Interspecies commensal interactions have nonlinear impacts on host immunity

Cell Host & Microbe - Tập 30 - Trang 988-1002.e6 - 2022
Tyler A. Rice1, Agata A. Bielecka1, Mytien T. Nguyen1, Connor E. Rosen1, Deguang Song1, Nicole D. Sonnert1, Yi Yang1, Yiyun Cao1, Varnica Khetrapal1, Jason R. Catanzaro2, Anjelica L. Martin1, Saleh A. Rashed1, Shana R. Leopold1, Liming Hao3, Xuezhu Yu4, David van Dijk4, Aaron M. Ring1, Richard A. Flavell1, Marcel R. de Zoete5, Noah W. Palm1
1Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
2Section of Pulmonology, Allergy, Immunology, and Sleep Medicine, Department of Pediatrics, Yale University School of Medicine, New Haven, CT 06520, USA
3Department of Pathology, Yale University School of Medicine, New Haven, CT 06520 USA
4Department of Computer Science, Yale University, New Haven, CT 06520, USA
5Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands

Tài liệu tham khảo

Ansaldo, 2019, Akkermansia muciniphila induces intestinal adaptive immune responses during homeostasis, Science, 364, 1179, 10.1126/science.aaw7479 Arnds, 2010, Development of a 16S rRNA-targeted probe set for Verrucomicrobia and its application for fluorescence in situ hybridization in a humic lake, Syst. Appl. Microbiol., 33, 139, 10.1016/j.syapm.2009.12.005 Atarashi, 2017, Ectopic colonization of oral bacteria in the intestine drives TH1 cell induction and inflammation, Science, 358, 359, 10.1126/science.aan4526 Atarashi, 2015, Th17 cell induction by adhesion of microbes to intestinal epithelial cells, Cell, 163, 367, 10.1016/j.cell.2015.08.058 Bajer, 2017, Distinct gut microbiota profiles in patients with primary sclerosing cholangitis and ulcerative colitis, World J. Gastroenterol., 23, 4548, 10.3748/wjg.v23.i25.4548 Becken, 2021, Genotypic and phenotypic diversity among human isolates of Akkermansia muciniphila, mBio, 12, 10.1128/mBio.00478-21 Belkaid, 2017, Homeostatic immunity and the microbiota, Immunity, 46, 562, 10.1016/j.immuni.2017.04.008 Brown, 2015, Diet and specific microbial exposure trigger features of environmental enteropathy in a novel murine model, Nat. Commun., 6, 7806, 10.1038/ncomms8806 Buffie, 2015, Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile, Nature, 517, 205, 10.1038/nature13828 Burkhardt, 2021, Quantifying the effect of experimental perturbations at single-cell resolution, Nat. Biotechnol., 39, 619, 10.1038/s41587-020-00803-5 Butler, 2018, Integrating single-cell transcriptomic data across different conditions, technologies, and species, Nat. Biotechnol., 36, 411, 10.1038/nbt.4096 Canny, 2006, Interactions of intestinal epithelial cells with bacteria and immune cells: methods to characterize microflora and functional consequences, Methods Mol. Biol., 341, 17 Caporaso, 2010, QIIME allows analysis of high-throughput community sequencing data, Nat. Methods, 7, 335, 10.1038/nmeth.f.303 Castro-Dopico, 2019, Anti-commensal IgG drives intestinal inflammation and type 17 immunity in ulcerative colitis, Immunity, 50, 1099, 10.1016/j.immuni.2019.02.006 Chai, 2017, Helicobacter species are potent drivers of colonic T cell responses in homeostasis and inflammation, Sci. Immunol., 2, eaal5068, 10.1126/sciimmunol.aal5068 Derrien, 2004, Akkermansia muciniphila gen. nov., sp. nov., a human intestinal mucin-degrading bacterium, Int. J. Syst. Evol. Microbiol., 54, 1469, 10.1099/ijs.0.02873-0 Donaldson, 2018, Gut microbiota utilize immunoglobulin A for mucosal colonization, Science, 360, 795, 10.1126/science.aaq0926 Everard, 2013, Cross-talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity, Proc. Natl. Acad. Sci. USA, 110, 9066, 10.1073/pnas.1219451110 Externest, 2000, Correlations between antibody immune responses at different mucosal effector sites are controlled by antigen type and dosage, Infect. Immun., 68, 3830, 10.1128/IAI.68.7.3830-3839.2000 Goodman, 2011, Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice, Proc. Natl. Acad. Sci. USA, 108, 6252, 10.1073/pnas.1102938108 Gould, 2018, Microbiome interactions shape host fitness, Proc. Natl. Acad. Sci. USA, 115, E11951, 10.1073/pnas.1809349115 Greetham, 2004, Allobaculum stercoricanis gen. nov., sp. nov., isolated from canine feces, Anaerobe, 10, 301, 10.1016/j.anaerobe.2004.06.004 Ha, 2020, Translocation of viable gut microbiota to mesenteric adipose drives formation of creeping fat in humans, Cell, 183, 666, 10.1016/j.cell.2020.09.009 Ji, 2020, Macroecological dynamics of gut microbiota, Nat. Microbiol., 5, 768, 10.1038/s41564-020-0685-1 Johansson, 2008, The inner of the two Muc2 mucin-dependent mucus layers in colon is devoid of bacteria, Proc. Natl. Acad. Sci. USA, 105, 15064, 10.1073/pnas.0803124105 Kamphuis, 2017, Mucus organisation is shaped by colonic content; a new view, Sci. Rep., 7, 8527, 10.1038/s41598-017-08938-3 Kau, 2015, Functional characterization of IgA-targeted bacterial taxa from undernourished Malawian children that produce diet-dependent enteropathy, Sci. Transl. Med., 7, 276ra24, 10.1126/scitranslmed.aaa4877 Kawamoto, 2014, Foxp3+ T cells regulate immunoglobulin A selection and facilitate diversification of bacterial species responsible for immune homeostasis, Immunity, 41, 152, 10.1016/j.immuni.2014.05.016 Kiner, 2021, Gut CD4(+) T cell phenotypes are a continuum molded by microbes, not by TH archetypes, Nat. Immunol., 22, 216, 10.1038/s41590-020-00836-7 Kolmogorov, 2019, Assembly of long, error-prone reads using repeat graphs, Nat. Biotechnol., 37, 540, 10.1038/s41587-019-0072-8 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 Kubinak, 2015, MyD88 signaling in T cells directs IgA-mediated control of the microbiota to promote health, Cell Host Microbe, 17, 153, 10.1016/j.chom.2014.12.009 Lee, 2020, Serum amyloid A proteins induce pathogenic Th17 cells and promote inflammatory disease, Cell, 180, 79, 10.1016/j.cell.2019.11.026 Lengfelder, 2019, Complex bacterial consortia reprogram the colitogenic activity of Enterococcus faecalis in a gnotobiotic mouse model of chronic, immune-mediated colitis, Front. Immunol., 10, 1420, 10.3389/fimmu.2019.01420 Letunic, 2021, Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation, Nucleic Acids Res, 49, W293, 10.1093/nar/gkab301 Liu, 2021, Akkermansia muciniphila exerts strain-specific effects on DSS-induced ulcerative colitis in mice, Front. Cell. Infect. Microbiol., 11, 698914, 10.3389/fcimb.2021.698914 Lozupone, 2012, Diversity, stability and resilience of the human gut microbiota, Nature, 489, 220, 10.1038/nature11550 McDonald, 2018, American gut: an open platform for citizen science microbiome research, mSystems, 3, 10.1128/mSystems.00031-18 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 Mi, 2019, PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools, Nucleic Acids Res., 47, D419, 10.1093/nar/gky1038 Miyauchi, 2020, Gut microorganisms act together to exacerbate inflammation in spinal cords, Nature, 585, 102, 10.1038/s41586-020-2634-9 Moor, 2016, Analysis of bacterial-surface-specific antibodies in body fluids using bacterial flow cytometry, Nat. Protoc., 11, 1531, 10.1038/nprot.2016.091 Palm, 2014, Immunoglobulin A coating identifies colitogenic bacteria in inflammatory bowel disease, Cell, 158, 1000, 10.1016/j.cell.2014.08.006 Parikh, 2019, Colonic epithelial cell diversity in health and inflammatory bowel disease, Nature, 567, 49, 10.1038/s41586-019-0992-y Peterson, 2007, IgA response to symbiotic bacteria as a mediator of gut homeostasis, Cell Host Microbe, 2, 328, 10.1016/j.chom.2007.09.013 Plichta, 2016, Transcriptional interactions suggest niche segregation among microorganisms in the human gut, Nat. Microbiol., 1, 16152, 10.1038/nmicrobiol.2016.152 Plovier, 2017, A purified membrane protein from Akkermansia muciniphila or the pasteurized bacterium improves metabolism in obese and diabetic mice, Nat. Med., 23, 107, 10.1038/nm.4236 Png, 2010, Mucolytic bacteria with increased prevalence in IBD mucosa augment in vitro utilization of mucin by other bacteria, Am. J. Gastroenterol., 105, 2420, 10.1038/ajg.2010.281 Routy, 2018, Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors, Science, 359, 91, 10.1126/science.aan3706 Schirmer, 2018, Compositional and temporal changes in the gut microbiome of pediatric ulcerative colitis patients are linked to disease course, Cell Host Microbe, 24, 600, 10.1016/j.chom.2018.09.009 van Muijlwijk, 2021, Identification of Allobaculum mucolyticum as a novel human intestinal mucin degrader, Gut Microbes, 13, 1966278, 10.1080/19490976.2021.1966278 Viladomiu, 2017, IgA-coated E. coli enriched in Crohn’s disease spondyloarthritis promote TH17-dependent inflammation, Sci. Transl. Med., 9, 10.1126/scitranslmed.aaf9655 Wick, 2017, Unicycler: resolving bacterial genome assemblies from short and long sequencing reads, PLOS Comput. Biol., 13, e1005595, 10.1371/journal.pcbi.1005595 Wilmore, 2018, Commensal microbes induce serum IgA responses that protect against polymicrobial sepsis, Cell Host Microbe, 23, 302, 10.1016/j.chom.2018.01.005 Xu, 2018, c-MAF-dependent regulatory T cells mediate immunological tolerance to a gut pathobiont, Nature, 554, 373, 10.1038/nature25500 Zegarra-Ruiz, 2019, A diet-sensitive commensal Lactobacillus strain Mediates TLR7-dependent systemic autoimmunity, Cell Host Microbe, 25, 113, 10.1016/j.chom.2018.11.009 Zeng, 2016, Gut microbiota-induced immunoglobulin G controls systemic infection by symbiotic bacteria and pathogens, Immunity, 44, 647, 10.1016/j.immuni.2016.02.006 Zhang, 2020, Alterations of Akkermansia muciniphila in the inflammatory bowel disease patients with washed microbiota transplantation, Appl. Microbiol. Biotechnol., 104, 10203, 10.1007/s00253-020-10948-7