflammatory process in the intestinal tissues of inflammatory bowel disease (IBD) patients, by providing stimulatory factors that trigger gut immune system activation. The aim of this study is to conduct a systematic review and meta-analysis to determine the prevalence of AIEC among patients with Crohn's disease (CD) and ulcerative colitis (UC). METHODS Electronic databases were searched up to February 2020 for relevant publications reporting the prevalence of AIEC in IBD patients. The prevalence rate of AIEC among CD and UC patients, the odds ratio (OR) and 95% confidence interval (CI) were calculated compared to non-IBD controls. RESULTS The final dataset included 12 studies, all investigating AIEC isolates from ileal/colonic specimens. The OR for prevalence of AIEC in CD patients was 3.27 (95% CI 1.79-5.9) compared with non-IBD controls. The overall pooled prevalence of AIEC among CD patients was 29% (95% CI 0.17-0.45), whereas this prevalence was calculated to be 9% (95% CI 0.03-0.19) in controls. Moreover, the prevalence of AIEC in UC subjects was calculated 12% (95% CI 0.01-0.34), while AIEC showed a prevalence of 5% (95% CI 0.0-0.17) among the controls. The OR for prevalence of AIEC in UC patients was 2.82 (95% CI 1.11-7.14) compared with controls. CONCLUSIONS There is a substantial increase in the prevalence of AIEC in IBD patients compared with controls. This review supports the growing evidence that AIEC could be involved in both CD and UC pathogenesis.
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Affiliation(s)
- Banafsheh Nadalian
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Abbas Yadegar
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamidreza Houri
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Meysam Olfatifar
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shabnam Shahrokh
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hidekazu Suzuki
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, School of Medicine, Tokai University, Isehara, Japan
| | - Mohammad Reza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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6
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Marques JG, Shokry E, Frivolt K, Werkstetter KJ, Brückner A, Schwerd T, Koletzko S, Koletzko B. Metabolomic Signatures in Pediatric Crohn's Disease Patients with Mild or Quiescent Disease Treated with Partial Enteral Nutrition: A Feasibility Study. SLAS Technol 2021; 26:165-177. [PMID: 33207993 PMCID: PMC7985853 DOI: 10.1177/2472630320969147] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 09/29/2020] [Accepted: 10/06/2020] [Indexed: 12/22/2022]
Abstract
Little is known about the metabolic response of pediatric Crohn's disease (CD) patients to partial enteral nutrition (PEN) therapy and the impact of disease activity and inflammation. We analyzed plasma samples from a nonrandomized controlled intervention study investigating the effect of partial enteral nutrition (PEN) on bone health and growth throughout one year with untargeted metabolomics using high-performance liquid chromatography (HPLC) coupled with high-resolution mass spectrometry (HRMS). Thirty-four paired samples from two time points (baseline and 12 months) were analyzed. Patients (median age: 13.9 years, range: 7-18.9 years, 44% females) were in remission or had mild disease activity. The intervention group received a casein-based formula for 12 months, providing ~25% of estimated daily energy requirements. Sparse partial least squares discriminant analysis (splsda) was applied for group discrimination and identifying sources of variation to identify the impact of PEN. We also investigated the correlation of metabolites with inflammation markers, including erythrocyte sedimentation rate (ESR), C-reactive protein (CRP), and fecal calprotectin. After 12 months, our results show substantial difference between PEN and non-PEN groups in the metabolome of CD patients in remission or with mild disease activity. Inflammatory markers were associated with individual compounds and chemical classes such as isoprenoids and phospholipids. Identified compounds comprise metabolites produced by human or bacterial metabolism, as well as xenobiotics recognized as flavoring agents and environmental contaminants and their biotransformation products. Further longitudinal studies that also include patients with higher disease activity are warranted to evaluate the suitability of these metabolic biomarkers for predicting disease activity.
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Affiliation(s)
- Jair Gonzalez Marques
- Department of Pediatrics, Dr. von Hauner Children’s Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Engy Shokry
- Department of Pediatrics, Dr. von Hauner Children’s Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Klara Frivolt
- Department of Pediatrics, Dr. von Hauner Children’s Hospital, University Hospital, LMU Munich, Munich, Germany
- Department of Paediatrics, Comenius University Medical School, Bratislava, Slovakia
| | - Katharina Julia Werkstetter
- Department of Pediatrics, Dr. von Hauner Children’s Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Annecarin Brückner
- Department of Pediatrics, Dr. von Hauner Children’s Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Tobias Schwerd
- Department of Pediatrics, Dr. von Hauner Children’s Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Sibylle Koletzko
- Department of Pediatrics, Dr. von Hauner Children’s Hospital, University Hospital, LMU Munich, Munich, Germany
- Department of Pediatrics, Gastroenterology and Nutrition, School of Medicine Collegium Medicum, University of Warmia and Mazury, Olsztyn, Poland
| | - Berthold Koletzko
- Department of Pediatrics, Dr. von Hauner Children’s Hospital, University Hospital, LMU Munich, Munich, Germany
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Metwaly A, Dunkel A, Waldschmitt N, Raj ACD, Lagkouvardos I, Corraliza AM, Mayorgas A, Martinez-Medina M, Reiter S, Schloter M, Hofmann T, Allez M, Panes J, Salas A, Haller D. Integrated microbiota and metabolite profiles link Crohn's disease to sulfur metabolism. Nat Commun 2020; 11:4322. [PMID: 32859898 PMCID: PMC7456324 DOI: 10.1038/s41467-020-17956-1] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 07/24/2020] [Indexed: 02/07/2023] Open
Abstract
Gut microbial and metabolite alterations have been linked to the pathogenesis of inflammatory bowel diseases. Here we perform a multi-omics microbiome and metabolite analysis of a longitudinal cohort of Crohn's disease patients undergoing autologous hematopoietic stem cell transplantation, and investigational therapy that induces drug free remission in a subset of patients. Via comparison of patients who responded and maintained remission, responded but experienced disease relapse and patients who did not respond to therapy, we identify shared functional signatures that correlate with disease activity despite the variability of gut microbiota profiles at taxonomic level. These signatures reflect the disease state when transferred to gnotobiotic mice. Taken together, the integration of microbiome and metabolite profiles from human cohort and mice improves the predictive modelling of disease outcome, and allows the identification of a network of bacteria-metabolite interactions involving sulfur metabolism as a key mechanism linked to disease activity in Crohn's disease.
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Affiliation(s)
- Amira Metwaly
- Chair of Nutrition and Immunology, Technical University of Munich, Freising-Weihenstephan, Germany
| | - Andreas Dunkel
- Leibniz-Institute for Food Systems Biology, Technical University of Munich, Freising, Germany
| | - Nadine Waldschmitt
- Chair of Nutrition and Immunology, Technical University of Munich, Freising-Weihenstephan, Germany
| | - Abilash Chakravarthy Durai Raj
- Helmholtz Zentrum München, German Research Center for Environmental Health, Research Unit Comparative Microbiome Analysis, Munich, Germany
| | - Ilias Lagkouvardos
- ZIEL Institute for Food and Health, Technical University of Munich, Freising, Germany
| | - Ana Maria Corraliza
- Inflammatory Bowel Disease Unit, Hospital Clínic de Barcelona, IDIBAPS, CIBERehd, Barcelona, Spain
| | - Aida Mayorgas
- Inflammatory Bowel Disease Unit, Hospital Clínic de Barcelona, IDIBAPS, CIBERehd, Barcelona, Spain
| | | | - Sinah Reiter
- Chair of Food Chemistry and Molecular Sensory Science, Technical University of Munich, Freising, Germany
| | - Michael Schloter
- Helmholtz Zentrum München, German Research Center for Environmental Health, Research Unit Comparative Microbiome Analysis, Munich, Germany
| | - Thomas Hofmann
- Chair of Food Chemistry and Molecular Sensory Science, Technical University of Munich, Freising, Germany
| | - Matthieu Allez
- APHP, Hôpital Saint Louis, Department of Gastroenterology, INSERM UMRS 1160, Paris Diderot, Sorbonne Paris-Cité University, Paris, France
| | - Julian Panes
- Inflammatory Bowel Disease Unit, Hospital Clínic de Barcelona, IDIBAPS, CIBERehd, Barcelona, Spain
| | - Azucena Salas
- Inflammatory Bowel Disease Unit, Hospital Clínic de Barcelona, IDIBAPS, CIBERehd, Barcelona, Spain
| | - Dirk Haller
- Chair of Nutrition and Immunology, Technical University of Munich, Freising-Weihenstephan, Germany.
- ZIEL Institute for Food and Health, Technical University of Munich, Freising, Germany.
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8
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Xu Y, Zhang M, Zhang J, Sun Z, Ran L, Ban Y, Wang B, Hou X, Zhai S, Ren L, Wang M, Hu J. Differential intestinal and oral microbiota features associated with gestational diabetes and maternal inflammation. Am J Physiol Endocrinol Metab 2020; 319:E247-E253. [PMID: 31891538 DOI: 10.1152/ajpendo.00266.2019] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Maternal microbiota is involved in many metabolic diseases. However, its role in the pathophysiology of gestational diabetes mellitus (GDM) remains unclear. In this case-control study, we performed a 16S rRNA sequencing-based microbial survey to compare the intestinal and oral microflora at third trimester during pregnancy between 30 GDM and 31 normal controls. Sequentially, a correlation-based network analysis was further performed to explore the interactions among microbiota, maternal and infant blood sugar, and inflammatory markers. Our results show that, compared with controls, the GDM cases showed significant differences in β-diversity and increased Gammaproteobacteria and Hemophilus in intestinal microbiota. Furthermore, the GDM cases showed lower α-diversity, increased Selenomonas and Bifidobacterium, and decreased Fusobacteria and Leptotrichia in oral microbiota. The ROC curve showed the area under the curve to be equal to 0.70 and 0.66 when using oral Leptotrichia or gut Hemophilus, respectively, to predict GDM status. In addition, the components and topography of microbial cooccurrence and coexclusion network were quite distinct by GDM status. In summary, intestinal and oral microorganisms in pregnant women are closely related to the status of GDM in the third trimester of pregnancy. The changes of intestinal and oral microbial features may be noninvasive biomarkers for monitoring the health management of GDM pregnancy.
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Affiliation(s)
- Yajuan Xu
- Department of Obstetrics and Gynaecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Miao Zhang
- Department of Obstetrics and Gynaecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jingzhe Zhang
- Department of Obstetrics and Gynaecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zongzong Sun
- Department of Obstetrics and Gynaecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Limin Ran
- Department of Obstetrics and Gynaecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yanjie Ban
- Department of Obstetrics and Gynaecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Biao Wang
- Department of Obstetrics and Gynaecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiaofeng Hou
- Department of Obstetrics and Gynaecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shanshan Zhai
- Department of Obstetrics and Gynaecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Lidan Ren
- Department of Obstetrics and Gynaecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Mengqi Wang
- Department of Obstetrics and Gynaecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jianzhong Hu
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York
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9
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Bosi A, Banfi D, Bistoletti M, Giaroni C, Baj A. Tryptophan Metabolites Along the Microbiota-Gut-Brain Axis: An Interkingdom Communication System Influencing the Gut in Health and Disease. Int J Tryptophan Res 2020; 13:1178646920928984. [PMID: 32577079 PMCID: PMC7290275 DOI: 10.1177/1178646920928984] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 05/02/2020] [Indexed: 12/12/2022] Open
Abstract
The ‘microbiota-gut-brain axis’ plays a fundamental role in maintaining host homeostasis, and different immune, hormonal, and neuronal signals participate to this interkingdom communication system between eukaryota and prokaryota. The essential aminoacid tryptophan, as a precursor of several molecules acting at the interface between the host and the microbiota, is fundamental in the modulation of this bidirectional communication axis. In the gut, tryptophan undergoes 3 major metabolic pathways, the 5-HT, kynurenine, and AhR ligand pathways, which may be directly or indirectly controlled by the saprophytic flora. The importance of tryptophan metabolites in the modulation of the gastrointestinal tract is suggested by several preclinical and clinical studies; however, a thorough revision of the available literature has not been accomplished yet. Thus, this review attempts to cover the major aspects on the role of tryptophan metabolites in host-microbiota cross-talk underlaying regulation of gut functions in health conditions and during disease states, with particular attention to 2 major gastrointestinal diseases, such as irritable bowel syndrome (IBS) and inflammatory bowel disease (IBD), both characterized by psychiatric disorders. Research in this area opens the possibility to target tryptophan metabolism to ameliorate the knowledge on the pathogenesis of both diseases, as well as to discover new therapeutic strategies based either on conventional pharmacological approaches or on the use of pre- and probiotics to manipulate the microbial flora.
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Affiliation(s)
- Annalisa Bosi
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Davide Banfi
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Michela Bistoletti
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Cristina Giaroni
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Andreina Baj
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
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10
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Barrios-Villa E, Martínez de la Peña CF, Lozano-Zaraín P, Cevallos MA, Torres C, Torres AG, Rocha-Gracia RDC. Comparative genomics of a subset of Adherent/Invasive Escherichia coli strains isolated from individuals without inflammatory bowel disease. Genomics 2019; 112:1813-1820. [PMID: 31689478 DOI: 10.1016/j.ygeno.2019.10.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 09/05/2019] [Accepted: 10/22/2019] [Indexed: 02/07/2023]
Abstract
There is increased evidence demonstrating the association between Crohn's Disease (CD), a type of Inflammatory Bowel Disease (IBD), and non-diarrheagenic Adherent/Invasive Escherichia coli (AIEC) isolates. AIEC strains are phenotypically characterized by their adhesion, invasion and intra-macrophage survival capabilities. In the present study, the genomes of five AIEC strains isolated from individuals without IBD (four from healthy donors and one from peritoneal liquid) were sequenced and compared with AIEC prototype strains (LF82 and NRG857c), and with extra-intestinal uropathogenic strain (UPEC CFT073). Non-IBD-AIEC strains showed an Average Nucleotide Identity up to 98% compared with control strains. Blast identities of the five non-IBD-AIEC strains were higher when compared to AIEC and UPEC reference strains than with another E. coli pathotypes, suggesting a relationship between them. The SNPs phylogeny grouped the five non-IBD-AIEC strains in one separated cluster, which indicates the emergence of these strains apart from the AIEC group. Additionally, four genomic islands not previously reported in AIEC strains were identified. An incomplete Type VI secretion system was found in non-IBD-AIEC strains; however, the Type II secretion system was complete. Several groups of genes reported in AIEC strains were searched in the five non-IBD-AIEC strains, and the presence of fimA, fliC, fuhD, chuA, irp2 and cvaC were confirmed. Other virulence factors were detected in non-IBD-AIEC strains, which were absent in AIEC reference strains, including EhaG, non-fimbrial adhesin 1, PapG, F17D-G, YehA/D, FeuC, IucD, CbtA, VgrG-1, Cnf1 and HlyE. Based on the differences in virulence determinants and SNPs, it is plausible to suggest that non-IBD AIEC strains belong to a different pathotype.
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Affiliation(s)
- Edwin Barrios-Villa
- Posgrado en Microbiología, Laboratorio de Microbiología Hospitalaria y de la Comunidad, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Claudia Fabiola Martínez de la Peña
- Posgrado en Microbiología, Laboratorio de Biología Molecular de Enteropatógenos, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Patricia Lozano-Zaraín
- Posgrado en Microbiología, Laboratorio de Microbiología Hospitalaria y de la Comunidad, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Miguel A Cevallos
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Carmen Torres
- Área de Bioquímica y Biología Molecular, Universidad de La Rioja, Logroño, Spain
| | - Alfredo G Torres
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Rosa Del Carmen Rocha-Gracia
- Posgrado en Microbiología, Laboratorio de Microbiología Hospitalaria y de la Comunidad, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico.
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11
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Ghaly S, Hart PH, Lawrance IC. Inflammatory bowel diseases: interrelationships between dietary vitamin D, exposure to UV radiation and the fecal microbiome. Expert Rev Gastroenterol Hepatol 2019; 13:1039-1048. [PMID: 31657973 DOI: 10.1080/17474124.2019.1685874] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Introduction: Environmental factors and an altered fecal microbiome are believed to be central to the pathogenesis of inflammatory bowel diseases (IBD). Vitamin D and ultraviolet radiation (UVR) are environmental factors that are associated by several pathways, including changes to the gastrointestinal microbiome, with the development and course of IBD.Area covered: This review explores the interaction of vitamin D, and UVR, with the intestinal innate and adaptive immune systems, and how they may influence the gut microbiome and the subsequent development, and progression, of IBD.Expert opinion: Vitamin D and UVR both regulate innate and adaptive immunity through a combination of common and independent mechanisms, with the overall effect being the promotion of immune tolerance. Vitamin D, and to a lesser extent UVR, can modify the gastrointestinal microbiome either directly, or through immune-mediated mechanisms and this may explain the effect on intestinal inflammation in animal models of IBD and some clinical studies. Thus, both vitamin D and UVR exposure can be considered potential 'master regulators' of gastrointestinal immunity, fine-tuning the complex interaction between genetics, host immunity and the gut microbiome. Further research and increased understanding of environment-host interactions is essential to achieving the ultimate goal of preventing and curing IBD.
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Affiliation(s)
- Simon Ghaly
- Department of Gastroenterology, St Vincent's Hospital, Sydney, Australia.,St. Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, Australia.,Faculty of Health and Medical Sciences, University of Western Australia, Perth, Australia.,Inflammation, Telethon Kids Institute, Nedlands, Australia
| | - Prue H Hart
- Inflammation, Telethon Kids Institute, Nedlands, Australia
| | - Ian C Lawrance
- Inflammation, Telethon Kids Institute, Nedlands, Australia.,Centre for Inflammatory Bowel Disease, St John of God Hospital, Subiaco, Australia
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12
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Di Caro S, Fragkos KC, Keetarut K, Koo HF, Sebepos-Rogers G, Saravanapavan H, Barragry J, Rogers J, Mehta SJ, Rahman F. Enteral Nutrition in Adult Crohn's Disease: Toward a Paradigm Shift. Nutrients 2019; 11:E2222. [PMID: 31540038 PMCID: PMC6770416 DOI: 10.3390/nu11092222] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 09/05/2019] [Accepted: 09/08/2019] [Indexed: 02/06/2023] Open
Abstract
Medical and surgical treatments for Crohn's disease are associated with toxic effects. Medical therapy aims for mucosal healing and is achievable with biologics, immunosuppressive therapy, and specialised enteral nutrition, but not with corticosteroids. Sustained remission remains a therapeutic challenge. Enteral nutrition, containing macro- and micro-nutrients, is nutritionally complete, and is provided in powder or liquid form. Enteral nutrition is a low-risk and minimally invasive therapy. It is well-established and recommended as first line induction therapy in paediatric Crohn's disease with remission rates of up to 80%. Other than in Japan, enteral nutrition is not routinely used in the adult population among Western countries, mainly due to unpalatable formulations which lead to poor compliance. This study aims to offer a comprehensive review of available enteral nutrition formulations and the literature supporting the use and mechanisms of action of enteral nutrition in adult Crohn's disease patients, in order to support clinicians in real world decision-making when offering/accepting treatment. The mechanisms of actions of enteral feed, including their impact on the gut microbiome, were explored. Barriers to the use of enteral nutrition, such as compliance and the route of administration, were considered. All available enteral preparations have been comprehensively described as a practical guide for clinical use. Likewise, guidelines are reported and discussed.
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Affiliation(s)
- Simona Di Caro
- Intestinal Failure Service, GI Services, University College London Hospitals NHS Foundation Trust, 250 Euston Road, London NW1 2PG, UK.
| | - Konstantinos C Fragkos
- Intestinal Failure Service, GI Services, University College London Hospitals NHS Foundation Trust, 250 Euston Road, London NW1 2PG, UK.
| | - Katie Keetarut
- Department of Dietetics, University College London Hospitals NHS Foundation Trust, 250 Euston Road, London NW1 2PG, UK.
| | - Hui Fen Koo
- UCL Medical School, 74 Huntley Street, Bloomsbury, London WC1E 6DE, UK.
| | - Gregory Sebepos-Rogers
- Intestinal Failure Service, GI Services, University College London Hospitals NHS Foundation Trust, 250 Euston Road, London NW1 2PG, UK.
| | - Hajeena Saravanapavan
- Intestinal Failure Service, GI Services, University College London Hospitals NHS Foundation Trust, 250 Euston Road, London NW1 2PG, UK.
| | - John Barragry
- Intestinal Failure Service, GI Services, University College London Hospitals NHS Foundation Trust, 250 Euston Road, London NW1 2PG, UK.
| | - Jennifer Rogers
- Intestinal Failure Service, GI Services, University College London Hospitals NHS Foundation Trust, 250 Euston Road, London NW1 2PG, UK.
| | - Shameer J Mehta
- Intestinal Failure Service, GI Services, University College London Hospitals NHS Foundation Trust, 250 Euston Road, London NW1 2PG, UK.
| | - Farooq Rahman
- Intestinal Failure Service, GI Services, University College London Hospitals NHS Foundation Trust, 250 Euston Road, London NW1 2PG, UK.
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13
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Palmela C, Chevarin C, Xu Z, Torres J, Sevrin G, Hirten R, Barnich N, Ng SC, Colombel JF. Adherent-invasive Escherichia coli in inflammatory bowel disease. Gut 2018; 67:574-587. [PMID: 29141957 DOI: 10.1136/gutjnl-2017-314903] [Citation(s) in RCA: 309] [Impact Index Per Article: 51.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 09/20/2017] [Accepted: 10/28/2017] [Indexed: 02/06/2023]
Abstract
Intestinal microbiome dysbiosis has been consistently described in patients with IBD. In the last decades, Escherichia coli, and the adherent-invasive E coli (AIEC) pathotype in particular, has been implicated in the pathogenesis of IBD. Since the discovery of AIEC, two decades ago, progress has been made in unravelling these bacteria characteristics and its interaction with the gut immune system. The mechanisms of adhesion of AIEC to intestinal epithelial cells (via FimH and cell adhesion molecule 6) and its ability to escape autophagy when inside macrophages are reviewed here. We also explore the existing data on the prevalence of AIEC in patients with Crohn's disease and UC, and the association between the presence of AIEC and disease location, activity and postoperative recurrence. Finally, we highlight potential therapeutic strategies targeting AIEC colonisation of gut mucosa, including the use of phage therapy, bacteriocins and antiadhesive molecules. These strategies may open new avenues for the prevention and treatment of IBD in the future.
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Affiliation(s)
- Carolina Palmela
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York City, New York, USA.,Division of Gastroenterology, Hospital Beatriz Ângelo, Loures, Portugal
| | - Caroline Chevarin
- Université Clermont Auvergne, Inserm U1071, USC-INRA 2018, M2iSH, CRNH Auvergne, F-63000 Clermont-Ferrand, France
| | - Zhilu Xu
- Department of Medicine and Therapeutics, Institute of Digestive Diseases, LKS Institute of Health Science, State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, China
| | - Joana Torres
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York City, New York, USA.,Division of Gastroenterology, Hospital Beatriz Ângelo, Loures, Portugal
| | - Gwladys Sevrin
- Université Clermont Auvergne, Inserm U1071, USC-INRA 2018, M2iSH, CRNH Auvergne, F-63000 Clermont-Ferrand, France
| | - Robert Hirten
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Nicolas Barnich
- Université Clermont Auvergne, Inserm U1071, USC-INRA 2018, M2iSH, CRNH Auvergne, F-63000 Clermont-Ferrand, France
| | - Siew C Ng
- Department of Medicine and Therapeutics, Institute of Digestive Diseases, LKS Institute of Health Science, State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, China
| | - Jean-Frederic Colombel
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
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14
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Alhagamhmad MH. Enteral Nutrition in the Management of Crohn's Disease: Reviewing Mechanisms of Actions and Highlighting Potential Venues for Enhancing the Efficacy. Nutr Clin Pract 2018; 33:483-492. [PMID: 29323428 DOI: 10.1002/ncp.10004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 09/12/2017] [Accepted: 10/10/2017] [Indexed: 12/16/2022] Open
Abstract
Crohn's disease (CD) is a chronic condition that affects the gut and has adverse effects on growth and development. There is a global increase in the incidence and prevalence rates, and several factors are believed to contribute to this rise, including dietary habits. In contrast, the use of enteral nutrition (EN) as an exclusive source of nutrition is increasingly becoming the preferred induction treatment of pediatric CD patients in part to address the nutrition complications. However, EN therapy is considered less effective in adults with CD. A better understanding of the molecular mechanisms of enteral therapy will help improve the clinical management of CD. It is increasingly becoming evident that the therapeutic utility of EN is in part due to the reversal of the microbial changes and the direct immunomodulatory effects. Moreover, there is a potential tendency for enhancing the efficacy of EN therapy by improving the palatability of the given formulas and, more important, by magnifying the anti-inflammatory properties. Recent observations have shown that the immunomodulatory effects of EN are mediated at least in part by blocking nuclear factor-κB. Furthermore, it is likely that several ingredients of EN contribute to this activity, in particular glutamine and arginine amino acids. In addition, manipulating the composition of EN therapy by altering concentrations of the key ingredients is found to have the potential for more efficient therapy. In this review, the underlying mechanisms of EN actions will be discussed further with a focus on the potential methods for enhancing the efficacy.
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Affiliation(s)
- Moftah H Alhagamhmad
- Faculty of Medicine, University of Benghazi (Al-Arab Medical University), Benghazi, Libya
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15
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McIlroy J, Ianiro G, Mukhopadhya I, Hansen R, Hold GL. Review article: the gut microbiome in inflammatory bowel disease-avenues for microbial management. Aliment Pharmacol Ther 2018; 47:26-42. [PMID: 29034981 DOI: 10.1111/apt.14384] [Citation(s) in RCA: 130] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 05/29/2017] [Accepted: 09/25/2017] [Indexed: 02/06/2023]
Abstract
BACKGROUND The concept of an altered collective gut microbiota rather than identification of a single culprit is possibly the most significant development in inflammatory bowel disease research. We have entered the "omics" era, which now allows us to undertake large-scale/high-throughput microbiota analysis which may well define how we approach diagnosis and treatment of inflammatory bowel disease (IBD) in the future, with a strong steer towards personalised therapeutics. AIM To assess current epidemiological, experimental and clinical evidence of the current status of knowledge relating to the gut microbiome, and its role in IBD, with emphasis on reviewing the evidence relating to microbial therapeutics and future microbiome modulating therapeutics. METHODS A Medline search including items 'intestinal microbiota/microbiome', 'inflammatory bowel disease', 'ulcerative colitis', 'Crohn's disease', 'faecal microbial transplantation', 'dietary manipulation' was performed. RESULTS Disease remission and relapse are associated with microbial changes in both mucosal and luminal samples. In particular, a loss of species richness in Crohn's disease has been widely observed. Existing therapeutic approaches broadly fall into 3 categories, namely: accession, reduction or indirect modulation of the microbiome. In terms of microbial therapeutics, faecal microbial transplantation appears to hold the most promise; however, differences in study design/methodology mean it is currently challenging to elegantly translate results into clinical practice. CONCLUSIONS Existing approaches to modulate the gut microbiome are relatively unrefined. Looking forward, the future of microbiome-modulating therapeutics looks bright with several novel strategies/technologies on the horizon. Taken collectively, it is clear that ignoring the microbiome in IBD is not an option.
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Affiliation(s)
- J McIlroy
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, UK
| | - G Ianiro
- Internal Medicine, Gastroenterology and Liver Unit, Gastroenterology Area, Fondazione Policlinico Universitario Gemelli, Università Cattolica del Sacro Cuore, Rome, Italy
| | - I Mukhopadhya
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, UK
| | - R Hansen
- Royal Hospital for Children, Glasgow, UK
| | - G L Hold
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, UK
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16
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Proteobacteria: A Common Factor in Human Diseases. BIOMED RESEARCH INTERNATIONAL 2017; 2017:9351507. [PMID: 29230419 PMCID: PMC5688358 DOI: 10.1155/2017/9351507] [Citation(s) in RCA: 631] [Impact Index Per Article: 90.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 10/16/2017] [Indexed: 12/11/2022]
Abstract
Microbiota represents the entire microbial community present in the gut host. It serves several functions establishing a mutualistic relation with the host. Latest years have seen a burst in the number of studies focusing on this topic, in particular on intestinal diseases. In this scenario, Proteobacteria are one of the most abundant phyla, comprising several known human pathogens. This review highlights the latest findings on the role of Proteobacteria not only in intestinal but also in extraintestinal diseases. Indeed, an increasing amount of data identifies Proteobacteria as a possible microbial signature of disease. Several studies demonstrate an increased abundance of members belonging to this phylum in such conditions. Major evidences currently involve metabolic disorders and inflammatory bowel disease. However, more recent studies suggest a role also in lung diseases, such as asthma and chronic obstructive pulmonary disease, but evidences are still scant. Notably, all these conditions are sustained by various degree of inflammation, which thus represents a core aspect of Proteobacteria-related diseases.
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17
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Hedin CR, van der Gast CJ, Stagg AJ, Lindsay JO, Whelan K. The gut microbiota of siblings offers insights into microbial pathogenesis of inflammatory bowel disease. Gut Microbes 2017; 8:359-365. [PMID: 28112583 PMCID: PMC5570433 DOI: 10.1080/19490976.2017.1284733] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Siblings of patients with Crohn's disease (CD) have elevated risk of developing CD and display aspects of disease phenotype, including faecal dysbiosis. In our recent article we have used 16S rRNA gene targeted high-throughput sequencing to comprehensively characterize the mucosal microbiota in healthy siblings of CD patients, and determine the influence of genotypic and phenotypic factors on the gut microbiota (dysbiosis). We have demonstrated that the core microbiota of both patients with CD and healthy siblings is significantly less diverse than controls. Faecalibacterium prausnitzii contributed most to core metacommunity dissimilarity between both patients and controls and between siblings and controls. Phenotype/genotype markers of CD risk significantly influenced microbiota variation between and within groups, of which genotype had the largest effect. Individuals with elevated CD-risk display mucosal dysbiosis characterized by reduced diversity of core microbiota and lower abundance of F. prausnitzii. The presence of this dysbiosis in healthy people at-risk of CD implicates microbiological processes in CD pathogenesis.
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Affiliation(s)
- Charlotte R. Hedin
- Department of Medicine, Karolinska University Hospital, Solna, Stockholm
| | | | - Andrew J. Stagg
- Queen Mary University of London, Centre for Immunobiology, Blizard Institute, London, UK
| | - James O. Lindsay
- Queen Mary University of London, Centre for Immunobiology, Blizard Institute, London, UK,Barts Health NHS Trust, Department of Gastroenterology, London, UK
| | - Kevin Whelan
- King's College London, Faculty of Life Sciences & Medicine, Diabetes and Nutritional Sciences Division, London, UK,CONTACT Kevin Whelan King's College London, 150 Stamford Street, London, SE1 9NH, United Kingdom
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18
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Dysbiosis in intestinal inflammation: Cause or consequence. Int J Med Microbiol 2016; 306:302-309. [PMID: 27012594 DOI: 10.1016/j.ijmm.2016.02.010] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 02/26/2016] [Accepted: 02/29/2016] [Indexed: 02/07/2023] Open
Abstract
The intestinal microbiota encompasses hundreds of bacterial species that constitute a relatively stable ecosystem. Alteration in the microbiota composition may arise from infections, immune defects, metabolic alterations, diet or antibiotic treatment. Dysbiosis is considered as an alteration in microbiota community structure and/or function, capable of causing/driving a detrimental distortion of microbe-host homeostasis. A variety of pathologies are associated with changes in the community structure and function of the gut microbiota, suggesting a link between dysbiosis and disease etiology. With an emphasis in this review on inflammatory bowel diseases (IBD), the non-trivial question is whether dysbiosis is the cause or consequence of inflammation. It is important to understand whether changes in microbial ecosystems are causally linked to the pathology and to what extend disease risk is predicable based on characteristic changes in community structure and/or function. Local changes in tissue integrity associated with focal areas of inflammation may result in the selection of a dysbiotic bacterial community associated with the propagation of a disease phenotype. This review outlines the role of dysbiosis in intestinal inflammation with particular focus on IBD-relevant gnotobiotic mouse models, the factors implicated in the development of dysbiosis and the means available to investigate dysbiosis in the context of human diseases.
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19
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Marchesi JR, Adams DH, Fava F, Hermes GDA, Hirschfield GM, Hold G, Quraishi MN, Kinross J, Smidt H, Tuohy KM, Thomas LV, Zoetendal EG, Hart A. The gut microbiota and host health: a new clinical frontier. Gut 2016; 65:330-9. [PMID: 26338727 PMCID: PMC4752653 DOI: 10.1136/gutjnl-2015-309990] [Citation(s) in RCA: 1401] [Impact Index Per Article: 175.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 07/16/2015] [Indexed: 12/15/2022]
Abstract
Over the last 10-15 years, our understanding of the composition and functions of the human gut microbiota has increased exponentially. To a large extent, this has been due to new 'omic' technologies that have facilitated large-scale analysis of the genetic and metabolic profile of this microbial community, revealing it to be comparable in influence to a new organ in the body and offering the possibility of a new route for therapeutic intervention. Moreover, it might be more accurate to think of it like an immune system: a collection of cells that work in unison with the host and that can promote health but sometimes initiate disease. This review gives an update on the current knowledge in the area of gut disorders, in particular metabolic syndrome and obesity-related disease, liver disease, IBD and colorectal cancer. The potential of manipulating the gut microbiota in these disorders is assessed, with an examination of the latest and most relevant evidence relating to antibiotics, probiotics, prebiotics, polyphenols and faecal microbiota transplantation.
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Affiliation(s)
- Julian R Marchesi
- School of Biosciences, Museum Avenue, Cardiff University, Cardiff, UK,Centre for Digestive and Gut Health, Imperial College London, London, UK
| | - David H Adams
- NIHR Biomedical Research Unit, Centre for Liver Research, University of Birmingham, Birmingham, UK
| | - Francesca Fava
- Nutrition and Nutrigenomics Group, Department of Food Quality and Nutrition, Research and Innovation Centre, Trento, Italy
| | - Gerben D A Hermes
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands,Top Institute Food and Nutrition (TIFN), Wageningen, The Netherlands
| | - Gideon M Hirschfield
- NIHR Biomedical Research Unit, Centre for Liver Research, University of Birmingham, Birmingham, UK
| | - Georgina Hold
- Division of Applied Medicine, School of Medicine and Dentistry, University of Aberdeen, Institute of Medical Sciences, Aberdeen, UK
| | - Mohammed Nabil Quraishi
- NIHR Biomedical Research Unit, Centre for Liver Research, University of Birmingham, Birmingham, UK
| | - James Kinross
- Section of Computational and Systems Medicine, Faculty of Medicine, Imperial College London, London, UK
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Kieran M Tuohy
- Nutrition and Nutrigenomics Group, Department of Food Quality and Nutrition, Research and Innovation Centre, Trento, Italy
| | | | - Erwin G Zoetendal
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands,Top Institute Food and Nutrition (TIFN), Wageningen, The Netherlands
| | - Ailsa Hart
- IBD Unit, St Mark's Hospital and Imperial College London, London, UK
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20
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Genome-based Definition of an Inflammatory Bowel Disease-associated Adherent-Invasive Escherichia coli Pathovar. Inflamm Bowel Dis 2016; 22:1-12. [PMID: 26444104 DOI: 10.1097/mib.0000000000000574] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
BACKGROUND Mucosal-associated Escherichia coli are commonly found in inflamed tissues during inflammatory bowel disease (IBD). These bacteria often possess an adherent and invasive phenotype but lack virulence-associated features of well-described intestinal E. coli pathogens, and are of diverse serology and phylotypes, making it difficult to correlate strain characteristics with exacerbations of disease. METHODS The genome sequences of 14 phenotypically assigned adherent-invasive Escherichia coli (AIEC) isolates obtained from intestinal biopsies of patients with IBD were compared with the genome sequences of 37 other pathogenic and commensal E. coli available from public databases. RESULTS Core genome-based phylogenetic analyses and genome-wide comparison of genetic content established the existence of a closely related cluster of AIEC strains with 3 distinct genetic insertions differentiating them from commensal E. coli. These strains are of the B2 phylotype have a variant type VI secretion system (T6SS-1), and are highly related to extraintestinal pathogenic E. coli, suggesting that these 2 clinically distinct pathovars have common virulence strategies. Four other mucosally adherent E. coli strains from patients with IBD were of diverse phylogenetic origins and lacked the 3 genetic features, suggesting that they are not related to the B2 AIEC cluster. Although AIEC are often considered as having a unique association with Crohn's disease, isolates from Crohn's disease and ulcerative colitis were genetically indistinguishable. CONCLUSIONS B2 AIEC thus represent a closely related cluster of IBD-associated E. coli strains that are distinct from normal commensal isolates, and which should be considered separately from the phenotypically similar but genetically distinct non-B2 AIEC strains when considering their association with intestinal pathogenesis.
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21
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Denizot J, Desrichard A, Agus A, Uhrhammer N, Dreux N, Vouret-Craviari V, Hofman P, Darfeuille-Michaud A, Barnich N. Diet-induced hypoxia responsive element demethylation increases CEACAM6 expression, favouring Crohn's disease-associated Escherichia coli colonisation. Gut 2015; 64:428-37. [PMID: 24898815 DOI: 10.1136/gutjnl-2014-306944] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Adherent-invasive Escherichia coli (AIEC) are abnormally predominant on Crohn's disease (CD) ileal mucosa. AIEC strains adhere to enterocytes via interaction between type 1 pili and CEACAM6 receptors abnormally expressed on CD ileal mucosa, leading to gut inflammation. We analysed whether epigenetic mechanisms are involved in the upregulation of CEACAM6 expression in intestinal epithelial cells (IECs). DESIGN Methylation of CEACAM6 promoter was analysed using bisulfite sequencing and site-specific methylation by SnapShot. pCpGfree reporter system was used to analyse CEACAM6 promoter activity. Transgenic mice expressing human CEACAM6 fed either standard food or a low-methyl diet (LMD) were orally challenged with 10(9) AIEC LF82. After 3 days, gut-associated AIEC and proinflammatory cytokines were quantified. RESULTS Analysis of CEACAM6 gene promoter revealed potentially methylated dinucleotide CpGs within HIF-1-responsive elements (HREs). Methylation levels of CpG within CEACAM6 promoter were inversely correlated with CEACAM6 expression in IEC expressing various levels of CEACAM6. We show the critical role of HRE methylation and transcription factor HIF-1 in the regulation of CEACAM6 gene in IEC. This was confirmed in transgenic mice expressing human CEACAM6 fed a LMD. LMD-dependent HRE demethylation led to abnormal gut expression of CEACAM6, favouring AIEC colonisation and subsequent inflammation. CONCLUSIONS HRE hypomethylation in CEACAM6 promoter correlates with high expression in IEC. Our findings suggest that abnormal DNA methylation leading to CEACAM6 increased expression and AIEC-mediated gut inflammation can be related to changes in nutritional habits, such as low intake in methyl donor molecules, leading to abnormal epigenetic marks in mouse model mimicking CD susceptibility.
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Affiliation(s)
- Jérémy Denizot
- Clermont Université, M2iSH, UMR 1071 INSERM/Université d'Auvergne, Clermont-Ferrand, France Unité Sous Contrat 2018 Institut National de la Recherche Agronomique, Clermont-Ferrand, France
| | - Alexis Desrichard
- Departments of Oncogenetics and Breast Oncology, Centre Jean Perrin, Clermont-Ferrand, France
| | - Allison Agus
- Clermont Université, M2iSH, UMR 1071 INSERM/Université d'Auvergne, Clermont-Ferrand, France Unité Sous Contrat 2018 Institut National de la Recherche Agronomique, Clermont-Ferrand, France
| | - Nancy Uhrhammer
- Departments of Oncogenetics and Breast Oncology, Centre Jean Perrin, Clermont-Ferrand, France
| | - Nicolas Dreux
- Clermont Université, M2iSH, UMR 1071 INSERM/Université d'Auvergne, Clermont-Ferrand, France Unité Sous Contrat 2018 Institut National de la Recherche Agronomique, Clermont-Ferrand, France
| | - Valérie Vouret-Craviari
- Institute for Research on Cancer and aging (IRCAN), Nice, France University of Nice-Sophia Antipolis, Nice, France
| | - Paul Hofman
- Institute for Research on Cancer and aging (IRCAN), Nice, France University of Nice-Sophia Antipolis, Nice, France Laboratory of Clinical and Experimental Pathology and Human Biobank, Pasteur Hospital, Nice, France
| | - Arlette Darfeuille-Michaud
- Clermont Université, M2iSH, UMR 1071 INSERM/Université d'Auvergne, Clermont-Ferrand, France Unité Sous Contrat 2018 Institut National de la Recherche Agronomique, Clermont-Ferrand, France Institut Universitaire de Technologie, Génie Biologique, Aubière, France Centre Hospitalier Universitaire Clermont-Ferrand, France
| | - Nicolas Barnich
- Clermont Université, M2iSH, UMR 1071 INSERM/Université d'Auvergne, Clermont-Ferrand, France Unité Sous Contrat 2018 Institut National de la Recherche Agronomique, Clermont-Ferrand, France Institut Universitaire de Technologie, Génie Biologique, Aubière, France
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Blais Lecours P, Marsolais D, Cormier Y, Berberi M, Haché C, Bourdages R, Duchaine C. Increased prevalence of Methanosphaera stadtmanae in inflammatory bowel diseases. PLoS One 2014; 9:e87734. [PMID: 24498365 PMCID: PMC3912014 DOI: 10.1371/journal.pone.0087734] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 12/28/2013] [Indexed: 12/12/2022] Open
Abstract
Background The gut microbiota is associated with the modulation of mucosal immunity and the etiology of inflammatory bowel diseases (IBD). Previous studies focused on the impact of bacterial species on IBD but seldom suspected archaea, which can be a major constituent of intestinal microbiota, to be implicated in the diseases. Recent evidence supports that two main archaeal species found in the digestive system of humans, Methanobrevibacter smithii (MBS) and Methanosphaera stadtmanae (MSS) can have differential immunogenic properties in lungs of mice; with MSS but not MBS being a strong inducer of the inflammatory response. We thus aimed at documenting the immunogenic potential of MBS and MSS in humans and to explore their association with IBD. Methods To validate the immunogenicity of MBS and MSS in humans, peripheral blood mononuclear cells from healthy subjects were stimulated with these two microorganisms and the production of inflammatory cytokine TNF was measured by ELISA. To verify MBS and MSS prevalence in IBD, stool samples from 29 healthy control subjects and 29 patients suffering from IBD were collected for DNA extraction. Plasma was also collected from these subjects to measure antigen-specific IgGs by ELISA. Quantitative PCR was used for bacteria, methanogens, MBS and MSS quantification. Results Mononuclear cells stimulated with MSS produced higher concentrations of TNF (39.5 ng/ml) compared to MBS stimulation (9.1 ng/ml). Bacterial concentrations and frequency of MBS-containing stools were similar in both groups. However, the number of stool samples positive for the inflammatory archaea MSS was higher in patients than in controls (47% vs 20%). Importantly, only IBD patients developed a significant anti-MSS IgG response. Conclusion The prevalence of MSS is increased in IBD patients and is associated with an antigen-specific IgG response.
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Affiliation(s)
- Pascale Blais Lecours
- Centre de recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Québec, Québec, Canada
| | - David Marsolais
- Centre de recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Québec, Québec, Canada
- Département de médecine, Faculté de médecine, Université Laval, Québec, QC, Canada
| | - Yvon Cormier
- Centre de recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Québec, Québec, Canada
- Département de médecine, Faculté de médecine, Université Laval, Québec, QC, Canada
| | | | | | | | - Caroline Duchaine
- Centre de recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Québec, Québec, Canada
- Département de biochimie, de microbiologie et de bioinformatique, Faculté des sciences et de génie, Université Laval, Québec, Québec, Canada
- * E-mail:
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Mukhopadhya I, Hansen R, El-Omar EM, Hold GL. IBD-what role do Proteobacteria play? Nat Rev Gastroenterol Hepatol 2012. [PMID: 22349170 DOI: 10.1038/nrgastro] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The gastrointestinal microbiota has come to the fore in the search for the causes of IBD. This shift has largely been driven by the finding of genetic polymorphisms involved in gastrointestinal innate immunity (particularly polymorphisms in NOD2 and genes involved in autophagy) and alterations in the composition of the microbiota that might result in inflammation (so-called dysbiosis). Microbial diversity studies have continually demonstrated an expansion of the Proteobacteria phylum in patients with IBD. Individual Proteobacteria, in particular (adherent-invasive) Escherichia coli, Campylobacter concisus and enterohepatic Helicobacter, have all been associated with the pathogenesis of IBD. In this Review, we comprehensively describe the various associations of Proteobacteria and IBD. We also examine the importance of pattern recognition in the extracellular innate immune response of the host with particular reference to Proteobacteria, and postulate that Proteobacteria with adherent and invasive properties might exploit host defenses, drive proinflammatory change, alter the intestinal microbiota in favor of dysbiosis and ultimately lead to the development of IBD.
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Affiliation(s)
- Indrani Mukhopadhya
- Gastrointestinal Research Group, Division of Applied Medicine, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK
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Abstract
The gastrointestinal microbiota has come to the fore in the search for the causes of IBD. This shift has largely been driven by the finding of genetic polymorphisms involved in gastrointestinal innate immunity (particularly polymorphisms in NOD2 and genes involved in autophagy) and alterations in the composition of the microbiota that might result in inflammation (so-called dysbiosis). Microbial diversity studies have continually demonstrated an expansion of the Proteobacteria phylum in patients with IBD. Individual Proteobacteria, in particular (adherent-invasive) Escherichia coli, Campylobacter concisus and enterohepatic Helicobacter, have all been associated with the pathogenesis of IBD. In this Review, we comprehensively describe the various associations of Proteobacteria and IBD. We also examine the importance of pattern recognition in the extracellular innate immune response of the host with particular reference to Proteobacteria, and postulate that Proteobacteria with adherent and invasive properties might exploit host defenses, drive proinflammatory change, alter the intestinal microbiota in favor of dysbiosis and ultimately lead to the development of IBD.
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Affiliation(s)
- Indrani Mukhopadhya
- Gastrointestinal Research Group, Division of Applied Medicine, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK
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Bifidobacterium animalis subsp. lactis fermented milk product reduces inflammation by altering a niche for colitogenic microbes. Proc Natl Acad Sci U S A 2010; 107:18132-7. [PMID: 20921388 DOI: 10.1073/pnas.1011737107] [Citation(s) in RCA: 166] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Intestinal health requires the coexistence of eukaryotic self with the gut microbiota and dysregulated host-microbial interactions can result in intestinal inflammation. Here, we show that colitis improved in T-bet(-/-)Rag2(-/-) mice that consumed a fermented milk product containing Bifidobacterium animalis subsp. lactis DN-173 010 strain. A decrease in cecal pH and alterations in short chain fatty acid profiles occurred with consumption, and there were concomitant increases in the abundance of select lactate-consuming and butyrate-producing bacteria. These metabolic shifts created a nonpermissive environment for the Enterobacteriaceae recently identified as colitogenic in a T-bet(-/-)Rag2(-/-) ulcerative colitis mouse model. In addition, 16S rRNA-based analysis of the T-bet(-/-)Rag2(-/-) fecal microbiota suggest that the structure of the endogenous gut microbiota played a key role in shaping the host response to the bacterial strains studied herein. We have identified features of the gut microbiota, at the membership and functional level, associated with response to this B. lactis-containing fermented milk product, and therefore this model provides a framework for evaluating and optimizing probiotic-based functional foods.
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Tannock GW. The bowel microbiota and inflammatory bowel diseases. Int J Inflam 2010; 2010:954051. [PMID: 21188223 PMCID: PMC3004003 DOI: 10.4061/2010/954051] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2010] [Accepted: 07/04/2010] [Indexed: 12/15/2022] Open
Abstract
The human bowel contains a large and biodiverse bacterial community known as the microbiota or microbiome. It seems likely that the microbiota, fractions of the microbiota, or specific species comprising the microbiota provide the antigenic fuel that drives the chronic immune inflammation of the bowel mucosa that is characteristic of Crohn's disease and ulcerative colitis. At least twenty years of microbiological research have been expended on analysis of the composition of the bowel microbiota of inflammatory bowel disease patients in comparison to that of control subjects. Despite extensive speculations about the aetiological role of dysbiosis in inflammatory bowel diseases, knowledge that can be easily translated into effective remedies for patients has not eventuated. The causes of this failure may be due to poorly defined and executed bacteriological studies, as well as the overwhelming complexity of a biome that contains hundreds of bacterial species and trillions of bacterial cells.
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Affiliation(s)
- Gerald W Tannock
- Department of Microbiology and Immunology, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
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