Abstract
Inflammasomes have emerged as central regulators of intestinal infection, immunity, and inflammation. Inflammasome activity mediates intestinal epithelial integrity, antimicrobial responses, and initiates inflammation through generation of the cytokines interleukin (IL-)1 and IL-18. Recent studies have identified an additional layer of inflammasome function in the intestine, namely, the control of intestinal microflora composition. Inflammasome-deficient mice show an aberrant microbial community which is dominantly transmissible to healthy mice. This dysbiosis in inflammasome-deficient mice has a profound impact on their physiology and pathophysiology, both locally in the intestine and systemically. Therefore, it is essential to consider the influence of the composition of microbial communities on experiments performed with inflammasome-deficient and other innate molecule-deficient mice, and to conduct experiments to control for potential dominant effects of the microflora on host responses. In this chapter, we provide experimental procedures to monitor inflammasome-mediated modifications of the intestinal microflora composition in mice and to test the resultant functional consequences of these changes in microbial communities and their transmission to cohoused mice.
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References
Martinon F, Burns K, Tschopp J (2002) The inflammasome: a molecular platform triggering activation of inflammatory caspases and processing of proIL-beta. Mol Cell 10(2):417–426
Strowig T, Henao-Mejia J, Elinav E, Flavell R (2012) Inflammasomes in health and disease. Nature 481(7381):278–286
Franchi L, Munoz-Planillo R, Nunez G (2012) Sensing and reacting to microbes through the inflammasomes. Nat Immunol 13(4):325–332
Zaki MH, Lamkanfi M, Kanneganti TD (2011) The Nlrp3 inflammasome: contributions to intestinal homeostasis. Trends Immunol 32(4):171–179
Elinav E, Strowig T, Kau AL, Henao-Mejia J, Thaiss CA, Booth CJ, Peaper DR, Bertin J, Eisenbarth SC, Gordon JI, Flavell RA (2011) NLRP6 inflammasome regulates colonic microbial ecology and risk for colitis. Cell 145(5):745–757
Henao-Mejia J, Elinav E, Jin C, Hao L, Mehal WZ, Strowig T, Thaiss CA, Kau AL, Eisenbarth SC, Jurczak MJ, Camporez JP, Shulman GI, Gordon JI, Hoffman HM, Flavell RA (2012) Inflammasome-mediated dysbiosis regulates progression of NAFLD and obesity. Nature 482(7384):179–185
Vijay-Kumar M, Aitken JD, Carvalho FA, Cullender TC, Mwangi S, Srinivasan S, Sitaraman SV, Knight R, Ley RE, Gewirtz AT (2010) Metabolic syndrome and altered gut microbiota in mice lacking toll-like receptor 5. Science 328(5975):228–231
Rakoff-Nahoum S, Medzhitov R (2008) Innate immune recognition of the indigenous microbial flora. Mucosal Immunol 1(Suppl 1):S10–S14
Mandar R, Mikelsaar M (1996) Transmission of mother’s microflora to the newborn at birth. Biol Neonate 69(1):30–35
Harris NL, Spoerri I, Schopfer JF, Nembrini C, Merky P, Massacand J, Urban JF Jr, Lamarre A, Burki K, Odermatt B, Zinkernagel RM, Macpherson AJ (2006) Mechanisms of neonatal mucosal antibody protection. J Immunol 177(9):6256–6262
Shi Y, Tyson GW, DeLong EF (2009) Metatranscriptomics reveals unique microbial small RNAs in the ocean’s water column. Nature 459(7244):266–269
Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, Glockner FO (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35(21):7188–7196
Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-Syed-Mohideen AS, McGarrell DM, Marsh T, Garrity GM, Tiedje JM (2009) The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37(Database issue):D141–D145
Kuczynski J, Lauber CL, Walters WA, Parfrey LW, Clemente JC, Gevers D, Knight R (2012) Experimental and analytical tools for studying the human microbiome. Nat Rev Genet 13(1):47–58
Quince C, Lanzen A, Davenport RJ, Turnbaugh PJ (2011) Removing noise from pyrosequenced amplicons. BMC Bioinformatics 12:38
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7(5):335–336
Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75(23):7537–7541
DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72(7):5069–5072
Lozupone C, Hamady M, Knight R (2006) UniFrac—an online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinformatics 7:371
Stecher B, Chaffron S, Kappeli R, Hapfelmeier S, Freedrich S, Weber TC, Kirundi J, Suar M, McCoy KD, von Mering C, Macpherson AJ, Hardt WD (2010) Like will to like: abundances of closely related species can predict susceptibility to intestinal colonization by pathogenic and commensal bacteria. PLoS Pathog 6(1):e1000711
Stecher B, Hardt WD (2011) Mechanisms controlling pathogen colonization of the gut. Curr Opin Microbiol 14(1):82–91
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Elinav, E., Thaiss, C.A., Flavell, R.A. (2013). Analysis of Microbiota Alterations in Inflammasome-Deficient Mice. In: De Nardo, C., Latz, E. (eds) The Inflammasome. Methods in Molecular Biology, vol 1040. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-523-1_14
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DOI: https://doi.org/10.1007/978-1-62703-523-1_14
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