451
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Balakrishnan B, Taneja V. Microbial modulation of the gut microbiome for treating autoimmune diseases. Expert Rev Gastroenterol Hepatol 2018; 12:985-996. [PMID: 30146910 DOI: 10.1080/17474124.2018.1517044] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Many studies have shown the relationship between autoimmune diseases and the gut microbiome in humans: those with autoimmune conditions display gut microbiome dysbiosis. The big question that needs to be addressed is if restoring eubiosis of the gut microbiota can help suppress the autoimmune condition by activating various immune regulatory mechanisms. Inducing these self-healing mechanisms should prolong good health in affected individuals. Area covered: Here, we review the available clinical and preclinical studies that have used selective bacteria for modulating gut microbiota for treating autoimmune diseases. The potential bacterial candidates and their mechanism of action in treating autoimmune diseases will be discussed. We searched for genetically modified and potential probiotics for diseases and discuss the most likely candidates. Expert commentary: To achieve eubiosis, manipulation of the gut microbiota must occur in some form. Several approaches for modulating gut microbiota include prebiotic diets, antimicrobial interventions, fecal microbiota transplants, and selective probiotics. One novel approach showing promising results is the use of selective bacterial candidates to modulate microbial composition. Use of single microbe for treatment has an advantage as compared to multi-species as microbes grow at different rates and if needed, a single microbe is easy to target.
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Affiliation(s)
| | - Veena Taneja
- a Department of Immunology , Mayo Clinic , Rochester , MN , USA
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452
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Picchianti-Diamanti A, Panebianco C, Salemi S, Sorgi ML, Di Rosa R, Tropea A, Sgrulletti M, Salerno G, Terracciano F, D'Amelio R, Laganà B, Pazienza V. Analysis of Gut Microbiota in Rheumatoid Arthritis Patients: Disease-Related Dysbiosis and Modifications Induced by Etanercept. Int J Mol Sci 2018; 19:ijms19102938. [PMID: 30261687 PMCID: PMC6213034 DOI: 10.3390/ijms19102938] [Citation(s) in RCA: 133] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 09/19/2018] [Accepted: 09/25/2018] [Indexed: 12/24/2022] Open
Abstract
A certain number of studies were carried out to address the question of how dysbiosis could affect the onset and development of rheumatoid arthritis (RA), but little is known about the reciprocal influence between microbiota composition and immunosuppressive drugs, and how this interaction may have an impact on the clinical outcome. The aim of this study was to characterize the intestinal microbiota in a groups of RA patients treatment-naïve, under methotrexate, and/or etanercept (ETN). Correlations between the gut microbiota composition and validated immunological and clinical parameters of disease activity were also evaluated. In the current study, a 16S analysis was employed to explore the gut microbiota of 42 patients affected by RA and 10 healthy controls. Disease activity score on 28 joints (DAS-28), erythrocyte sedimentation rate, C-reactive protein, rheumatoid factor, anti-cyclic citrullinated peptides, and dietary and smoking habits were assessed. The composition of the gut microbiota in RA patients free of therapy is characterized by several abnormalities compared to healthy controls. Gut dysbiosis in RA patients is associated with different serological and clinical parameters; in particular, the phylum of Euryarchaeota was directly correlated to DAS and emerged as an independent risk factor. Patients under treatment with ETN present a partial restoration of a beneficial microbiota. The results of our study confirm that gut dysbiosis is a hallmark of the disease, and shows, for the first time, that the anti-tumor necrosis factor alpha (TNF-α) ETN is able to modify microbial communities, at least partially restoring a beneficial microbiota.
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Affiliation(s)
- Andrea Picchianti-Diamanti
- Department of Clinical and Molecular Medicine, Sant'Andrea University Hospital, Sapienza University of Rome, 00185 Rome, Italy.
| | - Concetta Panebianco
- Gastroenterology Unit, IRCCS "Casa Sollievo della Sofferenza" Hospital, Viale dei Cappuccini, 1, 71013 San Giovanni Rotondo, Italy.
| | - Simonetta Salemi
- Department of Clinical and Molecular Medicine, Sant'Andrea University Hospital, Sapienza University of Rome, 00185 Rome, Italy.
| | - Maria Laura Sorgi
- Department of Clinical and Molecular Medicine, Sant'Andrea University Hospital, Sapienza University of Rome, 00185 Rome, Italy.
| | - Roberta Di Rosa
- Department of Clinical and Molecular Medicine, Sant'Andrea University Hospital, Sapienza University of Rome, 00185 Rome, Italy.
| | - Alessandro Tropea
- Department of Clinical and Molecular Medicine, Sant'Andrea University Hospital, Sapienza University of Rome, 00185 Rome, Italy.
| | - Mayla Sgrulletti
- Department of Clinical and Molecular Medicine, Sant'Andrea University Hospital, Sapienza University of Rome, 00185 Rome, Italy.
| | - Gerardo Salerno
- Department of Clinical and Molecular Medicine, Sant'Andrea University Hospital, Sapienza University of Rome, 00185 Rome, Italy.
| | - Fulvia Terracciano
- Gastroenterology Unit, IRCCS "Casa Sollievo della Sofferenza" Hospital, Viale dei Cappuccini, 1, 71013 San Giovanni Rotondo, Italy.
| | - Raffaele D'Amelio
- Department of Clinical and Molecular Medicine, Sant'Andrea University Hospital, Sapienza University of Rome, 00185 Rome, Italy.
| | - Bruno Laganà
- Department of Clinical and Molecular Medicine, Sant'Andrea University Hospital, Sapienza University of Rome, 00185 Rome, Italy.
| | - Valerio Pazienza
- Gastroenterology Unit, IRCCS "Casa Sollievo della Sofferenza" Hospital, Viale dei Cappuccini, 1, 71013 San Giovanni Rotondo, Italy.
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453
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Moris G, Arboleya S, Mancabelli L, Milani C, Ventura M, de Los Reyes-Gavilán CG, Gueimonde M. Fecal microbiota profile in a group of myasthenia gravis patients. Sci Rep 2018; 8:14384. [PMID: 30258104 PMCID: PMC6158187 DOI: 10.1038/s41598-018-32700-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 09/11/2018] [Indexed: 02/08/2023] Open
Abstract
The intestinal microbiota plays a key role in the maintenance of human health. Alterations in this microbiota have been described in several autoimmune diseases, including nervous system diseases. Nevertheless, the information regarding neuromuscular conditions is still limited. In this study, we aimed at characterizing the intestinal microbiota composition in myasthenia gravis patients (MG). To this end fecal samples were taken from ten patients, with antibodies against the acetylcholine receptor, and ten age and sex matched controls from the same population (Asturias region, Spain). Fecal samples were submitted to microbiota analyses by 16S rRNA gene profiling, bifidobacterial ITS-region profiling and qPCR. The fecal levels of short chain fatty acids were determined by gas chromatography. MG patients were found to harbor lower relative proportions of Verrucomicrobiaceae and Bifidobacteriaceae, among others, and increased of the phylum Bacteroidetes and the family Desulfovibrionaceae. The increase of these latter microbial groups was also confirmed at quantitative level by qPCR. In contrast, no statistically significant differences were found between MG patients and the control group in the bifidobacterial population at the species level or in short chain fatty acids profiles. Our data indicates an altered fecal microbiota pattern in MG patients and point out at specific microbiota targets for intervention in this population.
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Affiliation(s)
- German Moris
- Neurology Service, Asturias Central University Hospital (HUCA), SESPA, Oviedo, Asturias, Spain
| | - Silvia Arboleya
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), 33300, Villaviciosa, Asturias, Spain.,Diet, Microbiota and Health Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.,Microbiome Research Hub, University of Parma, Parma, Italy
| | - Clara G de Los Reyes-Gavilán
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), 33300, Villaviciosa, Asturias, Spain.,Diet, Microbiota and Health Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Miguel Gueimonde
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), 33300, Villaviciosa, Asturias, Spain. .,Diet, Microbiota and Health Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain.
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454
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Vogelzang A, Guerrini MM, Minato N, Fagarasan S. Microbiota - an amplifier of autoimmunity. Curr Opin Immunol 2018; 55:15-21. [PMID: 30248521 DOI: 10.1016/j.coi.2018.09.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 09/07/2018] [Indexed: 02/08/2023]
Abstract
Many studies describe dysbiosis as a change in the microbiota that accompanies autoimmune illnesses, but little is known about whether these changes are a cause or consequence of an altered immune state. The immune system actively shapes the composition of the microbiota, with divergent outcomes in healthy or autoimmune-prone individuals. The gut microbiota in turn acts as an acquired endocrine organ, influencing the physiology of the host via release of nutrients and chemical messengers. Dysbiosis arising from abnormal immune function can initiate or amplify autoimmunity through multiple mechanisms. We examine how the bidirectional relationship between resident microbes and the immune system contributes to autoimmune diseases.
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Affiliation(s)
- Alexis Vogelzang
- Laboratory for Mucosal Immunity, Center for Integrative Medical Sciences, RIKEN Yokohama Institute, Tsurumi Ward, Suehirocho, 1 Chome-7-22, Yokohama, Kanagawa Prefecture, 230-0045, Japan
| | - Matteo M Guerrini
- Laboratory for Mucosal Immunity, Center for Integrative Medical Sciences, RIKEN Yokohama Institute, Tsurumi Ward, Suehirocho, 1 Chome-7-22, Yokohama, Kanagawa Prefecture, 230-0045, Japan
| | - Nagahiro Minato
- Medical Innovation Center, Kyoto University Graduate School of Medicine, Sakyo Ward, Yoshida-Konoe, Kyoto, Kyoto Prefecture, 606-8501, Japan
| | - Sidonia Fagarasan
- Laboratory for Mucosal Immunity, Center for Integrative Medical Sciences, RIKEN Yokohama Institute, Tsurumi Ward, Suehirocho, 1 Chome-7-22, Yokohama, Kanagawa Prefecture, 230-0045, Japan.
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455
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Holers VM, Demoruelle MK, Kuhn KA, Buckner JH, Robinson WH, Okamoto Y, Norris JM, Deane KD. Rheumatoid arthritis and the mucosal origins hypothesis: protection turns to destruction. Nat Rev Rheumatol 2018; 14:542-557. [PMID: 30111803 PMCID: PMC6704378 DOI: 10.1038/s41584-018-0070-0] [Citation(s) in RCA: 225] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Individuals at high risk of developing seropositive rheumatoid arthritis (RA) can be identified for translational research and disease prevention studies through the presence of highly informative and predictive patterns of RA-related autoantibodies, especially anti-citrullinated protein antibodies (ACPAs), in the serum. In serologically positive individuals without arthritis, designated ACPA positive at risk, the presence of mucosal inflammatory processes associated with the presence of local ACPA production has been demonstrated. In other at-risk populations, local RA-related autoantibody production is present even in the absence of serum autoantibodies. Additionally, a proportion of at-risk individuals exhibit local mucosal ACPA production in the lung, as well as radiographic small-airway disease, sputum hypercellularity and increased neutrophil extracellular trap formation. Other mucosal sites in at-risk individuals also exhibit autoantibody production, inflammation and/or evidence of dysbiosis. As the proportion of individuals who exhibit such localized inflammation-associated ACPA production is substantially higher than the likelihood of an individual developing future RA, this finding raises the hypothesis that mucosal ACPAs have biologically relevant protective roles. Identifying the mechanisms that drive both the generation and loss of externally focused mucosal ACPA production and promote systemic autoantibody expression and ultimately arthritis development should provide insights into new therapeutic approaches to prevent RA.
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Affiliation(s)
- V Michael Holers
- Division of Rheumatology, University of Colorado-Denver, Aurora, CO, USA.
| | | | - Kristine A Kuhn
- Division of Rheumatology, University of Colorado-Denver, Aurora, CO, USA
| | | | - William H Robinson
- Division of Immunology and Rheumatology, Stanford University, Stanford, CA, USA
| | - Yuko Okamoto
- Division of Rheumatology, University of Colorado-Denver, Aurora, CO, USA
| | - Jill M Norris
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO, USA
| | - Kevin D Deane
- Division of Rheumatology, University of Colorado-Denver, Aurora, CO, USA
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456
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Dudics S, Langan D, Meka RR, Venkatesha SH, Berman BM, Che CT, Moudgil KD. Natural Products for the Treatment of Autoimmune Arthritis: Their Mechanisms of Action, Targeted Delivery, and Interplay with the Host Microbiome. Int J Mol Sci 2018; 19:ijms19092508. [PMID: 30149545 PMCID: PMC6164747 DOI: 10.3390/ijms19092508] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 08/12/2018] [Accepted: 08/18/2018] [Indexed: 12/16/2022] Open
Abstract
Rheumatoid arthritis (RA) is a chronic, debilitating illness characterized by painful swelling of the joints, inflammation of the synovial lining of the joints, and damage to cartilage and bone. Several anti-inflammatory and disease-modifying drugs are available for RA therapy. However, the prolonged use of these drugs is associated with severe side effects. Furthermore, these drugs are effective only in a proportion of RA patients. Hence, there is a need to search for new therapeutic agents that are effective yet safe. Interestingly, a variety of herbs and other natural products offer a vast resource for such anti-arthritic agents. We discuss here the basic features of RA pathogenesis; the commonly used animal models of RA; the mainstream drugs used for RA; the use of well-characterized natural products possessing anti-arthritic activity; the application of nanoparticles for efficient delivery of such products; and the interplay between dietary products and the host microbiome for maintenance of health and disease induction. We believe that with several advances in the past decade in the characterization and functional studies of natural products, the stage is set for widespread clinical testing and/or use of these products for the treatment of RA and other diseases.
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Affiliation(s)
- Steven Dudics
- Baltimore Veterans Affairs Medical Center, Baltimore, MD 21201, USA.
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
| | - David Langan
- Baltimore Veterans Affairs Medical Center, Baltimore, MD 21201, USA.
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
| | - Rakeshchandra R Meka
- Baltimore Veterans Affairs Medical Center, Baltimore, MD 21201, USA.
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
| | - Shivaprasad H Venkatesha
- Baltimore Veterans Affairs Medical Center, Baltimore, MD 21201, USA.
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
| | - Brian M Berman
- Family and Community Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
- Center for Integrative Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
| | - Chun-Tao Che
- Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, USA.
| | - Kamal D Moudgil
- Baltimore Veterans Affairs Medical Center, Baltimore, MD 21201, USA.
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
- Division of Rheumatology, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
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457
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Shan J, Peng L, Qian W, Xie T, Kang A, Gao B, Di L. Integrated Serum and Fecal Metabolomics Study of Collagen-Induced Arthritis Rats and the Therapeutic Effects of the Zushima Tablet. Front Pharmacol 2018; 9:891. [PMID: 30154719 PMCID: PMC6102586 DOI: 10.3389/fphar.2018.00891] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 07/23/2018] [Indexed: 11/18/2022] Open
Abstract
The Zushima tablet (ZT) has been used for decades in the clinical treatment of rheumatoid arthritis (RA) in China. However, its therapeutic mechanism is unclear. In this study, we aimed to explore the distinctive metabolic patterns in collagen-induced arthritis (CIA) rats and evaluate the therapeutic effects of ZT on RA using untargeted serum and fecal metabolomics approaches based on gas chromatography coupled with mass spectrometry. Body weight, hind paw swelling, TNF-α and IL-1β levels, arthritis scores, and histopathological parameters were assessed. In the metabolomics study, 31 altered metabolites in the serum and 30 in the feces were identified by comparing the model with the control group using statistical processing. These altered metabolites revealed that the tricarboxylic acid cycle, glycolysis metabolism, fatty acid metabolism, and purine metabolism were disturbed in CIA rats, and most of these altered metabolites including l-isoleucine, l-aspartic acid, pyruvic acid, cholic acid, and hypoxanthine, were rectified by ZT. Furthermore, short-chain fatty acids in feces were quantitatively determined, and the results showed that ZT could regulate the levels of propionate, butyrate, and valerate in CIA rats. Then, gut microbiota were analyzed by 16S rRNA analysis. Our results showed that Firmicutes and Bacteroidetes were the most abundant bacteria in rats. The levels of 19 types of bacteria at the family level were altered in RA rats, and most of them could be regulated by ZT. This study demonstrated that metabolomics analysis is a powerful tool for providing novel insight into RA and for elucidating the potential mechanism of ZT.
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Affiliation(s)
- Jinjun Shan
- Jiangsu Key Laboratory of Pediatric Respiratory Disease, Institute of Pediatrics, Nanjing University of Chinese Medicine, Nanjing, China.,Medical Metabolomics Center, Nanjing University of Chinese Medicine, Nanjing, China
| | - Linxiu Peng
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Wenjuan Qian
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Tong Xie
- Jiangsu Key Laboratory of Pediatric Respiratory Disease, Institute of Pediatrics, Nanjing University of Chinese Medicine, Nanjing, China.,Medical Metabolomics Center, Nanjing University of Chinese Medicine, Nanjing, China
| | - An Kang
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China.,Jiangsu Key Laboratory for Functional Substance of Chinese Medicine, Nanjing, China
| | - Bei Gao
- Genome Center of UC Davis, NIH West Coast Metabolomics Center, Davis, CA, United States
| | - Liuqing Di
- Jiangsu Key Laboratory of Pediatric Respiratory Disease, Institute of Pediatrics, Nanjing University of Chinese Medicine, Nanjing, China.,State Key Laboratory Cultivation Base for TCM Quality and Efficacy, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China.,Jiangsu Key Laboratory for Functional Substance of Chinese Medicine, Nanjing, China
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458
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The Anti-Inflammatory Mediator, Vasoactive Intestinal Peptide, Modulates the Differentiation and Function of Th Subsets in Rheumatoid Arthritis. J Immunol Res 2018; 2018:6043710. [PMID: 30155495 PMCID: PMC6092975 DOI: 10.1155/2018/6043710] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 07/19/2018] [Indexed: 12/15/2022] Open
Abstract
Genetic background, epigenetic modifications, and environmental factors trigger autoimmune response in rheumatoid arthritis (RA). Several pathogenic infections have been related to the onset of RA and may cause an inadequate immunological tolerance towards critical self-antigens leading to chronic joint inflammation and an imbalance between different T helper (Th) subsets. Vasoactive intestinal peptide (VIP) is a mediator that modulates all the stages comprised between the arrival of pathogens and Th cell differentiation in RA through its known anti-inflammatory and immunomodulatory actions. This “neuroimmunopeptide” modulates the pathogenic activity of diverse cell subpopulations involved in RA as lymphocytes, fibroblast-like synoviocytes (FLS), or macrophages. In addition, VIP decreases the expression of pattern recognition receptor (PRR) such as toll-like receptors (TLRs) in FLS from RA patients. These receptors act as sensors of pathogen-associated molecular pattern (PAMP) and damage-associated molecular pattern (DAMP) connecting the innate and adaptive immune system. Moreover, VIP modulates the imbalance between Th subsets in RA, decreasing pathogenic Th1 and Th17 subsets and favoring Th2 or Treg profile during the differentiation/polarization of naïve or memory Th cells. Finally, VIP regulates the plasticity between theses subsets. In this review, we provide an overview of VIP effects on the aforementioned features of RA pathology.
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459
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Medina G, Vera-Lastra O, Peralta-Amaro AL, Jiménez-Arellano MP, Saavedra MA, Cruz-Domínguez MP, Jara LJ. Metabolic syndrome, autoimmunity and rheumatic diseases. Pharmacol Res 2018; 133:277-288. [DOI: 10.1016/j.phrs.2018.01.009] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 01/16/2018] [Accepted: 01/18/2018] [Indexed: 12/14/2022]
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460
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Analysis of gut microbiota diversity and auxiliary diagnosis as a biomarker in patients with schizophrenia: A cross-sectional study. Schizophr Res 2018; 197:470-477. [PMID: 29352709 DOI: 10.1016/j.schres.2018.01.002] [Citation(s) in RCA: 195] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 12/26/2017] [Accepted: 01/01/2018] [Indexed: 12/20/2022]
Abstract
With the advent of sequencing technology, characterization of schizophrenia with underlying probing of gut microbiome can provide abundant clues for diagnosis and prognosis of schizophrenia. In this study, we first compared the difference of gut microbiota between schizophrenia patients and healthy controls by 16S rRNA sequencing. We further explored whether gut microbiota can be used as a biomarker to assist in the diagnosis of schizophrenia. We restricted inclusion criteria strictly to control confounding bias. Finally, we investigated differences in fecal microbiota between 64 schizophrenia patients and 53 healthy controls. At the phylum level, we found that the abundance of Proteobacteria in the schizophrenia patients was significantly increased. At the genus level, the relative abundance of Succinivibrio, Megasphaera, Collinsella, Clostridium, Klebsiella and Methanobrevibacter was significantly higher whereas the abundance of Blautia, Coprococcus, Roseburia was decreased compared to health controls. The receiver operating characteristic curve analysis demonstrated that 12 significant microbiota biomarkers were capable of being used as diagnostic factors for distinguishing the schizophrenia cohort from those in the control cohort (AUC = 0.837). We performed PICRUSt analysis and found that several metabolic pathways differed significantly between healthy controls and schizophrenia patients, including vitamin B6 and fatty acid. In conclusion, there are some difference of gut microbiota between schizophrenia patients and healthy controls and the insights from this study could be used to develop microbiota-based diagnosis for schizophrenia.
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461
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Xiao J, Chen L, Johnson S, Yu Y, Zhang X, Chen J. Predictive Modeling of Microbiome Data Using a Phylogeny-Regularized Generalized Linear Mixed Model. Front Microbiol 2018; 9:1391. [PMID: 29997602 PMCID: PMC6030386 DOI: 10.3389/fmicb.2018.01391] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 06/06/2018] [Indexed: 12/21/2022] Open
Abstract
Recent human microbiome studies have revealed an essential role of the human microbiome in health and disease, opening up the possibility of building microbiome-based predictive models for individualized medicine. One unique characteristic of microbiome data is the existence of a phylogenetic tree that relates all the microbial species. It has frequently been observed that a cluster or clusters of bacteria at varying phylogenetic depths are associated with some clinical or biological outcome due to shared biological function (clustered signal). Moreover, in many cases, we observe a community-level change, where a large number of functionally interdependent species are associated with the outcome (dense signal). We thus develop "glmmTree," a prediction method based on a generalized linear mixed model framework, for capturing clustered and dense microbiome signals. glmmTree uses the similarity between microbiomes, which is defined based on the microbiome composition and the phylogenetic tree, to predict the outcome. The effects of other predictive variables (e.g., age, sex) can be incorporated readily in the regression framework. Additional tuning parameters enable a data-adaptive approach to capture signals at different phylogenetic depth and abundance level. Simulation studies and real data applications demonstrated that "glmmTree" outperformed existing methods in the dense and clustered signal scenarios.
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Affiliation(s)
- Jian Xiao
- Division of Biomedical Statistics and Informatics and Center for Individualized Medicine, Mayo Clinic, Rochester, MN, United States
- School of Statistics and Mathematics, Zhongnan University of Economics and Law, Hubei, China
| | - Li Chen
- Department of Health Outcomes Research and Policy, Harrison School of Pharmacy, Auburn University, Auburn, AL, United States
| | - Stephen Johnson
- Division of Biomedical Statistics and Informatics and Center for Individualized Medicine, Mayo Clinic, Rochester, MN, United States
| | - Yue Yu
- Division of Biomedical Statistics and Informatics and Center for Individualized Medicine, Mayo Clinic, Rochester, MN, United States
| | - Xianyang Zhang
- Department of Statistics, Texas A&M University, College Station, TX, United States
| | - Jun Chen
- Division of Biomedical Statistics and Informatics and Center for Individualized Medicine, Mayo Clinic, Rochester, MN, United States
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462
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Abstract
PURPOSE OF REVIEW Accumulating evidence suggests that gut microbiota affect the development and function of the immune system and may play a role in the pathogenesis of autoimmune diseases. The purpose of this review is to summarize recent studies reporting gastrointestinal microbiota aberrations associated with the systemic sclerosis disease state. RECENT FINDINGS The studies described herein have identified common changes in gut microbial composition. Specifically, patients with SSc have decreased abundance of beneficial commensal genera (e.g., Faecalibacterium, Clostridium, and Bacteroides) and increased abundance of pathobiont genera (e.g., Fusobacterium, Prevotella, Erwinia). In addition, some studies have linked specific genera with the severity of gastrointestinal symptoms in systemic sclerosis. More research is needed to further characterize the gastrointestinal microbiota in systemic sclerosis and understand how microbiota perturbations can affect inflammation, fibrosis, and clinical outcomes. Interventional studies aimed at addressing/correcting these perturbations, either through dietary modification, pro/pre-biotic supplementation, or fecal transplantation, may lead to improved outcomes for patients with systemic sclerosis.
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Affiliation(s)
- Chiara Bellocchi
- Scleroderma Unit, Referral Center for Systemic Autoimmune Diseases, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico di Milano, University of Milan, Milan, Italy
| | - Elizabeth R Volkmann
- Division of Rheumatology, Department of Medicine, David Geffen School of Medicine, University of California, 1000 Veteran Avenue, Ste 32-59, Los Angeles, CA, 90095, USA.
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463
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Venturelli OS, Carr AC, Fisher G, Hsu RH, Lau R, Bowen BP, Hromada S, Northen T, Arkin AP. Deciphering microbial interactions in synthetic human gut microbiome communities. Mol Syst Biol 2018; 14:e8157. [PMID: 29930200 PMCID: PMC6011841 DOI: 10.15252/msb.20178157] [Citation(s) in RCA: 241] [Impact Index Per Article: 40.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Revised: 05/13/2018] [Accepted: 05/22/2018] [Indexed: 12/19/2022] Open
Abstract
The ecological forces that govern the assembly and stability of the human gut microbiota remain unresolved. We developed a generalizable model-guided framework to predict higher-dimensional consortia from time-resolved measurements of lower-order assemblages. This method was employed to decipher microbial interactions in a diverse human gut microbiome synthetic community. We show that pairwise interactions are major drivers of multi-species community dynamics, as opposed to higher-order interactions. The inferred ecological network exhibits a high proportion of negative and frequent positive interactions. Ecological drivers and responsive recipient species were discovered in the network. Our model demonstrated that a prevalent positive and negative interaction topology enables robust coexistence by implementing a negative feedback loop that balances disparities in monospecies fitness levels. We show that negative interactions could generate history-dependent responses of initial species proportions that frequently do not originate from bistability. Measurements of extracellular metabolites illuminated the metabolic capabilities of monospecies and potential molecular basis of microbial interactions. In sum, these methods defined the ecological roles of major human-associated intestinal species and illuminated design principles of microbial communities.
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Affiliation(s)
| | - Alex C Carr
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Garth Fisher
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ryan H Hsu
- California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, CA, USA
| | - Rebecca Lau
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Benjamin P Bowen
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Susan Hromada
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Trent Northen
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Adam P Arkin
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, CA, USA
- Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA
- Energy Biosciences Institute, University of California Berkeley, Berkeley, CA, USA
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464
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Bilen M, Beye M, Mbogning Fonkou MD, Khelaifia S, Cadoret F, Armstrong N, Nguyen TT, Delerce J, Daoud Z, Raoult D, Fournier PE. Genomic and phenotypic description of the newly isolated human species Collinsella bouchesdurhonensis sp. nov. Microbiologyopen 2018; 7:e00580. [PMID: 29900684 PMCID: PMC6182551 DOI: 10.1002/mbo3.580] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 11/15/2017] [Accepted: 11/21/2017] [Indexed: 12/19/2022] Open
Abstract
Using culturomics, a recently developed strategy based on diversified culture conditions for the isolation of previously uncultured bacteria, we isolated strain Marseille‐P3296T from a fecal sample of a healthy pygmy female. A multiphasic approach, taxono‐genomics, was used to describe the major characteristics of this anaerobic and gram‐positive bacillus that is unable to sporulate and is not motile. The genome of this bacterium is 1,878,572 bp‐long with a 57.94 mol% G + C content. On the basis of these characteristics and after comparison with its closest phylogenetic neighbors, we are confident that strain Marseille‐P3296T (=CCUG 70328 = CSUR P3296) is the type strain of a novel species for which we propose the name Collinsella bouchesdurhonensis sp. nov.
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Affiliation(s)
- Melhem Bilen
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France.,Clinical Microbiology Department, Faculty of Medicine and Medical sciences, University of Balamand, Amioun, Lebanon
| | - Mamadou Beye
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - Maxime Descartes Mbogning Fonkou
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - Saber Khelaifia
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - Frédéric Cadoret
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - Nicholas Armstrong
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - Thi Tien Nguyen
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - Jérémy Delerce
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - Ziad Daoud
- Clinical Microbiology Department, Faculty of Medicine and Medical sciences, University of Balamand, Amioun, Lebanon
| | - Didier Raoult
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France.,Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Pierre-Edouard Fournier
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
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465
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Hullar MAJ, Lampe JW, Torok-Storb BJ, Harkey MA. The canine gut microbiome is associated with higher risk of gastric dilatation-volvulus and high risk genetic variants of the immune system. PLoS One 2018; 13:e0197686. [PMID: 29889838 PMCID: PMC5995382 DOI: 10.1371/journal.pone.0197686] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 05/07/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Large and giant dog breeds have a high risk for gastric dilatation-volvulus (GDV) which is an acute, life-threatening condition. Previous work by our group identified a strong risk of GDV linked to specific alleles in innate and adaptive immune genes. We hypothesize that variation in the genes of the immune system act through modulation of the gut microbiome, or through autoimmune mechanisms, or both, to predispose dogs to this condition. Here, we investigate whether differences in the canine fecal microbiome are associated with GDV and are linked to previously identified risk alleles. METHODOLOGY/PRINCIPLE FINDINGS Fecal samples from healthy Great Danes (n = 38), and dogs with at least one occurrence of GDV (n = 37) were collected and analyzed by paired-end sequencing of the 16S rRNA gene. Dietary intake and temperament were estimated from a study-specific dietary and temperament questionnaire. Dogs with GDV had significantly more diverse fecal microbiomes than healthy control dogs. Alpha diversity was significantly increased in dogs with GDV, as well as dogs with at least one risk allele for DRB1 and TRL5. We found no significant association of dietary intake and GDV. Dogs with GDV showed a significant expansion of the rare lineage Actinobacteria (p = 0.004), as well as a significantly greater abundance of Firmicutes (p = 0.004) and a significantly lower abundance of Bacteroidetes (p<0.004). There was a significant difference in the abundance of 10 genera but after correction for multiple comparisons, none were significant. Bacterial phyla were significantly different between controls and dogs with GDV and at least one risk allele for DRB1 and TRL5. Actinobacteria were significantly higher in dogs with GDV and with one risk allele for DRB1 and TLR5 but not DLA88 genes. Furthermore, Collinsella was significantly increased in dogs with at least one risk allele for DRB1 and TLR5. Logistic regression showed that a model which included Actinobacteria, at least one risk allele,and temperament, explained 29% of the variation in risk of GDV in Great Danes. CONCLUSIONS The microbiome in GDV was altered by an expansion of a minor lineage and was associated with specific alleles of both innate and adaptive immunity genes. These associations are consistent with our hypothesis that immune genes may play a role in predisposition to GDV by altering the gut microbiome. Further research will be required to directly test the causal relationships of immune genes, the gut microbiome and GDV.
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Affiliation(s)
- Meredith A. J. Hullar
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Johanna W. Lampe
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Beverly J. Torok-Storb
- Department of Transplantation Biology, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Michael A. Harkey
- Department of Transplantation Biology, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
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466
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Luo Y, Blackledge WC. Microbiome-based mechanisms hypothesized to initiate obesity-associated rheumatoid arthritis. Obes Rev 2018; 19:786-797. [PMID: 29426061 DOI: 10.1111/obr.12671] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 12/11/2017] [Accepted: 12/18/2017] [Indexed: 02/05/2023]
Abstract
Worldwide, the growing obesity pandemic contributes to a range of chronic diseases. Recent epidemiological studies have suggested an association between obesity and the development of rheumatoid arthritis (RA), particularly among young women, whereby pro-inflammatory effects of adipokines provide one explanatory hypothesis. Yet, recent clinical and laboratory-based studies provide emerging evidence indicating microbiome involvement in RA initiation and development, including anti-citrullinated antibody formation and Th17 cell activation. Obesity and RA-associated microbiome alteration might provide a plausible link to address the impact of obesity to RA pathogenesis. The microbiome's influence on RA development - at mucosal as well as articular sites - and relevant pathophysiological mechanisms regarding obesity's association with RA are presented herein to discuss this hypothesis and aid understanding of obesity's role in RA development.
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Affiliation(s)
- Y Luo
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, China
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467
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Ostrov BE, Amsterdam D. Immunomodulatory interplay of the microbiome and therapy of rheumatic diseases. Immunol Invest 2018; 46:769-792. [PMID: 29058546 DOI: 10.1080/08820139.2017.1373828] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Modulation of the immune system by microbes, especially from the gastrointestinal tract, is increasingly considered a key factor in the onset, course and outcome of rheumatic diseases. The interplay of the microbiome, along with genetic predisposition and environmental exposure, is thought to be an important trigger for rheumatic diseases. Improved identification of the relationship of disease-specific genetic alterations and rheumatic diseases has potential diagnostic and therapeutic applications. Treatment of rheumatic disorders is influenced by microbial actions but this interplay can be challenging due to variable and unpredictable responses to therapies. Expanded knowledge of the microbiome now allows clinicians to more precisely select ideal medication regimens and to predict response to and toxicity from drugs. Rheumatic diseases and associated therapies were among the earliest microbiome interactions investigated, yet it is notable that current research is focused on clinical and immunological associations but, in comparison, a limited number of studies regarding the microbiome's impact on treatment for rheumatic diseases have been published. In the coming years, further knowledge of immunomodulating interactions between the microbiome and the immune system will aid our understanding of autoimmunity and will be increasingly important in selection of therapeutic agents for patients with autoimmune and rheumatic diseases. In this review, recent literature regarding the bidirectional immunomodulatory effects of the microbiome with rheumatic diseases and current understanding and gaps regarding the drug-microbiome interface in the management of these disorders is presented.
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Affiliation(s)
- Barbara E Ostrov
- a Pediatrics and Medicine, Pediatric Rheumatology, Department of Pediatrics, Rheumatology, Department of Medicine , Penn State College of Medicine , Hershey , PA , USA
| | - Daniel Amsterdam
- b Microbiology and Immunology, Pathology and Medicine , Jacobs School of Medicine and Biomedical Sciences, Chief of Service, Laboratory Medicine, Erie County Medical Center , Buffalo , NY , USA
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468
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Horng KR, Ganz HH, Eisen JA, Marks SL. Effects of preservation method on canine ( Canis lupus familiaris) fecal microbiota. PeerJ 2018; 6:e4827. [PMID: 29844978 PMCID: PMC5970549 DOI: 10.7717/peerj.4827] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 04/30/2018] [Indexed: 12/14/2022] Open
Abstract
Studies involving gut microbiome analysis play an increasing role in the evaluation of health and disease in humans and animals alike. Fecal sampling methods for DNA preservation in laboratory, clinical, and field settings can greatly influence inferences of microbial composition and diversity, but are often inconsistent and under-investigated between studies. Many laboratories have utilized either temperature control or preservation buffers for optimization of DNA preservation, but few studies have evaluated the effects of combining both methods to preserve fecal microbiota. To determine the optimal method for fecal DNA preservation, we collected fecal samples from one canine donor and stored aliquots in RNAlater, 70% ethanol, 50:50 glycerol:PBS, or without buffer at 25 °C, 4 °C, and −80 °C. Fecal DNA was extracted, quantified, and 16S rRNA gene analysis performed on Days 0, 7, 14, and 56 to evaluate changes in DNA concentration, purity, and bacterial diversity and composition over time. We detected overall effects on bacterial community of storage buffer (F-value = 6.87, DF = 3, P < 0.001), storage temperature (F-value=1.77, DF = 3, P = 0.037), and duration of sample storage (F-value = 3.68, DF = 3, P < 0.001). Changes in bacterial composition were observed in samples stored in −80 °C without buffer, a commonly used method for fecal DNA storage, suggesting that simply freezing samples may be suboptimal for bacterial analysis. Fecal preservation with 70% ethanol and RNAlater closely resembled that of fresh samples, though RNAlater yielded significantly lower DNA concentrations (DF = 8.57, P < 0.001). Although bacterial composition varied with temperature and buffer storage, 70% ethanol was the best method for preserving bacterial DNA in canine feces, yielding the highest DNA concentration and minimal changes in bacterial diversity and composition. The differences observed between samples highlight the need to consider optimized post-collection methods in microbiome research.
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Affiliation(s)
- Katti R Horng
- Department of Medical Microbiology and Immunology, University of California, Davis, Davis, CA, United States of America.,William R. Pritchard Veterinary Medical Teaching Hospital, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States of America
| | - Holly H Ganz
- Department of Evolution and Ecology, University of California, Davis, Davis, CA, United States of America.,AnimalBiome, Inc., Oakland, CA, United States of America
| | - Jonathan A Eisen
- Department of Evolution and Ecology, University of California, Davis, Davis, CA, United States of America
| | - Stanley L Marks
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States of America
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469
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Lu Y, Zhou X, Nardini C. Dissection of the module network implementation "LemonTree": enhancements towards applications in metagenomics and translation in autoimmune maladies. MOLECULAR BIOSYSTEMS 2018; 13:2083-2091. [PMID: 28809429 DOI: 10.1039/c7mb00248c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Under the current deluge of omics, module networks distinctively emerge as methods capable of not only identifying inherently coherent groups (modules), thus reducing dimensionality, but also hypothesizing cause-effect relationships between modules and their regulators. Module networks were first designed in the transcriptomic era and further exploited in the multi-omic context to assess (for example) miRNA regulation of gene expression. Despite a number of available implementations, expansion of module networks to other omics is constrained by a limited characterization of the solutions' (modules plus regulators) accuracy and stability - an immediate need for the better characterization of molecular biology complexity in silico. We hence carefully assessed for LemonTree - a popular and open source module network implementation - the dependency of the software performances (sensitivity, specificity, false discovery rate, solutions' stability) on the input parameters and on the data quality (sample size, expression noise) based on synthetic and real data. In the process, we uncovered and fixed an issue in the code for the regulator assignment procedure. We concluded this evaluation with a table of recommended parameter settings. Finally, we applied these recommended settings to gut-intestinal metagenomic data from rheumatoid arthritis patients, to characterize the evolution of the gut-intestinal microbiome under different pharmaceutical regimens (methotrexate and prednisone) and we inferred innovative clinical recommendations with therapeutic potential, based on the computed module network.
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Affiliation(s)
- Youtao Lu
- CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, P. R. China
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470
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Zhao N, Zhan X, Guthrie KA, Mitchell CM, Larson J. Generalized Hotelling's test for paired compositional data with application to human microbiome studies. Genet Epidemiol 2018; 42:459-469. [PMID: 29737047 DOI: 10.1002/gepi.22127] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/12/2018] [Accepted: 03/29/2018] [Indexed: 02/06/2023]
Abstract
The human microbiome is a dynamic system that changes due to diseases, medication, change in diet, etc. The paired design is a common approach to evaluate the microbial changes while controlling for the inherent differences between people. For example, microbiome data may be collected from the same individuals before and after a treatment. Two challenges exist in analyzing this type of data. First, microbiome data are compositional such that the reads for all taxa in each sample are constrained to sum to a constant. Second, the number of taxa can be much larger than the sample size. Few statistical methods exist to analyze such data besides methods that test one taxon at a time. In this paper, we propose to first conduct a log-ratio transformation of the compositions, and then develop a generalized Hotelling's test (GHT) to evaluate whether the average microbiome compositions are equivalent in the paired samples. We replace the sample covariance matrix in standard Hotelling's statistic by a shrinkage-based covariance, calculated as a weighted average of the sample covariance and a positive definite target matrix. The optimal weighting can be obtained for many commonly used target matrices. We develop a permutation procedure to assess the statistical significance. Extensive simulations show that our proposed method has well-controlled type I error and better power than a few ad hoc approaches. We apply our method to examine the vaginal microbiome changes in response to treatments for menopausal hot flashes. An R package " GHT" is freely available at https://github.com/zhaoni153/GHT.
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Affiliation(s)
- Ni Zhao
- Departments of Biostatistics, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Xiang Zhan
- Department of Public Health Sciences, Pennsylvania State University, Hershey, Pennsylvania, United States of America
| | - Katherine A Guthrie
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Caroline M Mitchell
- Vincent Center for Reproductive Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Joseph Larson
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
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471
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Guo Q, Wang Y, Xu D, Nossent J, Pavlos NJ, Xu J. Rheumatoid arthritis: pathological mechanisms and modern pharmacologic therapies. Bone Res 2018; 6:15. [PMID: 29736302 PMCID: PMC5920070 DOI: 10.1038/s41413-018-0016-9] [Citation(s) in RCA: 841] [Impact Index Per Article: 140.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Revised: 03/26/2018] [Accepted: 03/28/2018] [Indexed: 02/06/2023] Open
Abstract
Rheumatoid arthritis (RA) is a chronic systemic autoimmune disease that primarily affects the lining of the synovial joints and is associated with progressive disability, premature death, and socioeconomic burdens. A better understanding of how the pathological mechanisms drive the deterioration of RA progress in individuals is urgently required in order to develop therapies that will effectively treat patients at each stage of the disease progress. Here we dissect the etiology and pathology at specific stages: (i) triggering, (ii) maturation, (iii) targeting, and (iv) fulminant stage, concomitant with hyperplastic synovium, cartilage damage, bone erosion, and systemic consequences. Modern pharmacologic therapies (including conventional, biological, and novel potential small molecule disease-modifying anti-rheumatic drugs) remain the mainstay of RA treatment and there has been significant progress toward achieving disease remission without joint deformity. Despite this, a significant proportion of RA patients do not effectively respond to the current therapies and thus new drugs are urgently required. This review discusses recent advances of our understanding of RA pathogenesis, disease modifying drugs, and provides perspectives on next generation therapeutics for RA. The preclinical stages of rheumatoid arthritis (RA) represent a golden window for the development of therapies which could someday prevent the onset of clinical disease. The autoimmune processes underpinning RA usually begin many years before symptoms such as joint pain and stiffness emerge. Recent studies have identified some of the key cellular players driving these processes and begun to unpick how genetic and environmental risk factors combine to trigger them; they also suggest the existence of several distinct subtypes of RA, which require further exploration. Jiake Xu at the University of Western Australia in Perth and colleagues review current treatment strategies for RA and how such insights could ultimately lead to the earlier diagnosis of RA - as well as providing new opportunities for drug treatment and prevention through behavioral changes in high-risk individuals.
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Affiliation(s)
- Qiang Guo
- 1Department of Spine Surgery, Xiangya Hospital, Central South University, No. 87, Xiangya Road, 410008 Changsha, China.,2School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Nedlands, Western Australia 6009 Australia
| | - Yuxiang Wang
- 1Department of Spine Surgery, Xiangya Hospital, Central South University, No. 87, Xiangya Road, 410008 Changsha, China
| | - Dan Xu
- 2School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Nedlands, Western Australia 6009 Australia.,Musculoskeletal Health Network, Department of Health WA, 189 Royal Street, East Perth, WA 6004 Australia
| | - Johannes Nossent
- Musculoskeletal Health Network, Department of Health WA, 189 Royal Street, East Perth, WA 6004 Australia.,4School of Medicine, Faculty of Health and Medical Sciences, The University of Western Australia, Nedlands, Western Australia 6009 Australia
| | - Nathan J Pavlos
- 2School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Nedlands, Western Australia 6009 Australia
| | - Jiake Xu
- 2School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Nedlands, Western Australia 6009 Australia
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472
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Neff CP, Krueger O, Xiong K, Arif S, Nusbacher N, Schneider JM, Cunningham AW, Armstrong A, Li S, McCarter MD, Campbell TB, Lozupone CA, Palmer BE. Fecal Microbiota Composition Drives Immune Activation in HIV-infected Individuals. EBioMedicine 2018; 30:192-202. [PMID: 29650491 PMCID: PMC5952409 DOI: 10.1016/j.ebiom.2018.03.024] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 03/12/2018] [Accepted: 03/20/2018] [Indexed: 02/08/2023] Open
Abstract
The inflammatory properties of the enteric microbiota of Human Immunodeficiency Virus (HIV)-infected individuals are of considerable interest because of strong evidence that bacterial translocation contributes to chronic immune activation and disease progression. Altered enteric microbiota composition occurs with HIV infection but whether altered microbiota composition or increased intestinal permeability alone drives peripheral immune activation is controversial. To comprehensively assess the inflammatory properties of HIV-associated enteric microbiota and relate these to systemic immune activation, we developed methods to purify whole fecal bacterial communities (FBCs) from stool for use in in vitro immune stimulation assays with human cells. We show that the enteric microbiota of untreated HIV-infected subjects induce significantly higher levels of activated monocytes and T cells compared to seronegative subjects. FBCs from anti-retroviral therapy (ART)-treated HIV-infected individuals induced intermediate T cell activation, indicating an only partial correction of adaptive immune cell activation capacity of the microbiome with ART. In vitro activation levels correlated with activation levels and viral load in blood and were particularly high in individuals harboring specific gram-positive opportunistic pathogens. Blockade experiments implicated Tumor Necrosis Factor (TNF)-α and Toll-Like Receptor-2 (TLR2), which recognizes peptidoglycan, as strong mediators of T cell activation; This may contradict a previous focus on lipopolysaccharide as a primary mediator of chronic immune activation. These data support that increased inflammatory properties of the enteric microbiota and not increased permeability alone drives chronic inflammation in HIV.
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Affiliation(s)
- Charles Preston Neff
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Owen Krueger
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kathy Xiong
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Sabrina Arif
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Nichole Nusbacher
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Jennifer M Schneider
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Annie W Cunningham
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Abigail Armstrong
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Sam Li
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Martin D McCarter
- Department of Surgery, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Thomas B Campbell
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Catherine A Lozupone
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
| | - Brent E Palmer
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
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473
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Gomez-Arango LF, Barrett HL, Wilkinson SA, Callaway LK, McIntyre HD, Morrison M, Dekker Nitert M. Low dietary fiber intake increases Collinsella abundance in the gut microbiota of overweight and obese pregnant women. Gut Microbes 2018; 9:189-201. [PMID: 29144833 PMCID: PMC6219589 DOI: 10.1080/19490976.2017.1406584] [Citation(s) in RCA: 214] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
UNLABELLED The gut microbiota contributes to the regulation of glucose metabolism in pregnancy. Abundance of the genus Collinsella is positively correlated with circulating insulin; however, it is unclear what determines Collinsella abundance. This study aims to validate the correlation between Collinsella and insulin and to elucidate if macronutrient intake alters Collinsella abundance and gut microbiota composition. Gut microbiota profiles were assessed by 16S rRNA sequencing in 57 overweight and 73 obese pregnant women from the SPRING (Study of PRobiotics IN Gestational diabetes) trial at 16 weeks gestation and correlated with metabolic hormone levels and macronutrient intake. Gut microbiota composition in the top and bottom 10% of dietary fiber intake was evaluated through network analysis. Collinsella abundance correlated positively with circulating insulin (rho = 0.30, p = 0.0006), independent of maternal BMI, but negatively with dietary fiber intake (rho = -0.20, p = 0.025) in this cohort. Low dietary fiber intake was associated with a gut microbiota favoring lactate fermentation while high fiber intake promotes short-chain fatty acid-producing bacteria. Low dietary fiber may enable overgrowth of Collinsella and alter the overall fermentation pattern in gut microbiota. This suggests that dietary choices during pregnancy can modify the nutritional ecology of the gut microbiota, with potential deleterious effects on the metabolic and inflammatory health of the host. TRIAL REGISTRATION ANZCTR 12611001208998, registered 23/11/2011.
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Affiliation(s)
- Luisa F. Gomez-Arango
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, Australia,Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Helen L. Barrett
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, Australia,Faculty of Medicine, The University of Queensland, Brisbane, Australia,Obstetric Medicine, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - Shelley A. Wilkinson
- Mater Health Services, Nutrition and Dietetics, Mater Hospital, Brisbane, Australia,Mater Research Institute –University of Queensland, Brisbane, Australia
| | - Leonie K. Callaway
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, Australia,Faculty of Medicine, The University of Queensland, Brisbane, Australia,Obstetric Medicine, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - H. David McIntyre
- Faculty of Medicine, The University of Queensland, Brisbane, Australia,Mater Research Institute –University of Queensland, Brisbane, Australia
| | - Mark Morrison
- Faculty of Medicine, The University of Queensland, Brisbane, Australia,Diamantina Institute, The University of Queensland, Brisbane, Australia,School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Marloes Dekker Nitert
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, Australia,Diamantina Institute, The University of Queensland, Brisbane, Australia,CONTACT: Marloes Dekker Nitert School of Chemistry and Molecular Biosciences, Building 76–452. The University of Queensland Brisbane, QLD 4072, Australia
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474
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Bruserud Ø, Siddiqui H, Marthinussen MC, Chen T, Jonsson R, Oftedal BE, Olsen I, Husebye ES, Wolff AB. Oral microbiota in autoimmune polyendocrine syndrome type 1. J Oral Microbiol 2018; 10:1442986. [PMID: 29503707 PMCID: PMC5827717 DOI: 10.1080/20002297.2018.1442986] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 02/15/2018] [Indexed: 01/12/2023] Open
Abstract
Background: Autoimmune polyendocrine syndrome type-1 (APS-1) is a rare, childhood onset disease caused by mutations in the Autoimmune Regulator gene. The phenotypic expression is highly variable and includes disease manifestations in the oral cavity, including mucocutaneous candidiasis. Increasing evidence suggests a potential role of the skin, oral and gut microbiotas in the pathogenesis of autoimmunity. To date, no information exists regarding the oral microbiota in APS-1. Objective: To assess the bacterial microbiota of whole saliva in APS-1 patients by using high throughput sequencing. Design: Whole unstimulated saliva was collected from 10 APS-1 patients and 17 healthy controls and examined by high throughput sequencing of the hypervariable region V1-V2 of 16S rRNA using the 454 GS Junior system. Metastats (http://cbcb.umd.edu/software/metastats) was used to analyse the pyrosequencing reads. Results: A reduction in the total number of bacterial genera and species was detected in APS-1 compared to healthy controls. The proportion of the major phyla Firmicutes was higher (60% vs 41%, p = 0.002) and Bacteroidetes lower (15% vs 28%, p = 0.007) in APS-1 compared to healthy controls. On the genus level, Streptococcus and Gemella were prevalent in APS-1. Conclusion: Our findings indicate a significantly altered oral microbiota in APS-1.
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Affiliation(s)
- Øyvind Bruserud
- Department of Clinical Science, University of Bergen, Bergen, Norway
- K.G. Jebsen Center for Autoimmune Disorders, University of Bergen, Bergen, Norway
| | - Huma Siddiqui
- Department of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Mihaela Cuida Marthinussen
- Oral Health Centre of Expertise in Western Norway, Bergen, Norway
- Department of Clinical Dentistry, Faculty of Medicine, University of Bergen, Bergen, Norway
| | - Tsute Chen
- Department of Microbiology, Forsyth Institute, Cambridge, MA, USA
| | - Roland Jonsson
- Department of Rheumatology, Haukeland University Hospital, Bergen, Norway
- Broegelmann Research Laboratory, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Bergithe Eikeland Oftedal
- Department of Clinical Science, University of Bergen, Bergen, Norway
- K.G. Jebsen Center for Autoimmune Disorders, University of Bergen, Bergen, Norway
| | - Ingar Olsen
- Department of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Eystein Sverre Husebye
- Department of Clinical Science, University of Bergen, Bergen, Norway
- K.G. Jebsen Center for Autoimmune Disorders, University of Bergen, Bergen, Norway
- Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Anette Bøe Wolff
- Department of Clinical Science, University of Bergen, Bergen, Norway
- K.G. Jebsen Center for Autoimmune Disorders, University of Bergen, Bergen, Norway
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475
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Leite FLL, Singer RS, Ward T, Gebhart CJ, Isaacson RE. Vaccination Against Lawsonia intracellularis Decreases Shedding of Salmonella enterica serovar Typhimurium in Co-Infected Pigs and Alters the Gut Microbiome. Sci Rep 2018; 8:2857. [PMID: 29434295 PMCID: PMC5809363 DOI: 10.1038/s41598-018-21255-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 02/01/2018] [Indexed: 01/09/2023] Open
Abstract
Salmonella enterica serovar Typhimurium continues to be a major cause of foodborne illness worldwide and pork can serve as a source of infection. Co-infection of S. enterica with Lawsonia intracellularis, a common intestinal pathogen of swine, has been found as risk factor for increased S. enterica shedding. The objective of this study was to investigate if vaccination against L. intracellularis could lead to decreased S. Typhimurium shedding. To test this hypothesis, pigs were challenged with either S. Typhimurium or S. Typhimurium and L. intracellularis, with and without L. intracellularis vaccination (n = 9 per group). A non-challenged group served as a negative control. Vaccination decreased the shedding of S. Typhimurium in co-infected animals by 2.12 log10 organisms per gram of feces at 7 days post infection. Analysis of the microbiome showed that vaccination led to changes in the abundance of Clostridium species, including Clostridium butyricum, in addition to other compositional changes that may explain the protection mediated against S. Typhimurium. These results indicate that vaccination against L. intracellularis in co-infected herds may provide a new tool to increase food safety by helping to prevent S. enterica without the need for antibiotics.
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Affiliation(s)
- Fernando L L Leite
- Department of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, MN, USA
| | - Randall S Singer
- Department of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, MN, USA
| | - Tonya Ward
- Biotechnology Institute, University of Minnesota, St. Paul, MN, USA
| | - Connie J Gebhart
- Department of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, MN, USA
| | - Richard E Isaacson
- Department of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, MN, USA.
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476
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Smolen JS, Aletaha D, Barton A, Burmester GR, Emery P, Firestein GS, Kavanaugh A, McInnes IB, Solomon DH, Strand V, Yamamoto K. Rheumatoid arthritis. Nat Rev Dis Primers 2018; 4:18001. [PMID: 29417936 DOI: 10.1038/nrdp.2018.1] [Citation(s) in RCA: 1325] [Impact Index Per Article: 220.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Rheumatoid arthritis (RA) is a chronic, inflammatory, autoimmune disease that primarily affects the joints and is associated with autoantibodies that target various molecules including modified self-epitopes. The identification of novel autoantibodies has improved diagnostic accuracy, and newly developed classification criteria facilitate the recognition and study of the disease early in its course. New clinical assessment tools are able to better characterize disease activity states, which are correlated with progression of damage and disability, and permit improved follow-up. In addition, better understanding of the pathogenesis of RA through recognition of key cells and cytokines has led to the development of targeted disease-modifying antirheumatic drugs. Altogether, the improved understanding of the pathogenetic processes involved, rational use of established drugs and development of new drugs and reliable assessment tools have drastically altered the lives of individuals with RA over the past 2 decades. Current strategies strive for early referral, early diagnosis and early start of effective therapy aimed at remission or, at the least, low disease activity, with rapid adaptation of treatment if this target is not reached. This treat-to-target approach prevents progression of joint damage and optimizes physical functioning, work and social participation. In this Primer, we discuss the epidemiology, pathophysiology, diagnosis and management of RA.
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Affiliation(s)
- Josef S Smolen
- Division of Rheumatology, Department of Medicine 3, Medical University of Vienna, Waehringer Guertel 18-20, 1090 Vienna, Austria
| | - Daniel Aletaha
- Division of Rheumatology, Department of Medicine 3, Medical University of Vienna, Waehringer Guertel 18-20, 1090 Vienna, Austria
| | - Anne Barton
- Arthritis Research UK Centre for Genetics and Genomics and NIHR Manchester Biomedical Research Centre, Manchester Academic Health Sciences Centre, The University of Manchester and Central Manchester Foundation Trust, Manchester, UK
| | - Gerd R Burmester
- Department of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Paul Emery
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Chapel Allerton Hospital, Leeds, UK.,NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Gary S Firestein
- Division of Rheumatology, Allergy and Immunology, University of California-San Diego School of Medicine, La Jolla, CA, USA
| | - Arthur Kavanaugh
- Division of Rheumatology, Allergy and Immunology, University of California-San Diego School of Medicine, La Jolla, CA, USA
| | - Iain B McInnes
- Institute of Infection Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Daniel H Solomon
- Division of Rheumatology, Brigham and Women's Hospital, Boston, MA, USA
| | - Vibeke Strand
- Division of Immunology and Rheumatology, Stanford University, Palo Alto, CA, USA
| | - Kazuhiko Yamamoto
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
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477
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Rinaldi E, Consonni A, Guidesi E, Elli M, Mantegazza R, Baggi F. Gut microbiota and probiotics: novel immune system modulators in myasthenia gravis? Ann N Y Acad Sci 2018; 1413:49-58. [PMID: 29341125 DOI: 10.1111/nyas.13567] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 10/31/2017] [Accepted: 11/02/2017] [Indexed: 12/20/2022]
Abstract
Gut microorganisms (microbiota) live in symbiosis with the host and influence human nutrition, metabolism, physiology, and immune development and function. The microbiota prevents pathogen infection to the host, and in turn the host provides a niche for survival. The alteration of gut bacteria composition (dysbiosis) could contribute to the development of immune-mediated diseases by influencing the immune system activation and driving the pro- and anti-inflammatory responses in order to promote or counteract immune reactions. Probiotics are nonpathogenic microorganisms able to interact with the gut microbiota and provide health benefits; their use has recently been exploited to dampen immunological response in several experimental models of autoimmune diseases. Here, we focus on the relationships among commensal bacteria, probiotics, and the gut, describing the main interactions occurring with the immune system and recent data supporting the clinical efficacy of probiotic administration in rheumatoid arthritis, multiple sclerosis, and myasthenia gravis (MG) animal models. The encouraging results suggest that selected strains of probiotics should be evaluated in clinical trials as adjuvant therapy to restore the disrupted tolerance in myasthenia gravis.
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Affiliation(s)
- Elena Rinaldi
- Neurology IV-Neuroimmunology and Neuromuscular Diseases Unit, Neurological Institute "Carlo Besta," Milan, Italy
| | - Alessandra Consonni
- Neurology IV-Neuroimmunology and Neuromuscular Diseases Unit, Neurological Institute "Carlo Besta," Milan, Italy
| | - Elena Guidesi
- AAT-Advanced Analytical Technologies, Fiorenzuola d'Arda, Piacenza, Italy
| | - Marina Elli
- AAT-Advanced Analytical Technologies, Fiorenzuola d'Arda, Piacenza, Italy
| | - Renato Mantegazza
- Neurology IV-Neuroimmunology and Neuromuscular Diseases Unit, Neurological Institute "Carlo Besta," Milan, Italy
| | - Fulvio Baggi
- Neurology IV-Neuroimmunology and Neuromuscular Diseases Unit, Neurological Institute "Carlo Besta," Milan, Italy
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478
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Picchianti-Diamanti A, Rosado MM, D'Amelio R. Infectious Agents and Inflammation: The Role of Microbiota in Autoimmune Arthritis. Front Microbiol 2018; 8:2696. [PMID: 29387048 PMCID: PMC5776018 DOI: 10.3389/fmicb.2017.02696] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 12/26/2017] [Indexed: 12/17/2022] Open
Abstract
In higher vertebrates, mucosal sites at the border between the internal and external environments, directly interact with bacteria, viruses, and fungi. Through co-evolution, hosts developed mechanisms of tolerance or ignorance toward some infectious agents, because hosts established "gain of function" interactions with symbiotic bacteria. Indeed, some bacteria assist hosts in different functions, among which are digestion of complex carbohydrates, and absorption and supply of vitamins. There is no doubt that microbiota modulate innate and acquired immune responses starting at birth. However, variations in quality and quantity of bacterial species interfere with the equilibrium between inflammation and tolerance. In fact, correlations between gut bacteria composition and the severity of inflammation were first described for inflammatory bowel diseases and later extended to other pathologies. The genetic background, environmental factors (e.g., stress or smoking), and diet can induce strong changes in the resident bacteria which can expose the intestinal epithelium to a variety of different metabolites, many of which have unknown functions and consequences. In addition, alterations in gut permeability may allow pathogens entry, thereby triggering infection and/or chronic inflammation. In this context, a local event occurring at a mucosal site may be the triggering cause of an autoimmune reaction that eventually involves distant sites or organs. Recently, several studies attributed a pathogenic role to altered oral microbiota in rheumatoid arthritis (RA) and to gut dysbiosis in spondyloarthritis (SpA). There is also growing evidence that different drugs, such as antibiotics and immunosuppressants, can influence and be influenced by the diversity and composition of microbiota in RA and SpA patients. Hence, in complex disorders such RA and SpA, not only the genetic background, gender, and immunologic context of the individual are relevant, but also the history of infections and the structure of the microbial community at mucosal sites should be considered. Here the role of the microbiota and infections in the initiation and progression of chronic arthritis is discussed, as well as how these factors can influence a patient's response to synthetic and biologic immunosuppressive therapy.
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Affiliation(s)
- Andrea Picchianti-Diamanti
- Department of Clinical and Molecular Medicine, Sant'Andrea University Hospital, Sapienza University of Rome, Rome, Italy
| | | | - Raffaele D'Amelio
- Department of Clinical and Molecular Medicine, Sant'Andrea University Hospital, Sapienza University of Rome, Rome, Italy
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479
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Abstract
Vertebrates harbor both symbiotic and pathogenic bacteria on the body and various mucosal surfaces. Of these surfaces, the intestine has the most diverse composition. This composition is dependent upon various environmental and genetic factors, with diet exerting the maximum influence. Significant roles of the intestinal bacteria are to stimulate the development of a competent mucosal immune system and to maintain tolerance within the intestine. One manner in which this is achieved is by the establishment of epithelial integrity by microbiota found in healthy individuals (healthy microbiota); however, in the case of a disrupted intestinal microbiome (dysbiosis), which can be caused by various conditions, the epithelial integrity is compromised. This decreased epithelial integrity can then lead to luminal products crossing the barrier, generating a systemic proinflammatory response. In addition to epithelial integrity, healthy intestinal commensals metabolize indigestible dietary substrates and produce short-chain fatty acids, which are bacterial metabolites that are essential for colonic health and regulating the function of the intestinal immune system. Intestinal commensals are also capable of producing neuroactive molecules and neurotransmitters that can affect the function of the vagus nerve. The observations that intestinal dysbiosis is associated with different diseases of the nervous system, suggests that cross-talk occurs amongst the gut, the nervous system, and the immune system.
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Affiliation(s)
- Eric Marietta
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
- Department of Immunology, Mayo Clinic, Rochester, MN, USA
| | - Irina Horwath
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Veena Taneja
- Department of Immunology, Mayo Clinic, Rochester, MN, USA.
- Division of Rheumatology, Mayo Clinic, Rochester, MN, USA.
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480
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Tackling Pain Associated with Rheumatoid Arthritis: Proton-Sensing Receptors. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1099:49-64. [PMID: 30306514 DOI: 10.1007/978-981-13-1756-9_5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Rheumatoid arthritis (RA), characterized by chronic inflammation of synovial joints, is often associated with ongoing pain and increased pain sensitivity. Chronic pain that comes with RA turns independent, essentially becoming its own disease. It could partly explain that a significant number (50%) of RA patients fail to respond to current RA therapies that focus mainly on suppression of joint inflammation. The acute phase of pain seems to associate with joint inflammation in early RA. In established RA, the chronic phase of pain could be linked to inflammatory components of neuron-immune interactions and noninflammatory components. Accumulating evidence suggests that the initial inflammation and autoimmunity in RA (preclinical RA) begin outside of the joint and may originate at mucosal sites and alterations in the composition of microbiota located at mucosal sites could be essential for mucosal inflammation, triggering joint inflammation. Fibroblast-like synoviocytes in the inflamed joint respond to cytokines to release acidic components, lowering pH in synovial fluid. Extracellular proton binds to proton-sensing ion channels, and G-protein-coupled receptors in joint nociceptive fibers may contribute to sensory transduction and release of neurotransmitters, leading to pain and hyperalgesia. Activation of peripheral sensory neurons or nociceptors further modulates inflammation, resulting in neuroinflammation or neurogenic inflammation. Peripheral and central nerves work with non-neuronal cells (such as immune cells, glial cells) in concert to contribute to the chronic phase of RA-associated pain. This review will discuss actions of proton-sensing receptors on neurons or non-neuronal cells that modulate RA pathology and associated chronic pain, and it will be beneficial for the development of future therapeutic treatments.
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481
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Freedman SN, Shahi SK, Mangalam AK. The "Gut Feeling": Breaking Down the Role of Gut Microbiome in Multiple Sclerosis. Neurotherapeutics 2018; 15:109-125. [PMID: 29204955 PMCID: PMC5794701 DOI: 10.1007/s13311-017-0588-x] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Multiple sclerosis (MS) is a chronic neuroinflammatory disease of the central nervous system with unknown etiology. Recently, the gut microbiota has emerged as a potential factor in the development of MS, with a number of studies having shown that patients with MS exhibit gut dysbiosis. The gut microbiota helps the host remain healthy by regulating various functions, including food metabolism, energy homeostasis, maintenance of the intestinal barrier, inhibition of colonization by pathogenic organisms, and shaping of both mucosal and systemic immune responses. Alteration of the gut microbiota, and subsequent changes in its metabolic network that perturb this homeostasis, may lead to intestinal and systemic disorders such as MS. Here we discuss the findings of recent MS microbiome studies and potential mechanisms through which gut microbiota can predispose to, or protect against, MS. These findings highlight the need of an improved understanding of the interactions between the microbiota and host for developing therapies based on gut commensals with which to treat MS.
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Affiliation(s)
- Samantha N Freedman
- Interdisciplinary Graduate Program in Immunology, University of Iowa, Iowa City, IA, USA
- Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Shailesh K Shahi
- Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Ashutosh K Mangalam
- Interdisciplinary Graduate Program in Immunology, University of Iowa, Iowa City, IA, USA.
- Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.
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482
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Kapitan M, Niemiec MJ, Steimle A, Frick JS, Jacobsen ID. Fungi as Part of the Microbiota and Interactions with Intestinal Bacteria. Curr Top Microbiol Immunol 2018; 422:265-301. [PMID: 30062595 DOI: 10.1007/82_2018_117] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The human microbiota consists of bacteria, archaea, viruses, and fungi that build a highly complex network of interactions between each other and the host. While there are many examples for commensal bacterial influence on host health and immune modulation, little is known about the role of commensal fungi inside the gut community. Up until now, fungal research was concentrating on opportunistic diseases caused by fungal species, leaving the possible role of fungi as part of the microbiota largely unclear. Interestingly, fungal and bacterial abundance in the gut appear to be negatively correlated and disruption of the bacterial microbiota is a prerequisite for fungal overgrowth. The mechanisms behind bacterial colonization resistance are likely diverse, including direct antagonism as well as bacterial stimulation of host defense mechanisms. In this work, we will review the current knowledge of the development of the intestinal bacterial and fungal community, the influence of the microbiota on human health and disease, and the role of the opportunistic yeast C. albicans. We will furthermore discuss the possible benefits of commensal fungal colonization. Finally, we will summarize the recent findings on bacterial-fungal interactions.
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Affiliation(s)
- Mario Kapitan
- Research Group Microbial Immunology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
- Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany
| | - M Joanna Niemiec
- Research Group Microbial Immunology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
- Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany
| | - Alexander Steimle
- Interfaculty Institute for Microbiology and Infection Medicine, Tübingen, Germany
| | - Julia S Frick
- Interfaculty Institute for Microbiology and Infection Medicine, Tübingen, Germany
| | - Ilse D Jacobsen
- Research Group Microbial Immunology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany.
- Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany.
- Institute for Microbiology, Friedrich Schiller University, Jena, Germany.
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483
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Jazayeri O, Daghighi SM, Rezaee F. Lifestyle alters GUT-bacteria function: Linking immune response and host. Best Pract Res Clin Gastroenterol 2017; 31:625-635. [PMID: 29566905 DOI: 10.1016/j.bpg.2017.09.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 09/03/2017] [Indexed: 02/07/2023]
Abstract
Microbiota in human is a "mixture society" of different species (i.e. bacteria, viruses, funguses) populations with a different way of relationship classification to Human. Human GUT serves as the host of the majority of different bacterial populations (GUT flora, more than 500 species), which are with us ("from the beginning") in an innate manner known as the commensal (no harm to each other) and symbiotic (mutual benefit) relationship. A homeostatic balance of host-bacteria relationship is very important and vital for a normal health process. However, this beneficial relationship and delicate homeostatic state can be disrupted by the imbalance of microbiome-composition of gut microbiota, expressing a pathogenic state. A strict homeostatic balance of microbiome-composition strongly depends on several factors; 1- lifestyle, 2- geography, 3- ethnicities, 4- "mom" as prime of the type of bacterial colonization in infant and 5- the disease. With such diversity in individuals combined with huge number of different bacterial species and their interactions, it is wise to perform an in-depth systems biology (e.g. genomics, proteomics, glycomics, and etcetera) analysis of personalized microbiome. Only in this way, we are able to generate a map of complete GUT microbiota and, in turn, to determine its interaction with host and intra-interaction with pathogenic bacteria. A specific microbiome analysis provides us the knowledge to decipher the nature of interactions between the GUT microbiota and the host and its response to the invading bacteria in a pathogenic state. The GUT-bacteria composition is independent of geography and ethnicity but lifestyle well affects GUT-bacteria composition and function. Microbiome knowledge obtained by systems biology also helps us to change the behavior of GUT microbiota in response to the pathogenic microbes as protection. Functional microbiome changes in response to environmental factors will be discussed in this review.
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Affiliation(s)
- Omid Jazayeri
- Department of Molecular and Cell Biology, Faculty of Basic Science, University of Mazandaran, Babolsar, Iran
| | - S Mojtaba Daghighi
- Department of Pharmaceutical Biomaterials and Medical Biomaterials Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran; Pharmaceutical Sciences Research Center, Tehran University of Medical Sciences, Iran
| | - Farhad Rezaee
- Department of Gastroenterology-Hepatology, Erasmus Medical Center, Rotterdam, The Netherlands; Department of Cell Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
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484
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Kashyap PC, Chia N, Nelson H, Segal E, Elinav E. Microbiome at the Frontier of Personalized Medicine. Mayo Clin Proc 2017; 92:1855-1864. [PMID: 29202942 PMCID: PMC5730337 DOI: 10.1016/j.mayocp.2017.10.004] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 09/13/2017] [Accepted: 10/09/2017] [Indexed: 12/21/2022]
Abstract
The genomic revolution promises to transform our approach to treat patients by individualizing treatments, reducing adverse events, and decreasing health care costs. The early advances using this have been realized primarily by optimizing preventive and therapeutic approaches in cancer using human genome sequencing. The ability to characterize the microbiome, which includes all the microbes that reside within and upon us and all their genetic elements, using next-generation sequencing allows us to now incorporate this important contributor to human disease into developing new preventive and therapeutic strategies. In this review we highlight the importance of the microbiome in all aspects of human disease, including pathogenesis, phenotype, prognosis, and response to treatment, as well as their role as diagnostic and therapeutic biomarkers. We provide a role for next-generation sequencing in both precise microbial identification of infectious diseases and characterization of microbial communities and their function. Taken together, the microbiome is emerging as an integral part of precision medicine approach as it not only contributes to interindividual variability in all aspects of a disease but also represents a potentially modifiable factor that is amenable to targeting by therapeutics.
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Affiliation(s)
- Purna C Kashyap
- Enteric Neuroscience Program, Department of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN.
| | | | - Heidi Nelson
- Department of Surgery, Mayo Clinic, Rochester, MN
| | - Eran Segal
- Department of Computer Science, Weizmann Institute of Science, Rehovot, Israel
| | - Eran Elinav
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
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485
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Rogier R, Evans-Marin H, Manasson J, van der Kraan PM, Walgreen B, Helsen MM, van den Bersselaar LA, van de Loo FA, van Lent PL, Abramson SB, van den Berg WB, Koenders MI, Scher JU, Abdollahi-Roodsaz S. Alteration of the intestinal microbiome characterizes preclinical inflammatory arthritis in mice and its modulation attenuates established arthritis. Sci Rep 2017; 7:15613. [PMID: 29142301 PMCID: PMC5688157 DOI: 10.1038/s41598-017-15802-x] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 11/02/2017] [Indexed: 12/12/2022] Open
Abstract
Perturbations of the intestinal microbiome have been observed in patients with new-onset and chronic autoimmune inflammatory arthritis. However, it is currently unknown whether these alterations precede the development of arthritis or are rather a consequence of disease. Modulation of intestinal microbiota by oral antibiotics or germ-free condition can prevent arthritis in mice. Yet, the therapeutic potential of modulation of the microbiota after the onset of arthritis is not well characterized. We here show that the intestinal microbial community undergoes marked changes in the preclinical phase of collagen induced arthritis (CIA). The abundance of the phylum Bacteroidetes, specifically families S24-7 and Bacteroidaceae was reduced, whereas Firmicutes and Proteobacteria, such as Ruminococcaceae, Lachnospiraceae and Desulfovibrinocaceae, were expanded during the immune-priming phase of arthritis. In addition, we found that the abundance of lamina propria Th17, but not Th1, cells is highly correlated with the severity of arthritis. Elimination of the intestinal microbiota during established arthritis specifically reduced intestinal Th17 cells and attenuated arthritis. These effects were associated with reduced serum amyloid A expression in ileum and synovial tissue. Our observations suggest that intestinal microbiota perturbations precede arthritis, and that modulation of the intestinal microbiota after the onset of arthritis may offer therapeutic opportunities.
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Affiliation(s)
- Rebecca Rogier
- Department of Rheumatology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Heather Evans-Marin
- Department of Medicine, Division of Rheumatology, New York University School of Medicine, New York, United States
| | - Julia Manasson
- Department of Medicine, Division of Rheumatology, New York University School of Medicine, New York, United States
| | - Peter M van der Kraan
- Department of Rheumatology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Birgitte Walgreen
- Department of Rheumatology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Monique M Helsen
- Department of Rheumatology, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Fons A van de Loo
- Department of Rheumatology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Peter L van Lent
- Department of Rheumatology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Steven B Abramson
- Department of Medicine, Division of Rheumatology, New York University School of Medicine, New York, United States
| | - Wim B van den Berg
- Department of Rheumatology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marije I Koenders
- Department of Rheumatology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jose U Scher
- Department of Medicine, Division of Rheumatology, New York University School of Medicine, New York, United States
| | - Shahla Abdollahi-Roodsaz
- Department of Rheumatology, Radboud University Medical Center, Nijmegen, The Netherlands.
- Department of Medicine, Division of Rheumatology, New York University School of Medicine, New York, United States.
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486
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Bernstein CN, Forbes JD. Gut Microbiome in Inflammatory Bowel Disease and Other Chronic Immune-Mediated Inflammatory Diseases. Inflamm Intest Dis 2017; 2:116-123. [PMID: 30018962 PMCID: PMC5988152 DOI: 10.1159/000481401] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Since the description of the normal human gut microbiome in healthy individuals using broad-range polymerase chain reaction, there has been great advancement in the techniques used to conduct microbiome research and applications of this research across health, gastrointestinal diseases, and nongastrointestinal diseases. SUMMARY AND KEY MESSAGES In inflammatory bowel disease (IBD), studies have reported gut dysbiosis meaning that the microbial composition, diversity, and richness are altered. Persons with IBD harbor on average 25% fewer microbial genes than healthy persons. Reduced diversity has been reported in both the fecal and mucosal microbiome of IBD. Crohn disease and ulcerative colitis are systemic diseases with immunological alterations in both intestinal and circulating compartments. As knowledge about the impact of the gut microbiome on the intestinal and systemic immune response has grown, researchers have begun exploring how the gut microbiome may impact on other systemic conditions. Considering the role of microbes especially on regulatory T cells, it was plausible that the gut microbiome may have a role in other chronic immune-mediated inflammatory diseases. In this review, studies of the gut microbiome in other chronic immune-mediated inflammatory diseases are discussed including how the information can inform our understanding of the gut microbiome in IBD.
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Affiliation(s)
- Charles N. Bernstein
- University of Manitoba IBD Clinical and Research Centre, Winnipeg, Manitoba, Canada
- Department of Internal Medicine, Winnipeg, Manitoba, Canada
| | - Jessica D. Forbes
- University of Manitoba IBD Clinical and Research Centre, Winnipeg, Manitoba, Canada
- National Microbiology Laboratory, Public Health Agency of Canada, Canadian Science Centre for Human and Animal Health, Winnipeg, Manitoba, Canada
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487
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Role of human microbiome and selected bacterial infections in the pathogenesis of rheumatoid arthritis. Reumatologia 2017; 55:242-250. [PMID: 29332963 PMCID: PMC5746635 DOI: 10.5114/reum.2017.71641] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Accepted: 10/25/2017] [Indexed: 12/23/2022] Open
Abstract
Microorganisms inhabiting human body form a complex ecosystem. The mutual influence of the microbiome and the immune system of the host constitute the basis for numerous diseases, e.g. pseudomembranous colitis, inflammatory bowel disease, type 1 diabetes, atopic diseases, obesity, reactive arthritis. New molecular diagnostic methods and multi-center studies may help in understanding of the role of microbiota in health and disease. Rheumatoid arthritis has a multi-faceted etiology, and its causes are not entirely understood. There are indications for the influence of microbiomes of oral cavity, intestines, lungs and urinary tract on the development of rheumatoid arthritis. Interactions between microorganisms and human immune system play role in the pathogenesis of the disease.
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488
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The Role of High-Mobility Group Box-1 and Its Crosstalk with Microbiome in Rheumatoid Arthritis. Mediators Inflamm 2017; 2017:5230374. [PMID: 29200665 PMCID: PMC5672636 DOI: 10.1155/2017/5230374] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 07/16/2017] [Indexed: 02/06/2023] Open
Abstract
Rheumatoid arthritis (RA) is a chronic, definitely disabling, and potentially severe autoimmune disease. Although an increasing number of patients are affected, a key treatment for all patients has not been discovered. High-mobility group box-1 (HMGB1) is a nuclear protein passively and actively released by almost all cell types after several stimuli. HMGB1 is involved in RA pathogenesis, but a convincing explanation about its role and possible modulation in RA is still lacking. Microbiome and its homeostasis are altered in patients with RA, and the microbiota restoration has been proposed to patients with RA. The purpose of the present review is to analyze the available evidences regarding HMGB1 and microbiome roles in RA and the possible implications of the crosstalk between the nuclear protein and microbiome in understanding and possibly treating patients affected by this harmful condition.
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489
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Noyes NR, Weinroth ME, Parker JK, Dean CJ, Lakin SM, Raymond RA, Rovira P, Doster E, Abdo Z, Martin JN, Jones KL, Ruiz J, Boucher CA, Belk KE, Morley PS. Enrichment allows identification of diverse, rare elements in metagenomic resistome-virulome sequencing. MICROBIOME 2017; 5:142. [PMID: 29041965 PMCID: PMC5645900 DOI: 10.1186/s40168-017-0361-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 10/05/2017] [Indexed: 05/29/2023]
Abstract
BACKGROUND Shotgun metagenomic sequencing is increasingly utilized as a tool to evaluate ecological-level dynamics of antimicrobial resistance and virulence, in conjunction with microbiome analysis. Interest in use of this method for environmental surveillance of antimicrobial resistance and pathogenic microorganisms is also increasing. In published metagenomic datasets, the total of all resistance- and virulence-related sequences accounts for < 1% of all sequenced DNA, leading to limitations in detection of low-abundance resistome-virulome elements. This study describes the extent and composition of the low-abundance portion of the resistome-virulome, using a bait-capture and enrichment system that incorporates unique molecular indices to count DNA molecules and correct for enrichment bias. RESULTS The use of the bait-capture and enrichment system significantly increased on-target sequencing of the resistome-virulome, enabling detection of an additional 1441 gene accessions and revealing a low-abundance portion of the resistome-virulome that was more diverse and compositionally different than that detected by more traditional metagenomic assays. The low-abundance portion of the resistome-virulome also contained resistance genes with public health importance, such as extended-spectrum betalactamases, that were not detected using traditional shotgun metagenomic sequencing. In addition, the use of the bait-capture and enrichment system enabled identification of rare resistance gene haplotypes that were used to discriminate between sample origins. CONCLUSIONS These results demonstrate that the rare resistome-virulome contains valuable and unique information that can be utilized for both surveillance and population genetic investigations of resistance. Access to the rare resistome-virulome using the bait-capture and enrichment system validated in this study can greatly advance our understanding of microbiome-resistome dynamics.
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Affiliation(s)
- Noelle R Noyes
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Maggie E Weinroth
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA
| | - Jennifer K Parker
- Department of Clinical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Chris J Dean
- Department of Computer Sciences, Colorado State University, Fort Collins, CO, USA
| | - Steven M Lakin
- Department of Clinical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Robert A Raymond
- Department of Computer Sciences, Colorado State University, Fort Collins, CO, USA
| | - Pablo Rovira
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA
| | - Enrique Doster
- Department of Clinical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Zaid Abdo
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Jennifer N Martin
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA
| | - Kenneth L Jones
- Department of Pediatrics, Section of Hematology Oncology and Bone Marrow Transplant, University of Colorado School of Medicine, Aurora, CO, USA
| | - Jaime Ruiz
- Department of Computer and Information Science and Engineering, University of Florida, Gainesville, Florida, USA
| | - Christina A Boucher
- Department of Computer and Information Science and Engineering, University of Florida, Gainesville, Florida, USA
| | - Keith E Belk
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA
| | - Paul S Morley
- Department of Clinical Sciences, Colorado State University, Fort Collins, CO, USA.
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490
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Marietta E, Mangalam A, Murray J, Taneja V. Reply. Arthritis Rheumatol 2017; 70:321-322. [PMID: 28950432 DOI: 10.1002/art.40331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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491
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The role of gut microbiota in the pathogenesis of rheumatic diseases. Clin Rheumatol 2017; 37:25-34. [PMID: 28914372 DOI: 10.1007/s10067-017-3821-4] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 08/31/2017] [Accepted: 09/04/2017] [Indexed: 01/08/2023]
Abstract
Rheumatic diseases refer to many diseases with a loss of immune self-tolerance, leading to a chronic inflammation, degeneration, or metabolic derangement in multiple organs or tissues. The cause of rheumatic diseases remains to be elucidated, though both environmental and genetic factors are required for the development of rheumatic diseases. Over the past decades, emerging studies suggested that alteration of intestinal microbiota, known as gut dysbiosis, contributed to the occurrence or development of a range of rheumatic diseases, including rheumatoid arthritis, systemic lupus erythematosus, ankylosing spondylitis, systemic sclerosis, and Sjogren's syndrome, through profoundly affecting the balance between pro- and anti-inflammatory immune responses. In this article, we discussed the role of gut microbiota in the pathogenesis of rheumatic diseases based on a large number of experimental and clinical materials, thereby providing a new insight for microbiota-targeted therapies to prevent or cure rheumatic diseases.
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492
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Abstract
Until recently, human microbiology was based on the identification of single microbes, such as bacteria, fungi and viruses, frequently isolated from patients with acute or chronic infections. Novel culture-independent molecular biochemical analyses (genomics, transcriptomics, proteomics, metabolomics) allow today to detect and classify the diverse microorganisms in a given ecosystem (microbiota), such as the gastrointestinal tract, the skin, the airway system, the urogenital tract and others, and to assess all genomes in these ecosystems (microbiome) as well as their gene products. These analyses revealed that each individual has its own microbiota that plays a role in health and disease. In addition, they greatly contributed to the recent advances in the understanding of the pathogenesis of a wide range of human diseases. It is to be expected that these new insights will translate into diagnostic, therapeutic and preventive measures in the context of personalized/precision medicine.
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Affiliation(s)
- Hubert E Blum
- Department of Medicine II, University Hospital Freiburg, Hugstetter Strasse 55, D-79106 Freiburg, Germany.
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493
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de Oliveira GLV, Leite AZ, Higuchi BS, Gonzaga MI, Mariano VS. Intestinal dysbiosis and probiotic applications in autoimmune diseases. Immunology 2017; 152. [PMID: 28556916 PMCID: PMC5543467 DOI: 10.1111/imm.12765 10.1111/imm.12765] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
In humans, a complex interaction between the host immune system and commensal microbiota is required to maintain gut homeostasis. In this symbiotic relationship, the microbiota provides carbohydrate fermentation and digestion, vitamin synthesis and gut-associated lymphoid tissue development, as well as preventing colonization by pathobionts, whereas the host offers a niche and nutrients for the survival of the microbiota. However, when this mutualistic relationship is compromised and an altered interaction between immune cells and microorganisms occurs, the gut microbiota may cause or contribute to the establishment of infectious diseases and trigger autoimmune diseases. Researchers have made efforts to clarify the role of the microbiota in autoimmune disease development and find new therapeutic approaches to treat immune-mediated diseases. However, the exact mechanisms involved in the dysbiosis and breakdown of the gut epithelial barrier are currently unknown. Here, we provide a general overview of studies describing gut microbiota perturbations in animal models of autoimmune diseases, such as type 1 diabetes, multiple sclerosis, rheumatoid arthritis and systemic lupus erythematosus. Moreover, we include the main studies concerning dysbiosis in humans and a critical discussion of the existing data on the use of probiotics in these autoimmune diseases.
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Affiliation(s)
| | - Aline Zazeri Leite
- Microbiome Study GroupSchool of Health Sciences Dr Paulo PrataBarretosSão PauloBrazil
| | | | - Marina Ignácio Gonzaga
- Microbiome Study GroupSchool of Health Sciences Dr Paulo PrataBarretosSão PauloBrazil,Barretos Cancer HospitalBarretosSão PauloBrazil
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494
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Chen B, Sun L, Zhang X. Integration of microbiome and epigenome to decipher the pathogenesis of autoimmune diseases. J Autoimmun 2017; 83:31-42. [DOI: 10.1016/j.jaut.2017.03.009] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 03/15/2017] [Indexed: 02/07/2023]
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495
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Intestinal Dysbiosis and Rheumatoid Arthritis: A Link between Gut Microbiota and the Pathogenesis of Rheumatoid Arthritis. J Immunol Res 2017; 2017:4835189. [PMID: 28948174 PMCID: PMC5602494 DOI: 10.1155/2017/4835189] [Citation(s) in RCA: 166] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Revised: 06/17/2017] [Accepted: 07/12/2017] [Indexed: 12/22/2022] Open
Abstract
Characterization and understanding of gut microbiota has recently increased representing a wide research field, especially in autoimmune diseases. Gut microbiota is the major source of microbes which might exert beneficial as well as pathogenic effects on human health. Intestinal microbiome's role as mediator of inflammation has only recently emerged. Microbiota has been observed to differ in subjects with early rheumatoid arthritis compared to controls, and this finding has commanded this study as a possible autoimmune process. Studies with intestinal microbiota have shown that rheumatoid arthritis is characterized by an expansion and/or decrease of bacterial groups as compared to controls. In this review, we present evidence linking intestinal dysbiosis with the autoimmune mechanisms involved in the development of rheumatoid arthritis.
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496
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Colpitts SL, Kasper EJ, Keever A, Liljenberg C, Kirby T, Magori K, Kasper LH, Ochoa-Repáraz J. A bidirectional association between the gut microbiota and CNS disease in a biphasic murine model of multiple sclerosis. Gut Microbes 2017; 8:561-573. [PMID: 28708466 PMCID: PMC5730387 DOI: 10.1080/19490976.2017.1353843] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The gut microbiome plays an important role in the development of inflammatory disease as shown using experimental models of central nervous system (CNS) demyelination. Gut microbes influence the response of regulatory immune cell populations in the gut-associated lymphoid tissue (GALT), which drive protection in acute and chronic experimental autoimmune encephalomyelitis (EAE). Recent observations suggest that communication between the host and the gut microbiome is bidirectional. We hypothesized that the gut microbiota differs between the acute inflammatory and chronic progressive stages of a murine model of secondary-progressive multiple sclerosis (SP-MS). This non-obese diabetic (NOD) model of EAE develops a biphasic pattern of disease that more closely resembles the human condition when transitioning from relapsing-remitting (RR)-MS to SP-MS. We compared the gut microbiome of NOD mice with either mild or severe disease to that of non-immunized control mice. We found that the mice which developed a severe secondary form of EAE harbored a dysbiotic gut microbiome when compared with the healthy control mice. Furthermore, we evaluated whether treatment with a cocktail of broad-spectrum antibiotics would modify the outcome of the progressive stage of EAE in the NOD model. Our results indicated reduced mortality and clinical disease severity in mice treated with antibiotics compared with untreated mice. Our findings support the hypothesis that there are reciprocal effects between experimental CNS inflammatory demyelination and modification of the microbiome providing a foundation for the establishment of early therapeutic interventions targeting the gut microbiome that could potentially limit disease progression.
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Affiliation(s)
- Sara L. Colpitts
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH, USA
| | - Eli J. Kasper
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH, USA
| | - Abigail Keever
- Department of Biology, Eastern Washington University, Cheney, WA, USA
| | - Caleb Liljenberg
- Department of Biology, Eastern Washington University, Cheney, WA, USA
| | - Trevor Kirby
- Department of Biology, Eastern Washington University, Cheney, WA, USA
| | - Krisztian Magori
- Department of Biology, Eastern Washington University, Cheney, WA, USA
| | - Lloyd H. Kasper
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH, USA
| | - Javier Ochoa-Repáraz
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH, USA,Department of Biology, Eastern Washington University, Cheney, WA, USA,CONTACT Javier Ochoa-Repáraz Department of Biology, Eastern Washington University, Cheney, WA 99004, USA
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497
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Aggravation of collagen-induced arthritis by orally administered Porphyromonas gingivalis through modulation of the gut microbiota and gut immune system. Sci Rep 2017; 7:6955. [PMID: 28761156 PMCID: PMC5537233 DOI: 10.1038/s41598-017-07196-7] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 06/23/2017] [Indexed: 01/14/2023] Open
Abstract
Porhyromonas gingivalis, a causative bacterium of periodontitis, is implicated in the etiology of rheumatoid arthritis (RA), mainly because of expressing peptidyl arginine deiminase (PAD) that generates RA-related autoantigens. However, compared with other periodontopathic bacteria, the precise role of P. gingivalis in RA is largely unknown. We found that orally administered P. gingivalis changed the gut microbiome with concomitant elevation of serum endotoxin and inflammatory markers, and impairment of the gut barrier function. Based on findings showing a relationship between gut microbiota and RA, we investigated whether the change of gut microbiota induced by P. gingivalis and Prevotella intermedia, another periodontopathic bacterium without PAD, is associated with collagen-induced arthritis (CIA). DBA/1J mice were orally administered with or without bacteria followed by induction of CIA. P. gingivalis, but not P. intermedia, administration significantly aggravated arthritis with increased interleukin-17 levels in sera and culture supernatants, increased Th17 cell proportions among mesenteric lymphocytes, and a significant change in the gut microbiome. However, P. gingivalis administration did not elevate the level of anti-citrullinated protein antibody. These results suggest a unique role of P. gingivalis in the link between periodontitis and RA by affecting the gut immune system and the gut microbiota composition.
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498
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Gut bacterial peptides with autoimmunity potential as environmental trigger for late onset complex diseases: In-silico study. PLoS One 2017; 12:e0180518. [PMID: 28678867 PMCID: PMC5498033 DOI: 10.1371/journal.pone.0180518] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 06/17/2017] [Indexed: 02/06/2023] Open
Abstract
Recent evidences suggest that human gut microbiota with major component as bacteria can induce immunity. It is also known that gut lining depletes with ageing and that there is increased risk of autoimmune and inflammatory disorders with ageing. It is therefore likely that both may be correlated as depletion of gut lining exposes the gut bacterial antigens to host immune mechanisms, which may induce immunity to certain bacterial proteins, but at the same time such immunity may also be auto-immunogenic to host. This autoimmunity may make a protein molecule nonfunctional and thereby may be involved in late onset metabolic, autoimmune and inflammatory disorders such as, Diabetes, Rheumatoid Arthritis, Hyperlipidemias and Cancer. In this in-silico study we found a large number of peptides identical between human and gut bacteria which were binding to HLA-II alleles, and hence, likely to be auto-immunogenic. Further we observed that such autoimmune candidates were enriched in bacterial species belonging to Firmicutes and Proteobacteria phyla, which lead us to conclude that these phyla may have higher disease impact in genetically predisposed individuals. Functional annotation of human proteins homologous to candidate gut-bacterial peptides showed significant enrichment in metabolic processes and pathways. Cognitive trait, Ageing, Alzheimer, Type 2 diabetes, Chronic Kidney Failure (CKF), Chronic Obstructive Pulmonary Disease (COPD) and various Cancers were the major diseases represented in the dataset. This dataset provides us with gut bacterial autoimmune candidates which can be studied for their clinical significance in late onset diseases.
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499
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Balakrishnan B, Luckey D, Marietta E, Karau M, Patel R, Murray J, Taneja V. Development of a real-time PCR method for quantification of Prevotella histicola from the gut. Anaerobe 2017; 48:37-41. [PMID: 28684342 DOI: 10.1016/j.anaerobe.2017.06.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 06/22/2017] [Accepted: 06/27/2017] [Indexed: 01/19/2023]
Abstract
We designed species-specific primers and developed a qPCR method for enumerating P. histicola from intestinal samples. The two designed primer sets showed specificity for the target 16S rRNA gene of P. histicola. The absolute qPCR method was sensitive to quantify as few as 103 colony-forming units (CFU) in the gut.
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Affiliation(s)
| | - David Luckey
- Department of Immunology, Mayo Clinic, Rochester, MN55905, USA
| | - Eric Marietta
- Department of Gastroenterology, Mayo Clinic, Rochester, MN55905, USA
| | - Melissa Karau
- Department of Clinical Microbiology, Mayo Clinic, Rochester, MN55905, USA
| | - Robin Patel
- Department of Clinical Microbiology, Mayo Clinic, Rochester, MN55905, USA
| | - Joseph Murray
- Department of Gastroenterology, Mayo Clinic, Rochester, MN55905, USA
| | - Veena Taneja
- Department of Immunology, Mayo Clinic, Rochester, MN55905, USA.
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500
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de Oliveira GLV, Leite AZ, Higuchi BS, Gonzaga MI, Mariano VS. Intestinal dysbiosis and probiotic applications in autoimmune diseases. Immunology 2017; 152:1-12. [PMID: 28556916 DOI: 10.1111/imm.12765] [Citation(s) in RCA: 178] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 05/19/2017] [Accepted: 05/24/2017] [Indexed: 12/13/2022] Open
Abstract
In humans, a complex interaction between the host immune system and commensal microbiota is required to maintain gut homeostasis. In this symbiotic relationship, the microbiota provides carbohydrate fermentation and digestion, vitamin synthesis and gut-associated lymphoid tissue development, as well as preventing colonization by pathobionts, whereas the host offers a niche and nutrients for the survival of the microbiota. However, when this mutualistic relationship is compromised and an altered interaction between immune cells and microorganisms occurs, the gut microbiota may cause or contribute to the establishment of infectious diseases and trigger autoimmune diseases. Researchers have made efforts to clarify the role of the microbiota in autoimmune disease development and find new therapeutic approaches to treat immune-mediated diseases. However, the exact mechanisms involved in the dysbiosis and breakdown of the gut epithelial barrier are currently unknown. Here, we provide a general overview of studies describing gut microbiota perturbations in animal models of autoimmune diseases, such as type 1 diabetes, multiple sclerosis, rheumatoid arthritis and systemic lupus erythematosus. Moreover, we include the main studies concerning dysbiosis in humans and a critical discussion of the existing data on the use of probiotics in these autoimmune diseases.
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Affiliation(s)
| | - Aline Zazeri Leite
- Microbiome Study Group, School of Health Sciences Dr Paulo Prata, Barretos, São Paulo, Brazil
| | - Bruna Stevanato Higuchi
- Microbiome Study Group, School of Health Sciences Dr Paulo Prata, Barretos, São Paulo, Brazil
| | - Marina Ignácio Gonzaga
- Microbiome Study Group, School of Health Sciences Dr Paulo Prata, Barretos, São Paulo, Brazil.,Barretos Cancer Hospital, Barretos, São Paulo, Brazil
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