Helicobacter pylori infection is associated with an altered gastric microbiota in children

Mucosal Immunology - Tập 10 - Trang 1169-1177 - 2017
K.M. Brawner1, R. Kumar2, C.A. Serrano3, T. Ptacek4, E. Lefkowitz2,4, C.D. Morrow5, D. Zhi6, KR Kyanam-Kabir-Baig1, L.E. Smythies1, P.R. Harris3, P.D. Smith1,4,7
1Department of Medicine (Gastroenterology), University of Alabama at Birmingham, Birmingham, Alabama, USA
2Center for Clinical and Translational Science (Biomedical Informatics), University of Alabama at Birmingham, Birmingham, Alabama, USA
3Department of Pediatric Gastroenterology and Nutrition, Pontificia Universidad Católica de Chile, Santiago, Chile
4Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
5Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
6Department of Biostatistics, University of Alabama at Birmingham, Birmingham, Alabama, USA
7VA Medical Center Research Service, Birmingham, Alabama, USA

Tài liệu tham khảo

Clemente, 2012, The impact of the gut microbiota on human health: an integrative view, Cell, 148, 1258, 10.1016/j.cell.2012.01.035 Cho, 2012, Antibiotics in early life alter the murine colonic microbiome and adiposity, Nature, 488, 621, 10.1038/nature11400 Brown, 2011, Gut microbiome metagenomics analysis suggests a functional model for the development of autoimmunity for type 1 diabetes, PLoS One, 6, e25792, 10.1371/journal.pone.0025792 Cox, 2014, Altering the intestinal microbiota during a critical developmental window has lasting metabolic consequences, Cell, 158, 705, 10.1016/j.cell.2014.05.052 de Goffau, 2013, Fecal microbiota composition differs between children with beta-cell autoimmunity and those without, Diabetes, 62, 1238, 10.2337/db12-0526 Wang, 2015, Non-lethal inhibition of gut microbial trimethylamine production for the treatment of atherosclerosis, Cell, 163, 1585, 10.1016/j.cell.2015.11.055 Gevers, 2014, The treatment-naive microbiome in new-onset Crohn's disease, Cell Host Microbe, 15, 382, 10.1016/j.chom.2014.02.005 Kostic, 2015, The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes, Cell Host Microbe, 17, 260, 10.1016/j.chom.2015.01.001 Garrett, 2010, Homeostasis and inflammation in the intestine, Cell, 140, 859, 10.1016/j.cell.2010.01.023 Smith, 2013, The microbial metabolites, short-chain fatty acids, regulate colonic Treg cell homeostasis, Science, 341, 569, 10.1126/science.1241165 Furusawa, 2013, Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells, Nature, 504, 446, 10.1038/nature12721 Arpaia, 2013, Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation, Nature, 504, 451, 10.1038/nature12726 Mazmanian, 2005, An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system, Cell, 122, 107, 10.1016/j.cell.2005.05.007 Shen, 2012, Outer membrane vesicles of a human commensal mediate immune regulation and disease protection, Cell Host Microbe, 12, 509, 10.1016/j.chom.2012.08.004 Chu, 2016, Gene-microbiota interactions contribute to the pathogenesis of inflammatory bowel disease, Science, 352, 1116, 10.1126/science.aad9948 Donaldson, 2015, Gut biogeopgraphy of the bacterial microbiota, Nat. Rev. Microbiol., 14, 20, 10.1038/nrmicro3552 Salama, 2013, Life in the human stomach: persistence strategies of the bacterial pathogen Helicobacter pylori, Nat. Rev. Microbiol., 11, 385, 10.1038/nrmicro3016 Harris, 2013, Helicobacter pylori-associated hypochlorhydria in children, and development of iron deficiency, J. Clin. Pathol., 66, 343, 10.1136/jclinpath-2012-201243 Harris, 2008, Helicobacter pylori gastritis in children is associated with a regulatory T-cell response, Gastroenterology, 134, 491, 10.1053/j.gastro.2007.11.006 Serrano, 2013, Downregulated Th17 responses are associated with reduced gastritis in Helicobacter pylori-infected children, Mucosal Immunol., 6, 950, 10.1038/mi.2012.133 Brawner, 2014, Gastric microbiome and gastric cancer, Cancer J., 20, 211, 10.1097/PPO.0000000000000043 Bik, 2006, Molecular analysis of the bacterial microbiota in the human stomach, Proc. Natl. Acad. Sci. USA, 103, 732, 10.1073/pnas.0506655103 Maldonado-Contreras, 2011, Structure of the human gastric bacterial community in relation to Helicobacter pylori status, ISME J., 5, 574, 10.1038/ismej.2010.149 Olszak, 2012, Microbial exposure during early life has persistent effects on natural killer T cell function, Science, 336, 489, 10.1126/science.1219328 Lofgren, 2011, Lack of commensal flora in Helicobacter pylori-infected INS-GAS mice reduces gastritis and delays intraepithelial neoplasia, Gastroenterology, 140, 210, 10.1053/j.gastro.2010.09.048 Maynard, 2012, Reciprocal interactions of the intestinal microbiota and immune system, Nature, 489, 231, 10.1038/nature11551 Yatsunenko, 2012, Human gut microbiome viewed across age and geography, Nature, 486, 222, 10.1038/nature11053 Round, 2010, Inducible Foxp3+ regulatory T-cell development by a commensal bacterium of the intestinal microbiota, Proc. Natl. Acad. Sci. USA, 107, 12204, 10.1073/pnas.0909122107 Atarashi, 2011, Induction of colonic regulatory T cells by indigenous Clostridium species, Science, 331, 337, 10.1126/science.1198469 Geuking, 2011, Intestinal bacterial colonization induces mutualistic regulatory T cell responses, Immunity, 34, 794, 10.1016/j.immuni.2011.03.021 Atarashi, 2013, Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota, Nature, 500, 232, 10.1038/nature12331 Harakal, 2016, Regulatory T Cells Control Th2-Dominant Murine Autoimmune Gastritis, J. Immunol., 197, 27, 10.4049/jimmunol.1502344 Rubtsov, 2008, Regulatory T cell-derived interleukin-10 limits inflammation at environmental interfaces, Immunity, 28, 546, 10.1016/j.immuni.2008.02.017 Chaudhry, 2011, Interleukin-10 signaling in regulatory T cells is required for suppression of Th17 cell-mediated inflammation, Immunity, 34, 566, 10.1016/j.immuni.2011.03.018 Huber, 2011, Th17 cells express interleukin-10 receptor and are controlled by Foxp3(-) and Foxp3+ regulatory CD4+ T cells in an interleukin-10-dependent manner, Immunity, 34, 554, 10.1016/j.immuni.2011.01.020 Chen, 2003, Conversion of peripheral CD4+CD25- naive T cells to CD4+CD25+ regulatory T cells by TGF-beta induction of transcription factor Foxp3, J. Exp. Med., 198, 1875, 10.1084/jem.20030152 Fantini, 2006, Transforming growth factor beta induced FoxP3+ regulatory T cells suppress Th1 mediated experimental colitis, Gut, 55, 671, 10.1136/gut.2005.072801 Maynard, 2007, Regulatory T cells expressing interleukin 10 develop from Foxp3+ and Foxp3- precursor cells in the absence of interleukin 10, Nat. Immunol., 8, 931, 10.1038/ni1504 Eckburg, 2005, Diversity of the human intestinal microbial flora, Science, 308, 1635, 10.1126/science.1110591 The Human Microbiome Project Consortium, 2012, Structure, function and diversity of the healthy human microbiome, Nature, 486, 207, 10.1038/nature11234 Lim, 2015, Early life dynamics of the human gut virome and bacterial microbiome in infants, Nat. Med, 21, 1228, 10.1038/nm.3950 Bimczok, 2011, Stromal regulation of human gastric dendritic cells restricts the Th1 response to Helicobacter pylori, Gastroenterology, 141, 929, 10.1053/j.gastro.2011.06.006 Bimczok, 2015, Human gastric epithelial ceels contribute to gastric immune regulation by providing retinoic acid to dendritic cells, Mucosal Immunol., 8, 533, 10.1038/mi.2014.86 Donia, 2015, Human Microbiota. Small molecules from the human microbiota, Science, 349, 1254766, 10.1126/science.1254766 Jaime, 2013, Frequency of Helicobacter pylori infection in 144 school age Chilean children, Rev. Med. Chil., 141, 1249, 10.4067/S0034-98872013001000003 Thome, 2016, Early-life compartmentalization of human T cell differentiation and regulatory function in mucosal and lymphoid tissues, Nat. Med, 22, 72, 10.1038/nm.4008 Arnold, 2011, Helicobacter pylori infection prevents allergic asthma in mouse models through the induction of regulatory T cells, J. Clin. Invest., 121, 3088, 10.1172/JCI45041 Oertli, 2012, DC-derived IL-18 drives Treg differentiation, murine Helicobacter pylori-specific immune tolerance, and asthma protection, J. Clin. Invest., 122, 1082, 10.1172/JCI61029 Yang, 2016, Different gastric microbiota compositions in two human populations with high and low gastric cancer risk in Colombia, Sci. Rep, 6, 18594, 10.1038/srep18594 Fuentes, 2014, Gene geography of Chile: regional distribution of American, European and African genetic contributions, Rev. Med. Chil., 142, 281, 10.4067/S0034-98872014000300001 Adimark. El Nivel Socioeconómico Esomar. Manual de Aplicación. Department of Economy (2006). Malfertheiner, 2007, Current concepts in the management of Helicobacter pylori infection: the Maastricht III Consensus Report, Gut, 56, 772, 10.1136/gut.2006.101634 Caporaso, 2011, Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample, Proc. Natl. Acad. Sci. USA, 108, 4516, 10.1073/pnas.1000080107 Kozich, 2013, Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform, Appl. Environ. Microbiol., 79, 5112, 10.1128/AEM.01043-13 Kumar, 2014, Getting started with microbiome analysis: sample acquisition to bioinformatics, Curr. Protoc. Hum. Genet., 82, 18.11 Edgar, 2010, Search and clustering orders of magnitude faster than BLAST, Bioinformatics, 26, 2460, 10.1093/bioinformatics/btq461 McDonald, 2012, An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea, ISME J., 6, 610, 10.1038/ismej.2011.139 Wang, 2007, Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy, Appl. Environ. Microbiol., 73, 5261, 10.1128/AEM.00062-07 Caporaso, 2010, PyNAST: a flexible tool for aligning sequences to a template alignment, Bioinformatics, 26, 266, 10.1093/bioinformatics/btp636