Analysis of microbiota alterations in inflammasome-deficient mice

Methods in Molecular Biology

Volumn 1040, Issue , 2013, Pages 185-194

  Elinav, Eran ^a,b   Thaiss, Christoph A ^a,c   Flavell, Richard A ^a,d  

^a YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b WEIZMANN INSTITUTE OF SCIENCE   (Israel)

^c ETH ZURICH   (Switzerland)

^d HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

16S RNA sequencing; Cohousing; Dysbiosis; Inflammasome; Intestine; Microflora

Indexed keywords

INFLAMMASOME;

ANIMAL EXPERIMENT; ARTICLE; CONTROLLED STUDY; DNA SEQUENCE; FEMALE; GENOTYPE; INNATE IMMUNITY; INTESTINE FLORA; LACTOBACILLACEAE; MICROBIAL COLONIZATION; MICROBIAL COMMUNITY; MICROBIOME; MOUSE; NEWBORN; NONHUMAN; PREVOTELLACEAE; PRIORITY JOURNAL;

EID: 84880474099     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-523-1_14     Document Type: Article

References (21)

1. Martinon F, Burns K, Tschopp J (2002) The infl ammasome: A molecular platform triggering activation of infl ammatory caspases and processing of proIL-beta. Mol Cell 10(2): 417-426
2. Strowig T, Henao-Mejia J, Elinav E, Flavell R (2012) Infl ammasomes in health and disease. Nature 481(7381):278-286
3. Franchi L, Munoz-Planillo R, Nunez G (2012) Sensing and reacting to microbes through the infl ammasomes. Nat Immunol 13(4): 325-332
4. Zaki MH, Lamkanfi M, Kanneganti TD (2011) The Nlrp3 infl ammasome: Contributions to intestinal homeostasis. Trends Immunol 32(4):171-179
5. 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 infl ammasome regulates colonic microbial ecology and risk for colitis. Cell 145(5):745-757
6. 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) Infl ammasome-mediated dysbiosis regulates progression of NAFLD and obesity. Nature 482(7384):179-185
7. 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
8. Rakoff-Nahoum S, Medzhitov R (2008) Innate immune recognition of the indigenous microbial fl ora. Mucosal Immunol 1(Suppl 1): S10-S14
9. Mandar R, Mikelsaar M (1996) Transmission of mother's microfl ora to the newborn at birth. Biol Neonate 69(1):30-35
10. 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
11. Shi Y, Tyson GW, DeLong EF (2009) Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column. Nature 459(7244):266-269
12. 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
13. 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
14. 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
15. Quince C, Lanzen A, Davenport RJ, Turnbaugh PJ (2011) Removing noise from pyrosequenced amplicons. BMC Bioinformatics 12:38
16. 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
17. 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
18. 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
19. Lozupone C, Hamady M, Knight R (2006) UniFrac - an online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinformatics 7:371
20. 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
21. Stecher B, Hardt WD (2011) Mechanisms controlling pathogen colonization of the gut. Curr Opin Microbiol 14(1):82-91