Research Techniques Made Simple: Bacterial 16S Ribosomal RNA Gene Sequencing in Cutaneous Research

Journal of Investigative Dermatology

Volumn 136, Issue , 2016, Pages e23-e27

  Jo, Jay Hyun ^a   Kennedy, Elizabeth A ^a   Kong, Heidi H ^a  

^a NATIONAL CANCER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL RNA; RNA 16S;

GENETIC LINKAGE; HUMAN; MICROBIAL COMMUNITY; NONHUMAN; PRIORITY JOURNAL; RNA GENE; RNA SEQUENCE; SHORT SURVEY; SKIN FLORA; SKIN FUNCTION; STUDY DESIGN; BACTERIUM; DNA SEQUENCE; FEMALE; GENETICS; HIGH THROUGHPUT SEQUENCING; MALE; METHODOLOGY; MICROBIOLOGY; MICROFLORA; PROCEDURES; SENSITIVITY AND SPECIFICITY; SKIN;

BACTERIA; FEMALE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MALE; MICROBIOTA; RESEARCH DESIGN; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS, DNA; SKIN;

EID: 84977765268     PISSN: 0022202X     EISSN: 15231747     Source Type: Journal    
DOI: 10.1016/j.jid.2016.01.005     Document Type: Short Survey

References (23)

1. Belkaid, Y., Segre, J.A., Dialogue between skin microbiota and immunity. Science 346 (2014), 954–959.
2. Caporaso, J.G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F.D., Costello, E., et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7 (2010), 335–336.
3. Cogen, A.L., Yamasaki, K., Sanchez, K.M., Dorschner, R.A., Lai, Y., MacLeod, D.T., et al. Selective antimicrobial action is provided by phenol-soluble modulins derived from Staphylococcus epidermidis, a normal resident of the skin. J Invest Dermatol 130 (2010), 192–200.
4. Conlan, S., Kong, H.H., Segre, J.A., Species-level analysis of DNA sequence data from the NIH Human Microbiome Project. PloS One, 7, 2012, e47075.
5. DeSantis, T.Z., Hugenholtz, P., Larsen, N., Rojas, M., Brodie, E.L., Keller, K., et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72 (2006), 5069–5072.
6. Fredricks, D.N., Microbial ecology of human skin in health and disease. J Investig Dermatol Symp Proc 6 (2001), 167–169.
7. Goodrich, J.K., Di Rienzi, S.C., Poole, A.C., Koren, O., Walters, W.A., Caporaso, J.G., et al. Conducting a microbiome study. Cell 158 (2014), 250–262.
8. Grice, E.A., Kong, H.H., Conlan, S., Deming, C.B., Davis, J., Young, A.C., et al. Topographical and temporal diversity of the human skin microbiome. Science 324 (2009), 1190–1192.
9. Grice, E.A., Kong, H.H., Renaud, G., Young, A.C., NISC Comparative Sequencing Program, Bouffard, G.G., et al. A diversity profile of the human skin microbiota. Genome Res 18 (2008), 1043–1050.
10. Grice, E.A., Segre, J.A., The skin microbiome. Nat Rev Microbiol 9 (2011), 244–253.
11. Kong, H.H., Skin microbiome: genomics-based insights into the diversity and role of skin microbes. Trends Mol Med 17 (2011), 320–328.
12. Kong, H.H., Oh, J., Deming, C., Conlan, S., Grice, E.A., Beatson, M.A., et al. Temporal shifts in the skin microbiome associated with disease flares and treatment in children with atopic dermatitis. Genome Res 22 (2012), 850–859.
13. Kong, H.H., Segre, J.A., Skin microbiome: looking back to move forward. J Invest Dermatol 132 (2012), 933–939.
14. Leyden, J.J., McGinley, K.J., Nordstrom, K.M., Webster, G.F., Skin microflora. J Invest Dermatol 88 (1987), 65s–72s.
15. McOrist, A.L., Jackson, M., Bird, A.R., A comparison of five methods for extraction of bacterial DNA from human faecal samples. J Microbiol Methods 50 (2002), 131–139.
16. Nagy, I., Pivarcsi, A., Koreck, A., Szell, M., Urban, E., Kemeny, L., Distinct strains of Propionibacterium acnes induce selective human beta-defensin-2 and interleukin-8 expression in human keratinocytes through toll-like receptors. J Invest Dermatol 124 (2005), 931–938.
17. Oh, J., Conlan, S., Polley, E.C., Segre, J.A., Kong, H.H., Shifts in human skin and nares microbiota of healthy children and adults. Genome Med, 4, 2012, 77.
18. Oh, J., Freeman, A.F., NISC Comparative Sequencing Program, Park, M., Sokolic, R., Candotti, F., et al. The altered landscape of the human skin microbiome in patients with primary immunodeficiencies. Genome Res 23 (2013), 2103–2114.
19. Pruesse, E., Quast, C., Knittel, K., Fuchs, B.M., Ludwig, W., Peplies, J., et al. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35 (2007), 7188–7196.
20. Salter, S.J., Cox, M.J., Turek, E.M., Calus, S.T., Cookson, W.O., Moffatt, M.F., et al. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol, 12, 2014, 87.
21. Scharschmidt, T.C., List, K., Grice, E.A., Szabo, R., NISC Comparative Sequencing Program, Renaud, G., et al. Matriptase-deficient mice exhibit ichthyotic skin with a selective shift in skin microbiota. J Invest Dermatol 129 (2009), 2435–2442.
22. Schloss, P.D., Westcott, S.L., Ryabin, T., Hall, J.R., Hartmann, M., Hollister, E.B., et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75 (2009), 7537–7541.
23. Weiss, S., Amir, A., Hyde, E.R., Metcalf, J.L., Song, S.J., Knight, R., Tracking down the sources of experimental contamination in microbiome studies. Genome Biol, 15, 2014, 564.