Barrier surfaces, such as the intestinal lining and the skin, are colonized by a diverse community of commensal microorganisms. Although commensal microorganisms clearly impact the host immune system, whether the immune system also shapes the commensal community is poorly understood. We used 16S rDNA deep sequencing to test whether mice with specific immune defects have an altered commensal microflora. Initially, skin swabs were obtained from wild-type and Langerhans Cell (LC) deficient mice. Despite the intimate contacts that LC make with the upper epidermis, no significant differences were observed in microbial community composition. Similarly, the skin of MyD88/TRIF？/？, Rag1？/？ and heterozygous littermate controls showed no alteration in their commensal communities. Next we examined mouth swabs and feces. We did not find a difference in the MyD88/TRIF？/？ mice. However, we did observe a significant shift in the microbial composition in the feces and mouths of Rag1？/？ mice. Thus, we conclude that the adaptive immune system modulates the microbial composition at mucosal surfaces in the steady-state but LC, adaptive immunity, and MyD88-dependent innate responses do not affect the skin microbiome revealing a major distinction between barrier sites.
References
[1]
Maneesh D, Higgins PD, Middha S, Rioux KP (2012) The human gut microbiome: current knowledge, challenges, and future directions. Transl Res 160: 246–257 doi:10.1016/j.trsl.2012.05.003.
[2]
Grice EA, Kong HH, Renaud G, Young AC (2008) NISC Comparative Sequencing Program, (2008) et al. A diversity profile of the human skin microbiota. Genome Res 18: 1043–1050 doi:10.1101/gr.075549.107.
[3]
Grice EA, Kong HH, Conlan S, Deming CB, Davis J, et al. (2009) Topographical and temporal diversity of the human skin microbiome. Science 324: 1190–1192 doi:10.1126/science.1171700.
[4]
Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, et al. (2007) The human microbiome project. Nature 449: 804–810 doi:10.1038/nature06244.
[5]
Huse SM, Ye Y, Zhou Y, Fodor AA (2012) A core human microbiome as viewed through 16S rRNA sequence clusters. PLoS ONE 7: e34242 doi:10.1371/journal.pone.0034242.
[6]
Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, et al. (2006) An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444: 1027–1031 doi:10.1038/nature05414.
[7]
Turnbaugh PJ, Gordon JI (2009) The core gut microbiome, energy balance and obesity. J Physiol (Lond) 587: 4153–4158 doi:10.1113/jphysiol.2009.174136.
[8]
Kong HH, Oh J, Deming C, Conlan S, Grice EA, et al. (2012) Temporal shifts in the skin microbiome associated with disease flares and treatment in children with atopic dermatitis. Genome Res 22: 850–859 doi:10.1101/gr.131029.111.
[9]
Marchesi JR, Dutilh BE, Hall N, Peters WHM, Roelofs R, et al. (2011) Towards the human colorectal cancer microbiome. PLoS ONE 6: e20447 doi:10.1371/journal.pone.0020447.
[10]
Henao-Mejia J, Elinav E, Jin C, Hao L, Mehal WZ, et al. (2012) Inflammasome-mediated dysbiosis regulates progression of NAFLD and obesity. Nature 482: 179–185 doi:10.1038/nature10809.
Marchesi JR (2011) Human distal gut microbiome. Environ Microbiol 13: 3088–3102 doi:10.1111/j.1462-2920.2011.02574.x.
[13]
Hildebrand F, Nguyen ATL, Brinkman B, Yunta RG, Cauwe B, et al. (2013) Inflammation-associated enterotypes, host genotype, cage and inter-individual effects drive gut microbiota variation in common laboratory mice. Genome Biol 14: R4 doi:10.1186/gb-2013-14-1-r4.
[14]
Thompson CL, Mikaelyan A, Brune A (2013) Immune-modulating gut symbionts are not “Candidatus Arthromitus”. Mucosal Immunol 6: 200–201 doi:10.1038/mi.2012.91.
[15]
Talham GL, Jiang HQ, Bos NA, Cebra JJ (1999) Segmented filamentous bacteria are potent stimuli of a physiologically normal state of the murine gut mucosal immune system. Infect Immun 67: 1992–2000.
[16]
Morgan XC, Segata N, Huttenhower C (2012) Biodiversity and functional genomics in the human microbiome. Trends Genet doi:10.1016/j.tig.2012.09.005.
[17]
Atarashi K, Tanoue T, Shima T, Imaoka A, Kuwahara T, et al. (2011) Induction of colonic regulatory T cells by indigenous Clostridium species. Science 331: 337–341 doi:10.1126/science.1198469.
[18]
Nagano Y, Itoh K, Honda K (2012) The induction of Treg cells by gut-indigenous Clostridium. Curr Opin Immunol 24: 392–397 doi:10.1016/j.coi.2012.05.007.
[19]
Chiba T, Seno H (2011) Indigenous clostridium species regulate systemic immune responses by induction of colonic regulatory T cells. Gastroenterology 141: 1114–1116 doi:10.1053/j.gastro.2011.07.013.
[20]
Round JL, Mazmanian SK (2010) Inducible Foxp3+ regulatory T-cell development by a commensal bacterium of the intestinal microbiota. Proc Natl Acad Sci USA 107: 12204–12209 doi:10.1073/pnas.0909122107.
[21]
Lai Y, Di Nardo A, Nakatsuji T, Leichtle A, Yang Y, et al. (2009) Commensal bacteria regulate Toll-like receptor 3-dependent inflammation after skin injury. Nat Med 15: 1377–1382 doi:10.1038/nm.2062.
[22]
Naik S, Bouladoux N, Wilhelm C, Molloy MJ, Salcedo R, et al. (2012) Compartmentalized Control of Skin Immunity by Resident Commensals. Science doi:10.1126/science.1225152.
[23]
Lai Y, Cogen AL, Radek KA, Park HJ, Macleod DT, et al. (2010) Activation of TLR2 by a small molecule produced by Staphylococcus epidermidis increases antimicrobial defense against bacterial skin infections. J Invest Dermatol 130: 2211–2221 doi:10.1038/jid.2010.123.
[24]
Lupp C, Robertson ML, Wickham ME, Sekirov I, Champion OL, et al. (2007) Host-mediated inflammation disrupts the intestinal microbiota and promotes the overgrowth of Enterobacteriaceae. Cell Host Microbe 2: 119–129 doi:10.1016/j.chom.2007.06.010.
[25]
Garrett WS, Lord GM, Punit S, Lugo-Villarino G, Mazmanian SK, et al. (2007) Communicable ulcerative colitis induced by T-bet deficiency in the innate immune system. Cell 131: 33–45 doi:10.1016/j.cell.2007.08.017.
[26]
Garrett WS, Glimcher LH (2009) T-bet？/？ RAG2？/？ ulcerative colitis: the role of T-bet as a peacekeeper of host-commensal relationships. Cytokine 48: 144–147 doi:10.1016/j.cyto.2009.07.007.
[27]
Elinav E, Strowig T, Kau AL, Henao-Mejia J, Thaiss CA, et al. (2011) NLRP6 inflammasome regulates colonic microbial ecology and risk for colitis. Cell 145: 745–757 doi:10.1016/j.cell.2011.04.022.
[28]
Scharschmidt TC, List K, Grice EA, Szabo R (2009) NISC Comparative Sequencing Program, (2009) et al. Matriptase-deficient mice exhibit ichthyotic skin with a selective shift in skin microbiota. J Invest Dermatol 129: 2435–2442 doi:10.1038/jid.2009.104.
[29]
Ubeda C, Lipuma L, Gobourne A, Viale A, Leiner I, et al. (2012) Familial transmission rather than defective innate immunity shapes the distinct intestinal microbiota of TLR-deficient mice. J Exp Med 209: 1445–1456 doi:10.1084/jem.20120504.
[30]
Kubo A, Nagao K, Yokouchi M, Sasaki H, Amagai M (2009) External antigen uptake by Langerhans cells with reorganization of epidermal tight junction barriers. J Exp Med 206: 2937–2946 doi:10.1084/jem.20091527.
[31]
Gorbachev AV, Fairchild RL (2004) CD4+ T cells regulate CD8+ T cell-mediated cutaneous immune responses by restricting effector T cell development through a Fas ligand-dependent mechanism. J Immunol 172: 2286–2295.
[32]
Chodaczek G, Papanna V, Zal MA, Zal T (2012) Body-barrier surveillance by epidermal γδ TCRs. Nat Immunol 13: 272–282 doi:10.1038/ni.2240.
[33]
Tortola L, Rosenwald E, Abel B, Blumberg H, Sch？fer M, et al. (2012) Psoriasiform dermatitis is driven by IL-36-mediated DC-keratinocyte crosstalk. J Clin Invest 122: 3965–3976 doi:10.1172/JCI63451.
[34]
Doss M, White MR, Tecle T, Hartshorn KL (2010) Human defensins and LL-37 in mucosal immunity. J Leukoc Biol 87: 79–92 doi:10.1189/jlb.0609382.
[35]
Sonnenberg GF, Fouser LA, Artis D (2010) Functional biology of the IL-22-IL-22R pathway in regulating immunity and inflammation at barrier surfaces. Adv Immunol 107: 1–29 doi:10.1016/B978-0-12-381300-8.00001-0.
[36]
Sonnenberg GF, Fouser LA, Artis D (2011) Border patrol: regulation of immunity, inflammation and tissue homeostasis at barrier surfaces by IL-22. Nat Immunol 12: 383–390 doi:10.1038/ni.2025.
Hamady M, Lozupone C, Knight R (2010) Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data. ISME J 4: 17–27 doi:10.1038/ismej.2009.97.
[39]
Gallo RL, Nakatsuji T (2011) Microbial symbiosis with the innate immune defense system of the skin. J Invest Dermatol 131: 1974–1980 doi:10.1038/jid.2011.182.
[40]
Dimitriu PA, Boyce G, Samarakoon A, Hartmann M, Johnson P, et al. (2013) Temporal stability of the mouse gut microbiota in relation to innate and adaptive immunity. Environ Microbiol Rep 5: 200–210 doi:10.1111/j.1758-2229.2012.00393.x.
[41]
Wade WG (2012) The oral microbiome in health and disease. Pharmacol Res doi:10.1016/j.phrs.2012.11.006.
[42]
Fritz JH, Rojas OL, Simard N, McCarthy DD, Hapfelmeier S, et al. (2012) Acquisition of a multifunctional IgA+ plasma cell phenotype in the gut. Nature 481: 199–203 doi:10.1038/nature10698.
[43]
Ivanov II, Frutos Rde L, Manel N, Yoshinaga K, Rifkin DB, et al. (2008) Specific microbiota direct the differentiation of IL-17-producing T-helper cells in the mucosa of the small intestine. Cell Host Microbe 4: 337–349 doi:10.1016/j.chom.2008.09.009.
[44]
Suzuki K, Meek B, Doi Y, Muramatsu M, Chiba T, et al. (2004) Aberrant expansion of segmented filamentous bacteria in IgA-deficient gut. Proc Natl Acad Sci USA 101: 1981–1986 doi:10.1073/pnas.0307317101.
[45]
Grice EA, Snitkin ES, Yockey LJ, Bermudez DM (2010) NISC Comparative Sequencing Program, (2010) et al. Longitudinal shift in diabetic wound microbiota correlates with prolonged skin defense response. Proc Natl Acad Sci USA 107: 14799–14804 doi:10.1073/pnas.1004204107.
[46]
Sogin ML, Morrison HG, Huber JA, Mark Welch D, Huse SM, et al. (2006) Microbial diversity in the deep sea and the underexplored “rare biosphere”. Proc Natl Acad Sci USA 103: 12115–12120 doi:10.1073/pnas.0605127103.
[47]
Huber JA, Mark Welch DB, Morrison HG, Huse SM, Neal PR, et al. (2007) Microbial population structures in the deep marine biosphere. Science 318: 97–100 doi:10.1126/science.1146689.
[48]
Hamady M, Walker JJ, Harris JK, Gold NJ, Knight R (2008) Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nat Methods 5: 235–237 doi:10.1038/nmeth.1184.
[49]
Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, et al. (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75: 7537–7541 doi:10.1128/AEM.01541-09.
[50]
Schloss PD, Gevers D, Westcott SL (2011) Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS ONE 6: e27310 doi:10.1371/journal.pone.0027310.
[51]
Huse SM, Welch DM, Morrison HG, Sogin ML (2010) Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environ Microbiol 12: 1889–1898 doi:10.1111/j.1462-2920.2010.02193.x.
[52]
Cole JR, Wang Q, Cardenas E, Fish J, Chai B, et al. (2009) The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37: D141–D145 doi:10.1093/nar/gkn879.
[53]
Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27: 2194–2200 doi:10.1093/bioinformatics/btr381.
[54]
Schloss PD (2010) The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies. PLoS Comput Biol 6: e1000844 doi:10.1371/journal.pcbi.1000844.
[55]
Hamilton MJ, Weingarden AR, Unno T, Khoruts A, Sadowsky MJ (2013) High-throughput DNA sequence analysis reveals stable engraftment of gut microbiota following transplantation of previously frozen fecal bacteria. Gut Microbes 4: 125–135 doi:10.4161/gmic.23571.
[56]
Flores GE, Henley JB, Fierer N (2012) A direct PCR approach to accelerate analyses of human-associated microbial communities. PLoS ONE 7: e44563 doi:10.1371/journal.pone.0044563.
[57]
Parks BW, Nam E, Org E, Kostem E, Norheim F, et al. (2013) Genetic control of obesity and gut microbiota composition in response to high-fat, high-sucrose diet in mice. Cell Metab 17: 141–152 doi:10.1016/j.cmet.2012.12.007.
[58]
Lozupone C, Stombaugh J, Gonzalez A, Ackermann G, Wendel D, et al. (2013) Meta-analyses of studies of the human microbiota. Genome Res doi:10.1101/gr.151803.112.
[59]
White JR, Nagarajan N, Pop M (2009) Statistical methods for detecting differentially abundant features in clinical metagenomic samples. PLoS Comput Biol 5: e1000352 doi:10.1371/journal.pcbi.1000352.
