Sender R, Fuchs S, Milo R. Revised estimates for the number of human and Bacteria cells in the body. PLoS Biol. 2016;14(8):e1002533.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lepage P, Leclerc MC, Joossens M, Mondot S, Blottière HM, Raes J, et al. A metagenomic insight into our gut’s microbiome. Gut. 2013;62(1):146–58.
Article
PubMed
Google Scholar
Vernocchi P, Del Chierico F, Putignani L. Gut microbiota profiling: metabolomics based approach to unravel compounds affecting human health. Front Microbiol. 2016;7:1144.
Article
PubMed
PubMed Central
Google Scholar
Tai N, Wong FS, Wen L. The role of gut microbiota in the development of type 1, obesity and type 2 diabetes mellitus. Rev Endocr Metab Disord. 2015;16(1):55–65.
Article
CAS
PubMed
PubMed Central
Google Scholar
Geuking MB, Köller Y, Rupp S, McCoy KD. The interplay between the gut microbiota and the immune system. Gut Microbes. 2014;5(3):411–8.
Article
PubMed
PubMed Central
Google Scholar
Matsuoka K, Kanai T. The gut microbiota and inflammatory bowel disease. Semin Immunopathol. 2015;37:47–55.
Article
CAS
PubMed
Google Scholar
Fujimura KE, Lynch SV. Microbiota in allergy and asthma and the emerging relationship with the gut microbiome. Cell Host Microbe. 2015 May 13;17(5):592–602.
Article
CAS
PubMed
PubMed Central
Google Scholar
Collins SM. A role for the gut microbiota in IBS. Nat Rev Gastroenterol Hepatol. 2014 Aug;11(8):497–505.
Article
CAS
PubMed
Google Scholar
Zhang X, Zhang D, Jia H, Feng Q, Wang D, Liang D, et al. The oral and gut microbiomes are perturbed in rheumatoid arthritis and partly normalized after treatment. Nat Med. 2015 Aug;21(8):895–905.
Article
CAS
PubMed
Google Scholar
Vieira SM, Pagovich OE, Kriegel MA. Diet, microbiota and autoimmune diseases. Lupus. 2014 May;23(6):518–26.
Article
CAS
PubMed
PubMed Central
Google Scholar
Miele L, Giorgio V, Alberelli MA, De Candia E, Gasbarrini A, Grieco A. Impact of gut microbiota on obesity, diabetes, and cardiovascular disease risk. Curr Cardiol Rep. 2015;17(12):120.
Article
PubMed
Google Scholar
Torres-Fuentes C, Schellekens H, Dinan TG, Cryan JF. The microbiota–gut–brain axis in obesity. Lancet Gastroenterol Hepatol. 2017;2(10):747–56.
Article
PubMed
Google Scholar
Mulak A, Bonaz B. Brain-gut-microbiota axis in Parkinson’s disease. World J Gastroenterol. 2015 Oct 7;21(37):10609–20.
Article
CAS
PubMed
PubMed Central
Google Scholar
Blanton LV, Barratt MJ, Charbonneau MR, Ahmed T, Gordon JI. Childhood undernutrition, the gut microbiota, and microbiota-directed therapeutics. Science. 2016 Jun 24;352(6293):1533.
Article
CAS
PubMed
Google Scholar
Zhang H, Sun L. When human cells meet bacteria: precision medicine for cancers using the microbiota. Am J Cancer Res. 2018;8(7):1157–75.
Article
PubMed
PubMed Central
Google Scholar
Panebianco C, Andriulli A, Pazienza V. Pharmacomicrobiomics: exploiting the drug-microbiota interactions in anticancer therapies. Microbiome. 2018 May 22;6(1):92.
Article
PubMed
PubMed Central
Google Scholar
Sivan A, Corrales L, Hubert N, Williams JB, Aquino-Michaels K, Earley ZM, et al. Commensal Bifidobacterium promotes antitumor immunity and facilitates anti-PD-L1 efficacy. Science. 2015 Nov 27;350(6264):1084–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Vétizou M, Pitt JM, Daillère R, Lepage P, Waldschmitt N, Flament C, et al. Anticancer immunotherapy by CTLA-4 blockade relies on the gut microbiota. Science. 2015 Nov 27;350(6264):1079–84.
Article
CAS
PubMed
PubMed Central
Google Scholar
Structure, Function and Diversity of the healthy human microbiome. Nature. 2012;486(7402):207–214.
Tanaka M, Nakayama J. Development of the gut microbiota in infancy and its impact on health in later life. Allergol Int. 2017 Oct 1;66(4):515–22.
Article
CAS
PubMed
Google Scholar
Indrio F, Martini S, Francavilla R, Corvaglia L, Cristofori F, Mastrolia SA, et al. Epigenetic matters: the link between early nutrition, microbiome, and long-term health development. Front Pediatr. 2017;5:178.
Article
PubMed
PubMed Central
Google Scholar
Perez-Muñoz ME, Arrieta M-C, Ramer-Tait AE, Walter J. A critical assessment of the “sterile womb” and “in utero colonization” hypotheses: implications for research on the pioneer infant microbiome. Microbiome. 2017;5(1):48.
Article
PubMed
PubMed Central
Google Scholar
Dominguez-Bello MG, Costello EK, Contreras M, Magris M, Hidalgo G, Fierer N, et al. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc Natl Acad Sci U S A. 2010 Jun 29;107(26):11971–5.
Article
PubMed
PubMed Central
Google Scholar
The Integrative Human Microbiome Project. Dynamic analysis of microbiome-host omics profiles during periods of human health and disease. Cell Host Microbe. 2014;16(3):276–89.
Article
CAS
Google Scholar
Browne HP, Forster SC, Anonye BO, Kumar N, Neville BA, Stares MD, et al. Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation. Nature. 2016 May 4;533(7604):543–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Goodman AL, Kallstrom G, Faith JJ, Reyes A, Moore A, Dantas G, et al. Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice. PNAS. 2011 Apr 12;108(15):6252–7.
Article
PubMed
PubMed Central
Google Scholar
Lagier J-C, Hugon P, Khelaifia S, Fournier P-E, La Scola B, Raoult D. The rebirth of culture in microbiology through the example of Culturomics to study human gut microbiota. Clin Microbiol Rev. 2015 Jan;28(1):237–64.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bilen M, Dufour J-C, Lagier J-C, Cadoret F, Daoud Z, Dubourg G, et al. The contribution of culturomics to the repertoire of isolated human bacterial and archaeal species. Microbiome. 2018 May 24;6(1):94.
Article
PubMed
PubMed Central
Google Scholar
Woese CR, Fox GE. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci U S A. 1977 Nov;74(11):5088–90.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cole JR, Wang Q, Fish JA, Chai B, McGarrell DM, Sun Y, et al. Ribosomal database project: data and tools for high throughput rRNA analysis. Nucleic Acids Res. 2014;42(Database issue):D633–42.
Article
CAS
PubMed
Google Scholar
DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol. 2006;72(7):5069–72.
Article
CAS
PubMed
PubMed Central
Google Scholar
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013 Jan;41(Database issue):D590–6.
CAS
PubMed
Google Scholar
Nguyen N-P, Warnow T, Pop M. White B. A perspective on 16S rRNA operational taxonomic unit clustering using sequence similarity. NPJ Biofilms Microbiomes. 2016;2:16004.
Article
PubMed
PubMed Central
Google Scholar
Edgar RC. UNOISE2: improved error-correction for Illumina 16S and ITS amplicon sequencing. bioRxiv. 2016:081257.
Amir A, McDonald D, Navas-Molina JA, Kopylova E, Morton JT, Xu ZZ, et al. Deblur rapidly resolves single-nucleotide community sequence patterns. mSystems. 2017;2(2):e00191–16.
Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP. DADA2: high resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13(7):581–3.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ma J, Prince A, Aagaard KM. Use of whole genome shotgun metagenomics: a practical guide for the microbiome-minded physician scientist. Semin Reprod Med. 2014 Jan;32(01):005–13.
Article
CAS
Google Scholar
Kembel SW, Wu M, Eisen JA, Green JL. Incorporating 16S gene copy number information improves estimates of microbial diversity and abundance. PLoS Comput Biol. 2012 Oct 25;8(10):e1002743.
Article
CAS
PubMed
PubMed Central
Google Scholar
Prakash T, Taylor TD. Functional assignment of metagenomic data: challenges and applications. Brief Bioinform. 2012 Nov;13(6):711–27.
Article
PubMed
PubMed Central
Google Scholar
D’Argenio V. Human microbiome acquisition and Bioinformatic challenges in metagenomic studies. Int J Mol Sci. 2018;19(2).
Langille MGI, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, et al. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol. 2013 Sep;31(9):814–21.
Article
CAS
PubMed
PubMed Central
Google Scholar
Aßhauer KP, Wemheuer B, Daniel R, Meinicke P. Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data. Bioinformatics. 2015 Sep 1;31(17):2882–4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Iwai S, Weinmaier T, Schmidt BL, Albertson DG, Poloso NJ, Dabbagh K, et al. Piphillin: improved prediction of metagenomic content by direct inference from human microbiomes. PLoS One. 2016 Nov 7;11(11):e0166104.
Article
CAS
PubMed
PubMed Central
Google Scholar
Matson V, Fessler J, Bao R, Chongsuwat T, Zha Y, Alegre M-L, et al. The commensal microbiome is associated with anti–PD-1 efficacy in metastatic melanoma patients. Science. 2018 Jan 5;359(6371):104–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Al-Asmakh M, Zadjali F. Use of germ-free animal models in microbiota-related research. J Microbiol Biotechnol. 2015 Oct 28;25(10):1583–8.
Article
PubMed
Google Scholar
Luczynski P, McVey Neufeld K-A, Oriach CS, Clarke G, Dinan TG, Cryan JF. Growing up in a bubble: using germ-free animals to assess the influence of the gut microbiota on brain and behavior. Int J Neuropsychopharmacol. 2016;19(8).
Deplancke B, Gaskins HR. Microbial modulation of innate defense: goblet cells and the intestinal mucus layer. Am J Clin Nutr. 2001 Jun 1;73(6):1131S–41S.
Article
CAS
PubMed
Google Scholar
Smith K, McCoy KD, Macpherson AJ. Use of axenic animals in studying the adaptation of mammals to their commensal intestinal microbiota. Semin Immunol. 2007;19(2):59–69.
Article
CAS
PubMed
Google Scholar
Manolios N, Geczy CL, Schrieber L. High endothelial venule morphology and function are inducible in germ-free mice: a possible role for interferon-gamma. Cell Immunol. 1988 Nov;117(1):136–51.
Article
CAS
PubMed
Google Scholar
Weinstein PD, Cebra JJ. The preference for switching to IgA expression by Peyer’s patch germinal center B cells is likely due to the intrinsic influence of their microenvironment. J Immunol. 1991;147(12):4126–35.
CAS
PubMed
Google Scholar
Lécuyer E, Rakotobe S, Lengliné-Garnier H, Lebreton C, Picard M, Juste C, et al. Segmented filamentous bacterium uses secondary and tertiary lymphoid tissues to induce gut IgA and specific T helper 17 cell responses. Immunity. 2014 Apr 17;40(4):608–20.
Article
CAS
PubMed
Google Scholar
Pabst O, Herbrand H, Friedrichsen M, Velaga S, Dorsch M, Berhardt G, et al. Adaptation of solitary intestinal lymphoid tissue in response to microbiota and chemokine receptor CCR7 signaling. J Immunol. 2006 Nov 15;177(10):6824–32.
Article
CAS
PubMed
Google Scholar
Bouskra D, Brézillon C, Bérard M, Werts C, Varona R, Boneca IG, et al. Lymphoid tissue genesis induced by commensals through NOD1 regulates intestinal homeostasis. Nature. 2008 Nov;456(7221):507–10.
Article
CAS
PubMed
Google Scholar
Pabst O, Herbrand H, Worbs T, Friedrichsen M, Yan S, Hoffmann MW, et al. Cryptopatches and isolated lymphoid follicles: dynamic lymphoid tissues dispensable for the generation of intraepithelial lymphocytes. Eur J Immunol. 2005;35(1):98–107.
Article
CAS
PubMed
Google Scholar
Macpherson AJ, Martinic MM, Harris N. The functions of mucosal T cells in containing the indigenous commensal flora of the intestine. Cell Mol Life Sci. 2002 Dec;59(12):2088–96.
Article
CAS
PubMed
Google Scholar
Macpherson AJ, Hunziker L, McCoy K, Lamarre A. IgA responses in the intestinal mucosa against pathogenic and non-pathogenic microorganisms. Microbes Infect. 2001 Oct;3(12):1021–35.
Article
CAS
PubMed
Google Scholar
Ivanov II, de Llanos Frutos R, Manel N, Yoshinaga K, Rifkin DB, Sartor RB, et al. Specific microbiota direct the differentiation of Th17 cells in the mucosa of the small intestine. Cell Host Microbe. 2008;4(4):337–49.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gorjifard S, Goldszmid RS. Microbiota—myeloid cell crosstalk beyond the gut. J Leukoc Biol. 2016;100(5):865–79.
Article
CAS
PubMed
PubMed Central
Google Scholar
Trompette A, Gollwitzer ES, Yadava K, Sichelstiel AK, Sprenger N, Ngom-Bru C, et al. Gut microbiota metabolism of dietary fiber influences allergic airway disease and hematopoiesis. Nat Med. 2014 Feb;20(2):159–66.
Article
CAS
PubMed
Google Scholar
Bauer H, Horowitz RE, Levenson SM, Popper H. The response of the lymphatic tissue to the microbial flora. Studies on germfree mice. Am J Pathol. 1963;42:471–83.
CAS
PubMed
PubMed Central
Google Scholar
Benveniste J, Lespinats G, Adam C, Salomon JC. Immunoglobulins in intact, immunized, and contaminated axenic mice: study of serum IgA. J Immunol. 1971;107(6):1647–55.
CAS
PubMed
Google Scholar
Mazmanian SK, Liu CH, Tzianabos AO, Kasper DL. An immunomodulatory molecule of symbiotic Bacteria directs maturation of the host immune system. Cell. 2005 Jul 15;122(1):107–18.
Article
CAS
PubMed
Google Scholar
Ivanov II, Atarashi K, Manel N, Brodie EL, Shima T, Karaoz U, et al. Induction of intestinal Th17 cells by segmented filamentous bacteria. Cell. 2009 Oct 30;139(3):485–98.
Article
CAS
PubMed
PubMed Central
Google Scholar
Atarashi K, Tanoue T, Ando M, Kamada N, Nagano Y, Narushima S, et al. Th17 cell induction by adhesion of microbes to intestinal epithelial cells. Cell. 2015 Oct 8;163(2):367–80.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tan TG, Sefik E, Geva-Zatorsky N, Kua L, Naskar D, Teng F, et al. Identifying species of symbiont bacteria from the human gut that, alone, can induce intestinal Th17 cells in mice. Proc Natl Acad Sci U S A. 2016 Dec 13;113(50):E8141–50.
Article
CAS
PubMed
PubMed Central
Google Scholar
Geva-Zatorsky N, Sefik E, Kua L, Pasman L, Tan TG, Ortiz-Lopez A, et al. Mining the human gut microbiota for immunomodulatory organisms. Cell. 2017 Feb 23;168(5):928–943.e11.
Article
CAS
PubMed
PubMed Central
Google Scholar
Round JL, Mazmanian SK. Inducible Foxp3+ regulatory T-cell development by a commensal bacterium of the intestinal microbiota. Proc Natl Acad Sci U S A. 2010 Jul 6;107(27):12204–9.
Article
PubMed
PubMed Central
Google Scholar
Atarashi K, Tanoue T, Shima T, Imaoka A, Kuwahara T, Momose Y, et al. Induction of colonic regulatory T cells by indigenous Clostridium species. Science. 2011 Jan 21;331(6015):337–41.
Article
CAS
PubMed
Google Scholar
Atarashi K, Tanoue T, Oshima K, Suda W, Nagano Y, Nishikawa H, et al. Treg induction by a rationally selected mixture of clostridia strains from the human microbiota. Nature. 2013 Aug;500(7461):232–6.
Article
CAS
PubMed
Google Scholar
Nguyen TLA, Vieira-Silva S, Liston A, Raes J. How informative is the mouse for human gut microbiota research? Dis Model Mech. 2015 Jan;8(1):1–16.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hugenholtz F, de Vos WM. Mouse models for human intestinal microbiota research: a critical evaluation. Cell Mol Life Sci. 2018;75(1):149–60.
Article
CAS
PubMed
Google Scholar
Xiao L, Feng Q, Liang S, Sonne SB, Xia Z, Qiu X, et al. A catalog of the mouse gut metagenome. Nat Biotechnol. 2015 Oct;33(10):1103–8.
Article
CAS
PubMed
Google Scholar
Gärtner K. The forestomach of rats and mice, an effective device supporting digestive metabolism in muridae (review). J Exp Anim Sci. 2002 Jan 1;42(1):1–20.
Article
Google Scholar
Treuting PM, Arends MJ, Dintzis SM. Lower Gastrointestinal Tract. In: Comparative Anatomy and Histology [Internet]. Elsevier; 2018 [cited 2019 Jan 21]. p. 213–28. Available from: https://linkinghub.elsevier.com/retrieve/pii/B9780128029008000129
Smith HF, Parker W, Kotzé SH, Laurin M. Multiple independent appearances of the cecal appendix in mammalian evolution and an investigation of related ecological and anatomical factors. Comptes Rendus Palevol. 2013 Aug 1;12(6):339–54.
Article
Google Scholar
Wang J, Wang J, Pang X, Zhao L, Tian L, Wang X. Sex differences in colonization of gut microbiota from a man with short-term vegetarian and inulin-supplemented diet in germ-free mice. Sci Rep. 2016 Oct 31;6:36137.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lundberg R, Bahl MI, Licht TR, Toft MF, Hansen AK. Microbiota composition of simultaneously colonized mice housed under either a gnotobiotic isolator or individually ventilated cage regime. Sci Rep. 2017 Feb 7;7:42245.
Article
CAS
PubMed
PubMed Central
Google Scholar
Macpherson AJ, McCoy KD. Standardised animal models of host microbial mutualism. Mucosal Immunol. 2015;8(3):476–86.
Article
CAS
PubMed
Google Scholar
Lagkouvardos I, Pukall R, Abt B, Foesel BU, Meier-Kolthoff JP, Kumar N, et al. The mouse intestinal bacterial collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota. Nat Microbiol. 2016 Oct;1(10):16131.
Article
CAS
PubMed
Google Scholar
Desai MS, Seekatz AM, Koropatkin NM, Kamada N, Hickey CA, Wolter M, et al. A dietary Fiber-deprived gut microbiota degrades the colonic mucus barrier and enhances pathogen susceptibility. Cell. 2016 Nov 17;167(5):1339–1353.e21.
Article
CAS
PubMed
PubMed Central
Google Scholar
Staley C, Kaiser T, Beura LK, Hamilton MJ, Weingarden AR, Bobr A, et al. Stable engraftment of human microbiota into mice with a single oral gavage following antibiotic conditioning. Microbiome. 2017;5(1):87.
Article
PubMed
PubMed Central
Google Scholar
Hintze KJ, Cox JE, Rompato G, Benninghoff AD, Ward RE, Broadbent J, et al. Broad scope method for creating humanized animal models for animal health and disease research through antibiotic treatment and human fecal transfer. Gut Microbes. 2014 Mar 1;5(2):183–91.
Article
PubMed
PubMed Central
Google Scholar
Schwarzer M, Srutkova D, Hermanova P, Leulier F, Kozakova H, Schabussova I. Diet matters: endotoxin in the diet impacts the level of allergic sensitization in germ-free mice. PLoS One. 2017 Jan 4;12(1):e0167786.
Article
PubMed
PubMed Central
Google Scholar
Hrncir T, Stepankova R, Kozakova H, Hudcovic T, Tlaskalova-Hogenova H. Gut microbiota and lipopolysaccharide content of the diet influence development of regulatory T cells: studies in germ-free mice. BMC Immunol. 2008 Nov 6;9(1):65.
Article
CAS
PubMed
PubMed Central
Google Scholar
Iida N, Dzutsev A, Stewart CA, Smith L, Bouladoux N, Weingarten RA, et al. Commensal bacteria control cancer response to therapy by modulating the tumor microenvironment. Science. 2013 Nov 22;342(6161):967–70.
Article
CAS
PubMed
PubMed Central
Google Scholar
Viaud S, Saccheri F, Mignot G, Yamazaki T, Daillère R, Hannani D, et al. The intestinal microbiota modulates the anticancer immune effects of cyclophosphamide. Science. 2013 Nov 22;342(6161):971–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jenq RR, Taur Y, Devlin SM, Ponce DM, Goldberg JD, Ahr KF, et al. Intestinal Blautia is associated with reduced death from graft-versus-host disease. Biol Blood and Marrow Transplant. 2015 Aug 1;21(8):1373–83.
Article
Google Scholar
Peled JU, Devlin SM, Staffas A, Lumish M, Khanin R, Littmann ER, et al. Intestinal microbiota and relapse after hematopoietic-cell transplantation. J Clin Oncol. 2017 May 20;35(15):1650–9.
Article
PubMed
PubMed Central
Google Scholar
Routy B, Chatelier EL, Derosa L, Duong CPM, Alou MT, Daillère R, et al. Gut microbiome influences efficacy of PD-1–based immunotherapy against epithelial tumors. Science. 2018;359(6371):91–7.
Article
CAS
PubMed
Google Scholar
Gopalakrishnan V, Spencer CN, Nezi L, Reuben A, Andrews MC, Karpinets TV, et al. Gut microbiome modulates response to anti–PD-1 immunotherapy in melanoma patients. Science. 2017:eaan4236.
Frankel AE, Coughlin LA, Kim J, Froehlich TW, Xie Y, Frenkel EP, et al. Metagenomic shotgun sequencing and unbiased Metabolomic profiling identify specific human gut microbiota and metabolites associated with immune checkpoint therapy efficacy in melanoma patients. Neoplasia. 2017 Sep 15;19(10):848–55.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chaput N, Lepage P, Coutzac C, Soularue E, Le Roux K, Monot C, et al. Baseline gut microbiota predicts clinical response and colitis in metastatic melanoma patients treated with ipilimumab. Ann Oncol. 2017 Jun 1;28(6):1368–79.
Article
CAS
PubMed
Google Scholar
Dubin K, Callahan MK, Ren B, Khanin R, Viale A, Ling L, et al. Intestinal microbiome analyses identify melanoma patients at risk for checkpoint-blockade-induced colitis. Nat Commun. 2016 Feb 2;7:10391.
Article
CAS
PubMed
PubMed Central
Google Scholar
Geller LT, Barzily-Rokni M, Danino T, Jonas OH, Shental N, Nejman D, et al. Potential role of intratumor bacteria in mediating tumor resistance to the chemotherapeutic drug gemcitabine. Science. 2017 Sep 15;357(6356):1156–60.
Article
CAS
PubMed
PubMed Central
Google Scholar
Balachandran VP, Łuksza M, Zhao JN, Makarov V, Moral JA, Remark R, et al. Identification of unique neoantigen qualities in long-term survivors of pancreatic cancer. Nature. 2017 Nov;551(7681):512.
Article
CAS
PubMed
PubMed Central
Google Scholar
Thaiss CA, Levy M, Grosheva I, Zheng D, Soffer E, Blacher E, et al. Hyperglycemia drives intestinal barrier dysfunction and risk for enteric infection. Science. 2018 Mar 23;359(6382):1376–83.
Article
CAS
PubMed
Google Scholar
Paulos CM, Wrzesinski C, Kaiser A, Hinrichs CS, Chieppa M, Cassard L, et al. Microbial translocation augments the function of adoptively transferred self/tumor-specific CD8+ T cells via TLR4 signaling. J Clin Invest. 2007;117(8):2197–204.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hall JA, Bouladoux N, Sun CM, Wohlfert EA, Blank RB, Zhu Q, et al. Commensal DNA limits regulatory T cell conversion and is a natural adjuvant of intestinal immune responses. Immunity. 2008 Oct 17;29(4):637–49.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rooks MG, Garrett WS. Gut microbiota, metabolites and host immunity. Nat Rev Immunol. 2016 Jun;16(6):341–52.
Article
CAS
PubMed
PubMed Central
Google Scholar
Morrison DJ, Preston T. Formation of short chain fatty acids by the gut microbiota and their impact on human metabolism. Gut Microbes. 2016;7(3):189–200.
Article
PubMed
PubMed Central
Google Scholar
den BG, van EK, Groen AK, Venema K, Reijngoud D-J, Bakker BM. The role of short-chain fatty acids in the interplay between diet, gut microbiota, and host energy metabolism. J Lipid Res. 2013;54(9):2325–40.
Article
CAS
Google Scholar
Iraporda C, Errea A, Romanin DE, Cayet D, Pereyra E, Pignataro O, et al. Lactate and short chain fatty acids produced by microbial fermentation downregulate proinflammatory responses in intestinal epithelial cells and myeloid cells. Immunobiology. 2015 Oct;220(10):1161–9.
Article
CAS
PubMed
Google Scholar
Gurav A, Sivaprakasam S, Bhutia YD, Boettger T, Singh N, Ganapathy V. Slc5a8, a Na+−coupled high-affinity transporter for short-chain fatty acids, is a conditional tumor suppressor in colon that protects against colitis and colon cancer under low-fiber dietary conditions. Biochem J. 2015;469(2):267–78.
Article
CAS
PubMed
Google Scholar
White CA, Pone EJ, Lam T, Tat C, Hayama KL, Li G, et al. HDAC inhibitors upregulate B cell microRNAs that silence AID and Blimp-1 expression for epigenetic modulation of antibody and autoantibody responses. J Immunol. 2014;193(12):5933–50.
Article
CAS
PubMed
Google Scholar
Arpaia N, Campbell C, Fan X, Dikiy S, van der Veeken J, deRoos P, et al. Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation. Nature. 2013 Dec 19;504(7480):451–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cohen LJ, Esterhazy D, Kim S-H, Lemetre C, Aguilar RR, Gordon EA, et al. Commensal bacteria make GPCR ligands that mimic human signalling molecules. Nature. 2017 Sep;549(7670):48–53.
Article
CAS
PubMed
PubMed Central
Google Scholar
Levy M, Thaiss CA, Elinav E. Metabolites: messengers between the microbiota and the immune system. Genes Dev. 2016 Jul 15;30(14):1589–97.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sano T, Huang W, Hall JA, Yang Y, Chen A, Gavzy SJ, et al. An IL-23R/IL-22 circuit regulates epithelial serum amyloid a to promote local effector Th17 responses. Cell. 2015 Oct 8;163(2):381–93.
Article
CAS
PubMed
PubMed Central
Google Scholar
Uribe-Herranz M, Bittinger K, Rafail S, Guedan S, Pierini S, Tanes C, et al. Gut microbiota modulates adoptive cell therapy via CD8α dendritic cells and IL-12. JCI Insight. 2018 Feb 22;3(4).
Tanoue T, Morita S, Plichta DR, Skelly AN, Suda W, Sugiura Y, et al. A defined commensal consortium elicits CD8 T cells and anti-cancer immunity. Nature. 2019:1.
Morton AM, Sefik E, Upadhyay R, Weissleder R, Benoist C, Mathis D. Endoscopic photoconversion reveals unexpectedly broad leukocyte trafficking to and from the gut. PNAS. 2014 May 6;111(18):6696–701.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wolchok JD, Chiarion-Sileni V, Gonzalez R, Rutkowski P, Grob J-J, Cowey CL, et al. Overall survival with combined Nivolumab and Ipilimumab in advanced melanoma. N Engl J Med. 2017 Oct 5;377(14):1345–56.
Article
CAS
PubMed
PubMed Central
Google Scholar
Arques JL, Hautefort I, Ivory K, Bertelli E, Regoli M, Clare S, et al. Salmonella induces Flagellin- and MyD88-dependent migration of Bacteria-capturing dendritic cells into the gut lumen. Gastroenterology. 2009 Aug 1;137(2):579–587.e2.
Article
PubMed
Google Scholar
McDole JR, Wheeler LW, McDonald KG, Wang B, Konjufca V, Knoop KA, et al. Goblet cells deliver luminal antigen to CD103+ dendritic cells in the small intestine. Nature. 2012;483(7389):345–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mowat AM, Agace WW. Regional specialization within the intestinal immune system. Nat Rev Immunol. 2014 Oct;14(10):667–85.
Article
CAS
PubMed
Google Scholar
Queirolo P, Morabito A, Laurent S, Lastraioli S, Piccioli P, Ascierto PA, et al. Association of CTLA-4 polymorphisms with improved overall survival in melanoma patients treated with CTLA-4 blockade: a pilot study. Cancer Investig. 2013 Jun 1;31(5):336–45.
Article
CAS
Google Scholar
Spranger S, Bao R, Gajewski TF. Melanoma-intrinsic β-catenin signalling prevents anti-tumour immunity. Nature. 2015 Jul;523(7559):231–5.
Article
CAS
PubMed
Google Scholar
Peng W, Chen JQ, Liu C, Malu S, Creasy C, Tetzlaff MT, et al. Loss of PTEN promotes resistance to T cell-mediated immunotherapy. Cancer Discov. 2016 Feb;6(2):202–16.
Article
CAS
PubMed
Google Scholar
Derosa L, Hellmann MD, Spaziano M, Halpenny D, Fidelle M, Rizvi H, et al. Negative association of antibiotics on clinical activity of immune checkpoint inhibitors in patients with advanced renal cell and non-small-cell lung cancer. Ann Oncol. 2018 Jun 1;29(6):1437–44.
Article
CAS
PubMed
PubMed Central
Google Scholar
Galloway-Peña JR, Jenq RR, Shelburne SA. Can Consideration of the Microbiome Improve Antimicrobial Utilization and Treatment Outcomes in the Oncology Patient? Clin Cancer Res. 2017;23(13):3263–8.
Article
PubMed
PubMed Central
Google Scholar
Rohlke F, Stollman N. Fecal microbiota transplantation in relapsing Clostridium difficile infection. Ther Adv Gastroenterol. 2012 Nov;5(6):403–20.
Article
Google Scholar
David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature. 2014 Jan;505(7484):559–63.
Article
CAS
PubMed
Google Scholar
Lim B, Zimmermann M, Barry NA, Goodman AL. Engineered regulatory systems modulate gene expression of human commensals in the gut. Cell. 2017 Apr 20;169(3):547–558.e15.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shepherd ES, DeLoache WC, Pruss KM, Whitaker WR, Sonnenburg JL. An exclusive metabolic niche enables strain engraftment in the gut microbiota. Nature. 2018;557(7705):434–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Guo C-J, Chang F-Y, Wyche TP, Backus KM, Acker TM, Funabashi M, et al. Discovery of reactive microbiota-derived metabolites that inhibit host proteases. Cell. 2017;168(3):517–526.e18.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mullard A. Oncologists tap the microbiome in bid to improve immunotherapy outcomes. Nat Rev Drug Discov. 2018 Feb 16;17:153–5.
Article
CAS
PubMed
Google Scholar
Wheeler ML, Limon JJ, Bar AS, Leal CA, Gargus M, Tang J, et al. Immunological consequences of intestinal fungal Dysbiosis. Cell Host Microbe. 2016 Jun 8;19(6):865–73.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li X, Leonardi I, Semon A, Doron I, Gao IH, Putzel GG, et al. Response to fungal Dysbiosis by gut-resident CX3CR1+ mononuclear phagocytes aggravates allergic airway disease. Cell Host Microbe. 2018 Dec 12;24(6):847–856.e4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Filyk HA, Osborne LC. The multibiome: the intestinal Ecosystem’s influence on immune homeostasis, health, and disease. EBioMedicine. 2016 Nov 1;13:46–54.
Article
PubMed
PubMed Central
Google Scholar
Monaco CL, Gootenberg DB, Zhao G, Handley SA, Ghebremichael MS, Lim ES, et al. Altered Virome and bacterial microbiome in human immunodeficiency virus-associated acquired immunodeficiency syndrome. Cell Host Microbe. 2016 Mar 9;19(3):311–22.
Article
CAS
PubMed
PubMed Central
Google Scholar
Norman JM, Handley SA, Baldridge MT, Droit L, Liu CY, Keller BC, et al. Disease-specific alterations in the enteric Virome in inflammatory bowel disease. Cell. 2015 Jan 29;160(3):447–60.
Article
CAS
PubMed
PubMed Central
Google Scholar
Richardson SJ, Horwitz MS. Is type 1 diabetes “going viral”? Diabetes. 2014 Jul 1;63(7):2203–5.
Article
PubMed
Google Scholar
Zhao G, Vatanen T, Droit L, Park A, Kostic AD, Poon TW, et al. Intestinal virome changes precede autoimmunity in type I diabetes-susceptible children. Proc Natl Acad Sci U S A. 2017 Jul 25;114(30):E6166–75.
Article
CAS
PubMed
PubMed Central
Google Scholar