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Hochuli N, Kadyan S, Park G, Patoine C, Nagpal R. Pathways linking microbiota-gut-brain axis with neuroinflammatory mechanisms in Alzheimer's pathophysiology. MICROBIOME RESEARCH REPORTS 2023; 3:9. [PMID: 38455083 PMCID: PMC10917618 DOI: 10.20517/mrr.2023.39] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 11/03/2023] [Accepted: 11/30/2023] [Indexed: 03/09/2024]
Abstract
Disturbances in the local and peripheral immune systems are closely linked to a wide range of diseases. In the context of neurodegenerative disorders such as Alzheimer's disease (AD), inflammation plays a crucial role, often appearing as a common manifestation despite the variability in the occurrence of other pathophysiological hallmarks. Thus, combating neuroinflammation holds promise in treating complex pathophysiological diseases like AD. Growing evidence suggests the gut microbiome's crucial role in shaping the pathogenesis of AD by influencing inflammatory mediators. Gut dysbiosis can potentially activate neuroinflammatory pathways through bidirectional signaling of the gut-brain axis; however, the precise mechanisms of this complex interweaved network remain largely unclear. In these milieus, this review attempts to summarize the contributing role of gut microbiome-mediated neuroinflammatory signals in AD pathophysiology, while also pondering potential mechanisms through which commensal and pathogenic gut microbes affect neuroinflammation. While certain taxa such as Roseburia and Escherichia have been strongly correlated with AD, other clades such as Bacteroides and Faecalibacterium exhibit variations at the species and strain levels. In order to disentangle the inflammatory aspects of neurodegeneration attributed to the gut microbiome, it is imperative that future mechanistic studies investigate the species/strain-level dependency of commensals, opportunistic, and pathogenic gut microbes that consistently show correlations with AD patients across multiple associative studies.
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Affiliation(s)
| | | | | | | | - Ravinder Nagpal
- Department of Health, Nutrition, and Food Sciences, College of Education, Health, and Human Sciences, Florida State University, Tallahassee, FL 32306, USA
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2
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Frau A, Ijaz UZ, Slater R, Jonkers D, Penders J, Campbell BJ, Kenny JG, Hall N, Lenzi L, Burkitt MD, Pierik M, Darby AC, Probert CSJ. Inter-kingdom relationships in Crohn's disease explored using a multi-omics approach. Gut Microbes 2022; 13:1930871. [PMID: 34241567 PMCID: PMC8274447 DOI: 10.1080/19490976.2021.1930871] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The etiology of Crohn's disease (CD) is multifactorial. Bacterial and fungal microbiota are involved in the onset and/or progression of the disease. A bacterial dysbiosis in CD patients is accepted; however, less is known about the mycobiome and the relationships between the two communities. We investigated the interkingdom relationships, their metabolic consequences, and the changes in the fungal community during relapse and remission in CD.Two cohorts were evaluated: a British cohort (n = 63) comprising CD and ulcerative colitis patients, and controls. The fungal and bacterial communities of biopsy and fecal samples were analyzed, with the fecal volatiles; datasets were also integrated; and a Dutch cohort (n = 41) comprising CD patients and healthy controls was analyzed for stability of the gut mycobiome.A dysbiosis of the bacterial community was observed in biopsies and stool. Results suggest Bacteroides is likely key in CD and may modulate Candida colonization. A dysbiosis of the fungal community was observed only in the Dutch cohort; Malassezia and Candida were increased in patients taking immunosuppressants. Longitudinal analysis showed an increase in Cyberlindnera in relapse. Saccharomyces was dominant in all fecal samples, but not in biopsies, some of which did not yield fungal reads; amino acid degradation was the main metabolic change associated with CD and both bacteria and fungi might be implicated.We have shown that Bacteroides and yeasts may play a role in CD; understanding their role and relationship in the disease would shed new light on the development and treatment of CD.
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Affiliation(s)
- Alessandra Frau
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK,CONTACT Alessandra Frau Department of Molecular and Clinical Cancer Medicine, Nuffield Building, Ashton Street, LiverpoolL69 3GE, UK
| | - Umer Z. Ijaz
- School of Engineering, University of Glasgow, Glasgow, UK,Umer Z. Ijaz School of Engineering, University of Glasgow, Glasgow, UK
| | - Rachael Slater
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Daisy Jonkers
- School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, Netherlands
| | - John Penders
- School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, Netherlands
| | - Barry J. Campbell
- Department of Infection & Microbiomes, University of Liverpool, Liverpool, UK
| | | | - Neil Hall
- Earlham Institute, Norwich, UK,School of Biological Sciences, University of East Anglia, Norwich, Norfolk, UK
| | - Luca Lenzi
- Centre for Genomic Research, University of Liverpool, Liverpool, UK
| | - Michael D. Burkitt
- Division of Diabetes, Endocrinology and Gastroenterology, University of Manchester, Manchester, UK
| | - Marieke Pierik
- School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, Netherlands
| | - Alistair C. Darby
- Department of Infection & Microbiomes, University of Liverpool, Liverpool, UK
| | - Christopher S. J. Probert
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
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3
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Fan TJ, Goeser L, Lu K, Faith JJ, Hansen JJ. Enterococcus faecalis Glucosamine Metabolism Exacerbates Experimental Colitis. Cell Mol Gastroenterol Hepatol 2021; 12:1373-1389. [PMID: 34246809 PMCID: PMC8479252 DOI: 10.1016/j.jcmgh.2021.06.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 06/18/2021] [Accepted: 06/21/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND & AIMS The inflammatory bowel diseases (IBDs), Crohn's disease and ulcerative colitis, are caused in part by aberrant immune responses to resident intestinal bacteria. Certain dietary components, including carbohydrates, are associated with IBDs and alter intestinal bacterial composition. However, the effects of luminal carbohydrates on the composition and colitogenic potential of intestinal bacteria are incompletely understood. We hypothesize that carbohydrate metabolism by resident proinflammatory intestinal bacteria enhances their growth and worsens intestinal inflammation. METHODS We colonized germ-free, wild-type, and colitis-susceptible interleukin-10 knockout mice (Il10-/-) with a consortium of resident intestinal bacterial strains and quantified colon inflammation using blinded histologic scoring and spontaneous secretion of IL12/23p40 by colon explants. We measured luminal bacterial composition using real-time 16S polymerase chain reaction, bacterial gene expression using RNA sequencing and real-time polymerase chain reaction, and luminal glucosamine levels using gas chromatography-mass spectrometry. RESULTS We show that a consortium of 8 bacterial strains induces severe colitis in Il10-/- mice and up-regulates genes associated with carbohydrate metabolism during colitis. Specifically, Enterococcus faecalis strain OG1RF is proinflammatory and strongly up-regulates OG1RF_11616-11610, an operon that encodes genes of a previously undescribed phosphotransferase system that we show imports glucosamine. Experimental colitis is associated with increased levels of luminal glucosamine and OG1RF_11616 causes worse colitis, not by increasing E faecalis numbers, but rather by mechanisms that require the presence of complex microbiota. CONCLUSIONS Further studies of luminal carbohydrate levels and bacterial carbohydrate metabolism during intestinal inflammation will improve our understanding of the pathogenesis of IBDs and may lead to the development of novel therapies for these diseases.
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Affiliation(s)
- Ting-Jia Fan
- Center for Gastrointestinal Biology and Disease, Chapel Hill, North Carolina; Department of Microbiology and Immunology, Chapel Hill, North Carolina
| | - Laura Goeser
- Center for Gastrointestinal Biology and Disease, Chapel Hill, North Carolina
| | - Kun Lu
- Department of Environmental Sciences and Engineering, Chapel Hill, North Carolina
| | - Jeremiah J Faith
- The Precision Immunology Institute, New York, New York; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jonathan J Hansen
- Center for Gastrointestinal Biology and Disease, Chapel Hill, North Carolina; Department of Microbiology and Immunology, Chapel Hill, North Carolina; Division of Gastroenterology and Hepatology, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.
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4
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Wang C, Zhao J, Zhang H, Lee YK, Zhai Q, Chen W. Roles of intestinal bacteroides in human health and diseases. Crit Rev Food Sci Nutr 2020; 61:3518-3536. [PMID: 32757948 DOI: 10.1080/10408398.2020.1802695] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Bacteroides, an abundant genus in the intestines of mammals, has been recently considered as the next generation probiotics (NGP) candidate due to its potential role in promoting host health. However, the role of Bacteroides in the development of intestinal dysfunctions such as diarrhea, inflammatory bowel disease, and colorectal cancer should not be overlooked. In the present study, we focused on nine most widely occurred and abundant Bacteroides species and discussed their roles in host immunity, glucose and lipid metabolism and the prevention or induction of diseases. Besides, we also discussed the current methods used in the safety evaluation of Bacteroides species and key opinions about the concerns of these strains for the future use.
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Affiliation(s)
- Chen Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, P.R. China.,School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, P.R. China.,School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, P.R. China.,School of Food Science and Technology, Jiangnan University, Wuxi, China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, China.,Research Institute, Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine, Wuxi, China.,(Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou, China
| | - Yuan-Kun Lee
- Department of Microbiology & Immunology, National University of Singapore, Singapore, Singapore
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, P.R. China.,School of Food Science and Technology, Jiangnan University, Wuxi, China.,International Joint Research Laboratory for Probiotics, Jiangnan University, Wuxi, China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, P.R. China.,School of Food Science and Technology, Jiangnan University, Wuxi, China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, China.,Beijing Innovation Centre of Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing, P.R. China
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5
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Durant L, Stentz R, Noble A, Brooks J, Gicheva N, Reddi D, O’Connor MJ, Hoyles L, McCartney AL, Man R, Pring ET, Dilke S, Hendy P, Segal JP, Lim DNF, Misra R, Hart AL, Arebi N, Carding SR, Knight SC. Bacteroides thetaiotaomicron-derived outer membrane vesicles promote regulatory dendritic cell responses in health but not in inflammatory bowel disease. MICROBIOME 2020; 8:88. [PMID: 32513301 PMCID: PMC7282036 DOI: 10.1186/s40168-020-00868-z] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 05/13/2020] [Indexed: 06/09/2023]
Abstract
BACKGROUND Bacteroides thetaiotaomicron (Bt) is a prominent member of the human intestinal microbiota that, like all gram-negative bacteria, naturally generates nanosized outer membrane vesicles (OMVs) which bud off from the cell surface. Importantly, OMVs can cross the intestinal epithelial barrier to mediate microbe-host cell crosstalk involving both epithelial and immune cells to help maintain intestinal homeostasis. Here, we have examined the interaction between Bt OMVs and blood or colonic mucosa-derived dendritic cells (DC) from healthy individuals and patients with Crohn's disease (CD) or ulcerative colitis (UC). RESULTS In healthy individuals, Bt OMVs stimulated significant (p < 0.05) IL-10 expression by colonic DC, whereas in peripheral blood-derived DC they also stimulated significant (p < 0.001 and p < 0.01, respectively) expression of IL-6 and the activation marker CD80. Conversely, in UC Bt OMVs were unable to elicit IL-10 expression by colonic DC. There were also reduced numbers of CD103+ DC in the colon of both UC and CD patients compared to controls, supporting a loss of regulatory DC in both diseases. Furthermore, in CD and UC, Bt OMVs elicited a significantly lower proportion of DC which expressed IL-10 (p < 0.01 and p < 0.001, respectively) in blood compared to controls. These alterations in DC responses to Bt OMVs were seen in patients with inactive disease, and thus are indicative of intrinsic defects in immune responses to this commensal in inflammatory bowel disease (IBD). CONCLUSIONS Overall, our findings suggest a key role for OMVs generated by the commensal gut bacterium Bt in directing a balanced immune response to constituents of the microbiota locally and systemically during health which is altered in IBD patients. Video Abstract.
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Affiliation(s)
- Lydia Durant
- Antigen Presentation Research Group, Imperial College London, Northwick Park & St. Mark’s Hospital Campus, Watford Rd, Harrow, Greater London HA1 3UJ UK
| | - Régis Stentz
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, NR4 7UQ UK
| | - Alistair Noble
- Antigen Presentation Research Group, Imperial College London, Northwick Park & St. Mark’s Hospital Campus, Watford Rd, Harrow, Greater London HA1 3UJ UK
| | - Johanne Brooks
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, NR4 7UQ UK
- Norwich Medical School, University of East Anglia, Norwich, NR4 7TJ UK
| | - Nadezhda Gicheva
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, NR4 7UQ UK
| | - Durga Reddi
- Antigen Presentation Research Group, Imperial College London, Northwick Park & St. Mark’s Hospital Campus, Watford Rd, Harrow, Greater London HA1 3UJ UK
| | - Matthew J. O’Connor
- Antigen Presentation Research Group, Imperial College London, Northwick Park & St. Mark’s Hospital Campus, Watford Rd, Harrow, Greater London HA1 3UJ UK
| | - Lesley Hoyles
- Department of Biosciences, Nottingham Trent University, Clifton Campus, Nottingham, NG11 8NS UK
| | - Anne L. McCartney
- Food Microbial Sciences Unit, University of Reading, Whiteknights, Reading, RG6 6UR UK
| | - Ripple Man
- St Mark’s Hospital, London North West University Healthcare NHS Trust, Harrow, Greater London HA1 3UJ UK
| | - E. Tobias Pring
- Antigen Presentation Research Group, Imperial College London, Northwick Park & St. Mark’s Hospital Campus, Watford Rd, Harrow, Greater London HA1 3UJ UK
- St Mark’s Hospital, London North West University Healthcare NHS Trust, Harrow, Greater London HA1 3UJ UK
| | - Stella Dilke
- Antigen Presentation Research Group, Imperial College London, Northwick Park & St. Mark’s Hospital Campus, Watford Rd, Harrow, Greater London HA1 3UJ UK
- St Mark’s Hospital, London North West University Healthcare NHS Trust, Harrow, Greater London HA1 3UJ UK
| | - Philip Hendy
- Antigen Presentation Research Group, Imperial College London, Northwick Park & St. Mark’s Hospital Campus, Watford Rd, Harrow, Greater London HA1 3UJ UK
- St Mark’s Hospital, London North West University Healthcare NHS Trust, Harrow, Greater London HA1 3UJ UK
| | - Jonathan P. Segal
- St Mark’s Hospital, London North West University Healthcare NHS Trust, Harrow, Greater London HA1 3UJ UK
| | - Dennis N. F. Lim
- St Mark’s Hospital, London North West University Healthcare NHS Trust, Harrow, Greater London HA1 3UJ UK
| | - Ravi Misra
- St Mark’s Hospital, London North West University Healthcare NHS Trust, Harrow, Greater London HA1 3UJ UK
| | - Ailsa L. Hart
- St Mark’s Hospital, London North West University Healthcare NHS Trust, Harrow, Greater London HA1 3UJ UK
| | - Naila Arebi
- St Mark’s Hospital, London North West University Healthcare NHS Trust, Harrow, Greater London HA1 3UJ UK
| | - Simon R. Carding
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, NR4 7UQ UK
- Norwich Medical School, University of East Anglia, Norwich, NR4 7TJ UK
| | - Stella C. Knight
- Antigen Presentation Research Group, Imperial College London, Northwick Park & St. Mark’s Hospital Campus, Watford Rd, Harrow, Greater London HA1 3UJ UK
- St Mark’s Hospital, London North West University Healthcare NHS Trust, Harrow, Greater London HA1 3UJ UK
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6
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Sitkin S, Pokrotnieks J. Gut Microbiota as a Host Defender and a Foe: The 2 Faces of Commensal Bacteroides thetaiotaomicron in Inflammatory Bowel Disease. Inflamm Bowel Dis 2019; 25:e71. [PMID: 30561647 DOI: 10.1093/ibd/izy377] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Affiliation(s)
- Stanislav Sitkin
- Department of Internal Diseases, Gastroenterology and Dietetics, North-Western State Medical University named after I.I. Mechnikov, St. Petersburg, Russia.,Research Department, Elpis SIA, Riga, Latvia
| | - Juris Pokrotnieks
- Department of Internal Diseases, Rīga Stradiņš University, Riga, Latvia.,Centre of Gastroenterology, Hepatology and Nutrition, Pauls Stradiņš Clinical University Hospital, Riga, Latvia
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7
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Ihekweazu FD, Fofanova TY, Queliza K, Nagy-Szakal D, Stewart CJ, Engevik MA, Hulten KG, Tatevian N, Graham DY, Versalovic J, Petrosino JF, Kellermayer R. Bacteroides ovatus ATCC 8483 monotherapy is superior to traditional fecal transplant and multi-strain bacteriotherapy in a murine colitis model. Gut Microbes 2019; 10:504-520. [PMID: 30663928 PMCID: PMC6748610 DOI: 10.1080/19490976.2018.1560753] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Background and aims: Bacteriotherapy aimed at addressing dysbiosis may be therapeutic for Inflammatory Bowel Diseases (IBDs). We sought to determine if defined Bacteroides-based bacteriotherapy could be an effective and consistent alternative to fecal microbiota transplantation (FMT) in a murine model of IBD. Methods: We induced experimental colitis in 8- 12-week-old C57BL/6 mice using 2-3% dextran sodium sulfate. Mice were simultaneously treated by oral gavage with a triple-Bacteroides cocktail, individual Bacteroides strains, FMT using stool from healthy donor mice, or their own stool as a control. Survival, weight loss and markers of inflammation (histology, serum amyloid A, cytokine production) were correlated to 16S rRNA gene profiling of fecal and mucosal microbiomes. Results: Triple-Bacteroides combination therapy was more protective against weight loss and mortality than traditional FMT therapy. B. ovatus ATCC8483 was more effective than any individual strain, or a combination of strains, in preventing weight loss, decreasing histological damage, dampening inflammatory response, and stimulating epithelial recovery. Irrespective of the treatment group, overall Bacteroides abundance associated with treatment success and decreased cytokine production while the presence of Akkermansia correlated with treatment failure. However, the therapeutic benefit associated with high Bacteroides abundance was negated in the presence of Streptococcus. Conclusions: Bacteroides ovatus monotherapy was more consistent and effective than traditional FMT at ameliorating colitis and stimulating epithelial recovery in a murine model of IBD. Given the tolerability of Bacteroides ovatus ATCC 8483 in an active, on-going human study, this therapy may be repurposed for the management of IBD in a clinically expedient timeline.
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Affiliation(s)
- Faith D. Ihekweazu
- Pediatric Gastroenterology, Hepatology and Nutrition, Baylor College of Medicine, Texas Children’s Hospital, Houston, TX, USA,CONTACT Faith D. Ihekweazu Pediatric Gastroenterology, Hepatology and Nutrition, Baylor College of Medicine, Texas Children’s Hospital, 1102 Bates Ave, FT860.28, Houston, TX 77030, USA
| | | | - Karen Queliza
- Pediatric Gastroenterology, Hepatology and Nutrition, Baylor College of Medicine, Texas Children’s Hospital, Houston, TX, USA
| | - Dorottya Nagy-Szakal
- Center for Infection and Immunity, Columbia University Mailman School of Public Health, New York, NY, USA
| | - Christopher J. Stewart
- Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA,Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Melinda A. Engevik
- Pediatric Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Kristina G. Hulten
- Pediatric Infectious Disease, Baylor College of Medicine, Texas Children’s Hospital, Houston, TX, USA
| | - Nina Tatevian
- Pathology and Laboratory Medicine, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - David Y. Graham
- Gastroenterology, Baylor College of Medicine, Houston, TX, USA
| | - James Versalovic
- Pediatric Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
| | | | - Richard Kellermayer
- Pediatric Gastroenterology, Hepatology and Nutrition, Baylor College of Medicine, Texas Children’s Hospital, Houston, TX, USA
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8
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Ihekweazu FD, Versalovic J. Development of the Pediatric Gut Microbiome: Impact on Health and Disease. Am J Med Sci 2018; 356:413-423. [PMID: 30384950 PMCID: PMC6268214 DOI: 10.1016/j.amjms.2018.08.005] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 08/10/2018] [Indexed: 02/07/2023]
Abstract
The intestinal microbiota are important in human growth and development. Microbial composition may yield insights into the temporal development of microbial communities and vulnerabilities to disorders of microbial ecology such as recurrent Clostridium difficile infection. Discoveries of key microbiome features of carbohydrate and amino acid metabolism are lending new insights into possible therapies or preventative strategies for inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS). In this review, we summarize the current understanding of the development of the pediatric gastrointestinal microbiome, the influence of the microbiome on the developing brain through the gut-brain axis, and the impact of dysbiosis on disease development. Dysbiosis is explored in the context of pediatric allergy and asthma, recurrent C. difficile infection, IBD, IBS, and metabolic disorders. The central premise is that the human intestinal microbiome plays a vital role in health and disease, beginning in the prenatal period and extending throughout childhood.
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Affiliation(s)
- Faith D. Ihekweazu
- Pediatric Gastroenterology, Hepatology and Nutrition, Baylor College of Medicine, Texas Children’s Hospital, 1102 Bates St., Houston, TX, 77030, USA.
| | - James Versalovic
- Pediatric Pathology and Immunology, Baylor College of Medicine, Texas Children’s Hospital 1102 Bates St., Houston, TX, 77030, USA.
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Mazzarella G, Perna A, Marano A, Lucariello A, Rotondi Aufiero V, Sorrentino A, Melina R, Guerra G, Taccone FS, Iaquinto G, De Luca A. Pathogenic Role of Associated Adherent-InvasiveEscherichia coliin Crohn's Disease. J Cell Physiol 2017; 232:2860-2868. [DOI: 10.1002/jcp.25717] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 11/30/2016] [Indexed: 12/12/2022]
Affiliation(s)
| | - Angelica Perna
- Department of Mental and Physical Health and Preventive Medicine; Section of Human Anatomy, Second University of Naples; Naples Italy
| | - Angela Marano
- Institute of Food Sciences-CNR; Lab. Immuno-Morphology; Avellino Italy
| | - Angela Lucariello
- Department of Mental and Physical Health and Preventive Medicine; Section of Human Anatomy, Second University of Naples; Naples Italy
| | | | - Alida Sorrentino
- Institute of Food Sciences-CNR; Lab. Immuno-Morphology; Avellino Italy
| | - Raffaele Melina
- Department of Gastroenterology; San G. Moscati Hospital; Avellino Italy
| | - Germano Guerra
- Department of Medicine and Health Sciences; University of Molise; Molise Italy
| | - Fabio Silvio Taccone
- Department of Intensive Care, Erasme Hospital; Université Libre de Bruxelles; Brussels Belgium
| | - Gaetano Iaquinto
- Division of Gastroenterology; Santa Rita Hospital; Atripalda (Av) Italy
| | - Antonio De Luca
- Department of Mental and Physical Health and Preventive Medicine; Section of Human Anatomy, Second University of Naples; Naples Italy
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10
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Loganes C, Valencic E, Pin A, Marini E, Martelossi S, Naviglio S, De Leo L, Not T, Monasta L, Tommasini A, Marcuzzi A. Ex vivo response to mucosal bacteria and muramyl dipeptide in inflammatory bowel disease. World J Gastroenterol 2016; 22:9734-9743. [PMID: 27956797 PMCID: PMC5124978 DOI: 10.3748/wjg.v22.i44.9734] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 08/12/2016] [Accepted: 09/06/2016] [Indexed: 02/06/2023] Open
Abstract
AIM To evaluate how mucosal bacteria impact on the spontaneous and muramyl dipeptide (MDP)-induced inflammation in Crohn’s disease (CD) and ulcerative colitis (UC).
METHODS Colonic mucosal biopsies were collected from children with active or remissive CD, UC and controls. Two tissue samples were taken from inflamed mucosal segments (in patients with active disease) or from non-inflamed mucosa [in patients in remission or in healthy controls (HC)]. Experiments were performed in the presence or absence of antibiotics, to assess whether the disease-associated microbiota can modulate the cytokine response ex vivo. For this purpose, each specimen was half-cut to compare spontaneous and MDP-induced inflammation in the presence of live bacteria (LB) or antibiotics. After 24 h of culture, an array of 17 cytokines was assessed in supernatants. Statistical analyses were performed to find significant differences in single cytokines or in patterns of cytokine response in the different groups.
RESULTS We demonstrated that subjects with CD display a spontaneous production of inflammatory cytokines including granulocyte-colony stimulating factor (G-CSF), interleukin (IL) 6, IL8, IL10 and IL12, that was not significantly influenced by the addition of antibiotics. UC specimens also displayed a trend of increased spontaneous secretion of several cytokines, which however was not significant due to broader variability among patients. After the addition of antibiotics, spontaneous IL8 secretion was significantly higher in UC than in controls. In HC, a trend towards the weakening of spontaneous IL8 production was observed in the presence of live mucosal bacteria with respect to the presence of antibiotics. In contrast, in the presence of LB UC showed an increasing trend of spontaneous IL8 production, while MDP stimulation resulted in lower IL8 production in the presence of antibiotics. We also showed that subjects with CD seem to have a lowered production of IL8 in response to MDP in the presence of LB. Only with the addition of antibiotics, likely reducing the contribution of LB, multivariate statistical analysis could identify the combination of measures of G-CSF, tumor necrosis factor alpha, IL4 and IL17 as a good discriminator between CD and UC.
CONCLUSION We showed that the presence of LB or antibiotics can significantly influence the inflammatory response ex vivo in inflammatory bowel diseases.
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11
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Basson A, Trotter A, Rodriguez-Palacios A, Cominelli F. Mucosal Interactions between Genetics, Diet, and Microbiome in Inflammatory Bowel Disease. Front Immunol 2016; 7:290. [PMID: 27531998 PMCID: PMC4970383 DOI: 10.3389/fimmu.2016.00290] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 07/19/2016] [Indexed: 12/12/2022] Open
Abstract
Numerous reviews have discussed gut microbiota composition changes during inflammatory bowel diseases (IBD), particularly Crohn’s disease (CD). However, most studies address the observed effects by focusing on studying the univariate connection between disease and dietary-induced alterations to gut microbiota composition. The possibility that these effects may reflect a number of other interconnected (i.e., pantropic) mechanisms, activated in parallel, particularly concerning various bacterial metabolites, is in the process of being elucidated. Progress seems, however, hampered by various difficult-to-study factors interacting at the mucosal level. Here, we highlight some of such factors that merit consideration, namely: (1) the contribution of host genetics and diet in altering gut microbiome, and in turn, the crosstalk among secondary metabolic pathways; (2) the interdependence between the amount of dietary fat, the fatty acid composition, the effects of timing and route of administration on gut microbiota community, and the impact of microbiota-derived fatty acids; (3) the effect of diet on bile acid composition, and the modulator role of bile acids on the gut microbiota; (4) the impact of endogenous and exogenous intestinal micronutrients and metabolites; and (5) the need to consider food associated toxins and chemicals, which can introduce confounding immune modulating elements (e.g., antioxidant and phytochemicals in oils and proteins). These concepts, which are not mutually exclusive, are herein illustrated paying special emphasis on physiologically inter-related processes.
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Affiliation(s)
- Abigail Basson
- Digestive Health Research Institute, Case Western Reserve University , Cleveland, OH , USA
| | - Ashley Trotter
- Digestive Health Research Institute, Case Western Reserve University, Cleveland, OH, USA; University Hospitals Case Medical Center, Cleveland, OH, USA
| | | | - Fabio Cominelli
- Digestive Health Research Institute, Case Western Reserve University, Cleveland, OH, USA; University Hospitals Case Medical Center, Cleveland, OH, USA
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Rahman K, Sasaki M, Nusrat A, Klapproth JMA. Crohn's disease-associated Escherichia coli survive in macrophages by suppressing NFκB signaling. Inflamm Bowel Dis 2014; 20:1419-25. [PMID: 24918323 PMCID: PMC4104147 DOI: 10.1097/mib.0000000000000096] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Epidemiological and genetic studies suggest a role for enteric flora in the pathogenesis of Crohn's disease (CD). Crohn's disease-associated Escherichia coli (CDEC) is characterized by their ability to invade epithelial cells and survive and induce high concentration of TNF-α from infected macrophages. However, the molecular mechanisms of CDEC survival in infected macrophages are not completely understood. METHODS Intracellular survival of CDEC strain LF82 isolated from inflamed ileum tissue, 13I isolated from inflamed colonic tissue, and control E. coli strains were tested in the murine macrophage cell line, J774A.1 by Gentamicin protection assay. Modulation of intracellular cell signaling pathways by the E. coli strains were assessed by western blot analysis and confocal microscopy. RESULTS 13I demonstrated increased survival in macrophages with 2.6-fold higher intracellular bacteria compared with LF82, yet both strains induced comparable levels of TNF-α. LF82 and 13I differentially modulated key mitogen-activated protein kinase pathways during the acute phase of infection; LF82 activated all 3 mitogen-activated protein kinase pathways, whereas 13I activated ERK1/2 pathway but not p38 and JNK pathways. Both 13I and LF82 suppressed nuclear translocation of NFκB compared with noninvasive E. coli strains during the acute phase of infection. However, unlike noninvasive E. coli strains, 13I and LF82 infection resulted in chronic activation of NFκB during the later phase of infection. CONCLUSIONS Our results showed that CDEC survive in macrophages by initially suppressing NFκB activation. However, persistence of bacterial within macrophages induces chronic activation of NFκB, which correlates with increased TNF-α secretion from infected macrophages.
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Affiliation(s)
- Khalidur Rahman
- Division of Digestive Diseases; Emory University, Atlanta, GA
- Atlanta VA Medical Center, Decatur, GA
| | - Maiko Sasaki
- Division of Digestive Diseases; Emory University, Atlanta, GA
- Atlanta VA Medical Center, Decatur, GA
| | - Asma Nusrat
- Epithelial Pathobiology and Mucosal Inflammation Research Unit, Department of Pathology and Laboratory Medicine; Emory University, Atlanta, GA
| | - Jan-Michael A. Klapproth
- Division of Digestive Diseases; Emory University, Atlanta, GA
- Atlanta VA Medical Center, Decatur, GA
- Contact (corresponding author): Division of Digestive Diseases, Suite 201, 615 Michael Street, Atlanta, GA 30322, U.S.A, Tel: (404) 727-5638, Fax: (404) 727-5767,
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Abstract
The epithelium of the gastrointestinal tract is one of the most versatile tissues in the organism, responsible for providing a tight barrier between dietary and bacterial antigens and the mucosal and systemic immune system while maintaining efficient digestive and absorptive processes to ensure adequate nutrient and energy supply. Inflammatory bowel diseases (Crohn's disease and ulcerative colitis) are associated with a breakdown of both functions, which in some cases are clearly interrelated. In this updated literature review, we focus on the effects of intestinal inflammation and the associated immune mediators on selected aspects of the transepithelial transport of macronutrients and micronutrients. The mechanisms responsible for nutritional deficiencies are not always clear and could be related to decreased intake, malabsorption, and excess losses. We summarize the known causes of nutrient deficiencies and the mechanism of inflammatory bowel disease-associated diarrhea. We also overview the consequences of impaired epithelial transport, which infrequently transcend its primary purpose to affect the gut microbial ecology and epithelial integrity. Although some of those regulatory mechanisms are relatively well established, more work needs to be done to determine how inflammatory cytokines can alter the transport process of nutrients across the gastrointestinal and renal epithelia.
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Pastorelli L, De Salvo C, Mercado JR, Vecchi M, Pizarro TT. Central role of the gut epithelial barrier in the pathogenesis of chronic intestinal inflammation: lessons learned from animal models and human genetics. Front Immunol 2013; 4:280. [PMID: 24062746 PMCID: PMC3775315 DOI: 10.3389/fimmu.2013.00280] [Citation(s) in RCA: 312] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 08/29/2013] [Indexed: 12/12/2022] Open
Abstract
The gut mucosa is constantly challenged by a bombardment of foreign antigens and environmental microorganisms. As such, the precise regulation of the intestinal barrier allows the maintenance of mucosal immune homeostasis and prevents the onset of uncontrolled inflammation. In support of this concept, emerging evidence points to defects in components of the epithelial barrier as etiologic factors in the pathogenesis of inflammatory bowel diseases (IBDs). In fact, the integrity of the intestinal barrier relies on different elements, including robust innate immune responses, epithelial paracellular permeability, epithelial cell integrity, as well as the production of mucus. The purpose of this review is to systematically evaluate how alterations in the aforementioned epithelial components can lead to the disruption of intestinal immune homeostasis, and subsequent inflammation. In this regard, the wealth of data from mouse models of intestinal inflammation and human genetics are pivotal in understanding pathogenic pathways, for example, that are initiated from the specific loss of function of a single protein leading to the onset of intestinal disease. On the other hand, several recently proposed therapeutic approaches to treat human IBD are targeted at enhancing different elements of gut barrier function, further supporting a primary role of the epithelium in the pathogenesis of chronic intestinal inflammation and emphasizing the importance of maintaining a healthy and effective intestinal barrier.
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Affiliation(s)
- Luca Pastorelli
- Department of Pathology, Case Western Reserve University School of Medicine , Cleveland, OH , USA ; Department of Biomedical Sciences for Health, University of Milan , Milan , Italy ; Gastroenterology and Digestive Endoscopy Unit, IRCCS Policlinico San Donato , San Donato Milanese , Italy
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Abstract
Recent translational studies have provided new insights into the pathogenesis of pediatric-onset inflammatory bowel disease. Registry studies have identified distinct clinical phenotypes with increasing age of onset; this has led to a revision of the clinical phenotyping system, now termed the Paris classification system. It is recognized that there are infantile (age, <1 years), very early onset (VEO) (age, 1-10 years), and early onset (age, 10-17 years) forms of disease. Rare genetic mutations affecting antimicrobial and anti-inflammatory pathways have been discovered in infantile and VEO forms, although genetic pathways identified in early onset disease have been similar to adult-onset inflammatory bowel disease. An increasing incidence in the infantile and VEO forms has suggested an important environmental influence. This is likely ultimately expressed through alterations in the enteric flora (dysbiosis) and dysregulated immune responses to the flora, which are recognized as a critical trigger for mucosal inflammation. These data should ultimately guide new pathogenic models of disease, which will inform both therapy in individual patients and disease prevention in their at-risk family members.
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Denson LA. How does knowledge from translational research impact our clinical care of pediatric inflammatory bowel disease patients? Curr Gastroenterol Rep 2012; 14:275-81. [PMID: 22422506 DOI: 10.1007/s11894-012-0258-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Recent translational studies have provided new insights into pathogenesis, disease behavior, and treatment responses in pediatric Inflammatory Bowel Disease (IBD). Registry studies have identified distinct clinical phenotypes with increasing age of onset; this has led to a revision of the clinical phenotyping system, now termed the Paris classification system. It is recognized that there are infantile (age <2 years), very early onset (VEO, age 2-10), and early onset (EO, age 10-17) forms of disease. Rare genetic mutations affecting anti-microbial and anti-inflammatory pathways have been discovered in infantile and VEO forms, while genetic pathways identified in EO disease have been similar to adult-onset IBD. Genetic and serologic patterns measured soon after diagnosis have been shown to be associated with more aggressive stricturing behavior; these patterns may now be used clinically to help predict disease course. More recently, clinical and genetic models have been developed that, if validated, could be used to predict treatment responses.
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Affiliation(s)
- Lee A Denson
- Pediatric Gastroenterology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA.
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The colitis-associated transcriptional profile of commensal Bacteroides thetaiotaomicron enhances adaptive immune responses to a bacterial antigen. PLoS One 2012; 7:e42645. [PMID: 22880065 PMCID: PMC3411805 DOI: 10.1371/journal.pone.0042645] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Accepted: 07/11/2012] [Indexed: 01/01/2023] Open
Abstract
Background Inflammatory bowel diseases (IBD) may be caused in part by aberrant immune responses to commensal intestinal microbes including the well-characterized anaerobic gut commensal Bacteroides thetaiotaomicron (B. theta). Healthy, germ-free HLA-B27 transgenic (Tg) rats develop chronic colitis when colonized with complex gut commensal bacteria whereas non-transgenic (nTg) rats remain disease-free. However, the role of B. theta in causing disease in Tg rats is unknown nor is much known about how gut microbes respond to host inflammation. Methods Tg and nTg rats were monoassociated with a human isolate of B. theta. Colonic inflammation was assessed by histologic scoring and tissue pro-inflammatory cytokine measurement. Whole genome transcriptional profiling of B. theta recovered from ceca was performed using custom GeneChips and data analyzed using dChip, Significance Analysis of Microarrays, and Gene Set Enrichment Analysis (GSEA) software. Western Blots were used to determine adaptive immune responses to a differentially expressed B. theta gene. Results B. theta monoassociated Tg rats, but not nTg or germ-free controls, developed chronic colitis. Transcriptional profiles of cecal B. theta were significantly different in Tg vs. nTg rats. GSEA revealed that genes in KEGG canonical pathways involved in bacterial growth and metabolism were downregulated in B. theta from Tg rats with colitis though luminal bacterial concentrations were unaffected. Bacterial genes in the Gene Ontology molecular function “receptor activity”, most of which encode nutrient binding proteins, were significantly upregulated in B. theta from Tg rats and include a SusC homolog that induces adaptive immune responses in Tg rats. Conclusions B. theta induces colitis in HLA-B27 Tg rats, which is associated with regulation of bacterial genes in metabolic and nutrient binding pathways that may affect host immune responses. These studies of the host-microbial dialogue may lead to the identification of novel microbial targets for IBD therapies.
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Edwards LA, O'Neill C, Furman MA, Hicks S, Torrente F, Pérez-Machado M, Wellington EM, Phillips AD, Murch SH. Enterotoxin-producing staphylococci cause intestinal inflammation by a combination of direct epithelial cytopathy and superantigen-mediated T-cell activation. Inflamm Bowel Dis 2012; 18:624-40. [PMID: 21887731 DOI: 10.1002/ibd.21852] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Accepted: 07/13/2011] [Indexed: 12/31/2022]
Abstract
BACKGROUND Enterotoxin-producing Staphylococcus aureus may cause severe inflammatory intestinal disease, particularly in infants or immunodeficient or elderly patients. They are also recognized to be associated with sudden infant death syndrome. Little is known, however, about mucosal responses to staphylococci. METHODS The mucosal lesion in three infants with staphylococcal enterocolitis was assessed by immunohistochemistry and electron microscopy. The organisms underwent extensive molecular analysis. Their toxins were assessed for capacity to induce T-cell activation and host mucosal responses examined by in vitro organ culture. Epithelial responses were studied by coculture with HEp-2 and Caco-2 cells. RESULTS Intestinal biopsies from the patients showed marked epithelial damage with mucosal inflammation. The three staphylococci, representing two distinct clones, were methicillin-sensitive, producing SEG/I enterotoxins and Rho-inactivating EDIN toxins. Their enterotoxins potently activated T cells, but only whole organisms could induce in vitro enteropathy, characterized by remarkable epithelial desquamation uninhibited by tacrolimus. EDIN-producing staphylococci, but not their supernatants, induced striking cytopathy in HEp-2 epithelial cells but not in Caco-2 cells. Although HEp-2 and Caco-2 cells produced similar IL-8, CCL20, and cathelicidin LL37 responses upon bacterial exposure, only Caco-2 cells expressed mRNA for the β-defensins HBD2 and HBD3, while HEp-2 cells were unable to do so. CONCLUSIONS Staphylococci induce enterocolitis by a combination of direct enterocyte cytopathy mediated by EDIN toxins, disrupting the epithelial barrier, and enterotoxin superantigen-induced mucosal T-cell activation. Gut epithelial production of β-defensins may contribute to host defense against invasive staphylococcal disease.
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Affiliation(s)
- Lindsey A Edwards
- Centre for Paediatric Gastroenterology Royal Free and University College Medical School, London, UK
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Edwards LA, Bajaj-Elliott M, Klein NJ, Murch SH, Phillips AD. Bacterial-epithelial contact is a key determinant of host innate immune responses to enteropathogenic and enteroaggregative Escherichia coli. PLoS One 2011; 6:e27030. [PMID: 22046438 PMCID: PMC3203933 DOI: 10.1371/journal.pone.0027030] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Accepted: 10/09/2011] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Enteropathogenic (EPEC) and Enteroaggregative (EAEC) E. coli have similar, but distinct clinical symptoms and modes of pathogenesis. Nevertheless when they infect the gastrointestinal tract, it is thought that their flagellin causes IL-8 release leading to neutrophil recruitment and gastroenteritis. However, this may not be the whole story as the effect of bacterial adherence to IEC innate response(s) remains unclear. Therefore, we have characterized which bacterial motifs contribute to the innate epithelial response to EPEC and EAEC, using a range of EPEC and EAEC isogenic mutant strains. METHODOLOGY Caco-2 and HEp-2 cell lines were exposed to prototypical EPEC strain E2348/69 or EAEC strain O42, in addition to a range of isogenic mutant strains. E69 [LPS, non-motile, non-adherent, type three secretion system (TTSS) negative, signalling negative] or O42 [non-motile, non-adherent]. IL-8 and CCL20 protein secretion was measured. Bacterial surface structures were assessed by negative staining Transmission Electron Microscopy. The Fluorescent-actin staining test was carried out to determine bacterial adherence. RESULTS Previous studies have reported a balance between the host pro-inflammatory response and microbial suppression of this response. In our system an overall balance towards the host pro-inflammatory response is seen with the E69 WT and to a greater extent O42 WT, which is in fit with clinical symptoms. On removal of the external EPEC structures flagella, LPS, BFP, EspA and EspC; and EAEC flagella and AAF, the host inflammatory response is reduced. However, removal of E69 lymphostatin increases the host inflammatory response suggesting involvement in the bacterial mediated anti-inflammatory response. CONCLUSION Epithelial responses were due to combinations of bacterial agonists, with host-bacterial contact a key determinant of these innate responses. Host epithelial recognition was offset by the microbe's ability to down-regulate the inflammatory response. Understanding the complexity of this host-microbial balance will contribute to improved vaccine design for infectious gastroenteritis.
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Affiliation(s)
- Lindsey A Edwards
- Centre for Paediatric Gastroenterology, Royal Free Hospital, London, United Kingdom.
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