Sampling of Intestinal Microbiota and Targeted Amplification of Bacterial 16S rRNA Genes for Microbial Ecologic Analysis

Current Protocols in Immunology

Volumn 2014, Issue , 2014, Pages 7.41.1-7.41.11

  Tong, Maomeng ^a   Jacobs, Jonathan P ^a   McHardy, Ian H ^a   Braun, Jonathan ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

16S rRNA; Illumina sequencing; Intestinal microbiota; Lavage; Mucosal microbiota

Indexed keywords

BACTERIAL RNA; RNA 16S;

ARTICLE; BACTERIAL GENE; DATA ANALYSIS; FECES ANALYSIS; GENE AMPLIFICATION; GENE SEQUENCE; HUMAN; INTESTINE BIOPSY; INTESTINE FLORA; INTESTINE LAVAGE; INTESTINE MUCOSA; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; ANIMAL; GENETICS; HIGH THROUGHPUT SEQUENCING; IMMUNOLOGY; MOUSE; NUCLEIC ACID AMPLIFICATION; PROCEDURES;

ANIMALS; GASTROINTESTINAL MICROBIOME; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MICE; NUCLEIC ACID AMPLIFICATION TECHNIQUES; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S;

EID: 84943324410     PISSN: 19343671     EISSN: 1934368X     Source Type: Journal    
DOI: 10.1002/0471142735.im0741s107     Document Type: Article

References (18)

1. Caporaso, J.G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F.D., Costello, E.K., Fierer, N., Pena, A.G., Goodrich, J.K., Gordon, J.I., Huttley, G.A., Kelley, S.T., Knights, D., Koenig, J.E., Ley, R.E., Lozupone, C.A., McDonald, D., Muegge, B.D., Pirrung, M., Reeder, J., Sevinsky, J.R., Turnbaugh, P.J., Walters, W.A., Widmann, J., Yatsunenko, T., Zaneveld, J., Knight, R. 2010. QIIME allows analysis of highthroughput community sequencing data. Nat. Methods 7:335-336.
2. Caporaso, J.G., Lauber, C.L., Walters, W.A., Berg-Lyons, D., Huntley, J., Fierer, N., Owens, S.M., Betley, J., Fraser, L., Bauer, M., Gormley, N., Gilbert, J.A., Smith, G., Knight, R. 2012. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 6:1621-1624.
3. Costello, E.K., Lauber, C.L., Hamady, M., Fierer, N., Gordon, J.I., Knight, R. 2009. Bacterial community variation in human body habitats across space and time. Science 326:1694-1697. Eckburg, P.B., Bik, E.M., Bernstein, C.N., Purdom, E., Dethlefsen, L., Sargent, M., Gill, S.R., Nelson, K.E., Relman, D.A. 2005. Diversity of the human intestinal microbial flora. Science 308:1635-1638.
4. Eckburg, P.B., Bik, E.M., Bernstein, C.N., Purdom, E., Dethlefsen, L., Sargent, M., Gill, S.R., Nelson, K.E., Relman, D.A. 2005. Diversity of the human intestinal microbial flora. Science 308:1635-1638
5. Erickson, A.R., Cantarel, B.L., Lamendella, R., Darzi, Y., Mongodin, E.F., Pan, C., Shah, M., Halfvarson, J., Tysk, C., Henrissat, B., Raes, J., Verberkmoes, N.C., Fraser, C.M., Hettich, R.L., Jansson, J.K. 2012. Integrated metagenomics/metaproteomics reveals human hostmicrobiota signatures of Crohn's disease. PloS One 7:e49138.
6. Frank, D.N., St Amand, A.L., Feldman, R.A., Boedeker, E.C., Harpaz, N., Pace, N.R. 2007. Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc. Natl. Acad. Sci. U.S.A. 104:13780-13785.
7. Johansson, M.E., Larsson, J.M., Hansson, G.C. 2011. The two mucus layers of colon are organized by the MUC2 mucin, whereas the outer layer is a legislator of host-microbial interactions. Proc. Natl. Acad. Sci. U.S.A. 108:4659-4665.
8. Kinross, J.M., Darzi, A.W., Nicholson, J.K. 2011. Gut microbiome-host interactions in health and disease. Genome Med. 3:14. Kuczynski, J., Stombaugh, J., Walters, W.A., Gonzalez, A., Caporaso, J.G., Knight, R. 2012. Using QIIME to analyze 16S rRNA gene sequences from microbial communities. Curr. Protoc. Microbiol. 27:E:1E.5:1E.5.1-1E.5.20.
9. Kuczynski, J., Stombaugh, J., Walters, W.A., Gonzalez, A., Caporaso, J.G., Knight, R. 2012. Using QIIME to analyze 16S rRNA gene sequences from microbial communities. Curr. Protoc. Microbiol. 27:E:1E.5:1E.5.1-1E.5.20
10. Langille, M.G., Zaneveld, J., Caporaso, J.G., Mc-Donald, D., Knights, D., Reyes, J.A., Clemente, J.C., Burkepile, D.E., Vega Thurber, R.L., Knight, R., Beiko, R.G., Huttenhower, C. 2013. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat. Biotechnol. 31:814-821.
11. Li, X., LeBlanc, J., Truong, A., Vuthoori, R., Chen, S.S., Lustgarten, J.L., Roth, B., Allard, J., Ippoliti, A., Presley, L.L., Borneman, J., Bigbee, W.L., Gopalakrishnan, V., Graeber, T.G., Elashoff, D., Braun, J., Goodglick, L. 2011. A metaproteomic approach to study humanmicrobial ecosystems at the mucosal luminal interface. PloS One 6:e26542.
12. McHardy, I., Goudarzi, M., Tong, M., Ruegger, P., Schwager, E., Weger, J., Graeber, T., Sonnenburg, J., Horvath, S., Huttenhower, C., Mc-Govern, D., Fornace, A., Borneman, J., Braun, J. 2013. Integrative analysis of the microbiome and metabolome of the human intestinal mucosal surface reveals exquisite interrelationships. Microbiome 1:17.
13. McHardy, I.H., Li, X., Tong, M., Ruegger, P., Jacobs, J., Borneman, J., Anton, P., Braun, J. 2013. HIV Infection is associated with compositional and functional shifts in the rectal mucosal microbiota. Microbiome 1:26.
14. Nicholson, J.K., Holmes, E., Kinross, J., Burcelin, R., Gibson, G., Jia, W., Pettersson, S. 2012. Host-gut microbiotametabolic interactions. Science 336:1262-1267.
15. Perez-Cobas, A.E., Gosalbes, M.J., Friedrichs, A., Knecht, H., Artacho, A., Eismann, K., Otto, W., Rojo, D., Bargiela, R., von Bergen, M., Neulinger, S.C., Daumer, C., Heinsen, F.A., Latorre, A., Barbas, C., Seifert, J., Dos Santos, V.M., Ott, S.J., Ferrer, M., Moya, A. 2012. Gut microbiota disturbance during antibiotic therapy: A multi-omic approach. Gut. Microbes 5:64-70.
16. Raes, J. and Bork, P. 2008. Molecular eco-systems biology: Towards an understanding of community function. Nat. Rev. Microbiol. 6:693-699.
17. Schloss, P.D., Westcott, S.L., Ryabin, T., Hall, J.R., Hartmann, M., Hollister, E.B., Lesniewski, R.A., Oakley, B.B., Parks, D.H., Robinson, C.J., Sahl, J.W., Stres, B., Thallinger, G.G., Van Horn, D.J., Weber, C.F. 2009. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75:7537-7541.
18. Tong, M., Li, X., Wegener Parfrey, L., Roth, B., Ippoliti, A., Wei, B., Borneman, J., McGovern, D.P., Frank, D.N., Li, E., Horvath, S., Knight, R., Braun, J. 2013. A modular organization of the human intestinal mucosal microbiota and its associationwith inflammatory bowel disease. PloS One 8:e80702.