Life on Human Surfaces: Skin Metagenomics

PLoS ONE

Volumn 8, Issue 6, 2013, Pages

  Mathieu, Alban ^a,b   Delmont, Tom O ^a   Vogel, Timothy M ^a   Robe, Patrick ^b   Nalin, Renaud ^b,c   Simonet, Pascal ^a  

^a ECOLE CENTRALE DE LYON   (France)

^b LibraGen   (France)

^c NONE

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ADULT; ARTICLE; BACTERIAL COLONIZATION; CONTROLLED STUDY; CORYNEBACTERIUM; HIGH THROUGHPUT SEQUENCING; HUMAN; MALE; METAGENOMICS; MICROBIAL COMMUNITY; POLYMERASE CHAIN REACTION; PROPIONIBACTERIUM; SKIN FLORA; SKIN SURFACE; STAPHYLOCOCCUS;

ADULT; BACTERIA; BASE SEQUENCE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MALE; METAGENOMICS; MICROBIOTA; MOLECULAR SEQUENCE ANNOTATION; MOLECULAR SEQUENCE DATA; PRINCIPAL COMPONENT ANALYSIS; SKIN;

BACTERIA (MICROORGANISMS); CORYNEBACTERIUM; PROPIONIBACTERIUM; STAPHYLOCOCCUS;

EID: 84878940197     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0065288     Document Type: Article

References (17)

1. Fredricks DN, (2001) Microbial Ecology of Human Skin in Health and Disease. J Investig Dermatol Symp Proc 6: 167-169.
2. Kuczynski J, Lauber CL, Walters WA, Parfrey LW, Clemente JC, et al. (2011) Experimental and analytical tools for studying the human microbiome. Nature Reviews Genetics 13: 47-58 doi:10.1038/nrg3129.
3. Costello EK, Lauber CL, Hamady M, Fierer N, Gordon JI, et al. (2009) Bacterial Community Variation in Human Body Habitats Across Space and Time. Science 326: 1694-1697 doi:10.1126/science.1177486.
4. Fierer N, Lauber CL, Zhou N, McDonald D, Costello EK, et al. (2010) Forensic identification using skin bacterial communities. Proceedings of the National Academy of Sciences 107: 6477-6481 doi:10.1073/pnas.1000162107.
5. Fierer N, Hamady M, Lauber CL, Knight R, (2008) The influence of sex, handedness, and washing on the diversity of hand surface bacteria. Proc Natl Acad Sci U S A 105: 17994-17999 doi:10.1073/pnas.0807920105.
6. Gao Z, Tseng C, Pei Z, Blaser MJ, (2007) Molecular analysis of human forearm superficial skin bacterial biota. Proceedings of the National Academy of Sciences 104: 2927-2932 doi:10.1073/pnas.0607077104.
7. 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.
8. Fitz-Gibbon S, Tomida S, Chiu B-H, Nguyen L, Du C, et al. (2013) Propionibacterium Acnes Strain Populations in the Human Skin Microbiome Associated with Acne. J Invest Dermatol. doi:10.1038/jid.2013.21.
9. Griffiths RI, Whiteley AS, O'Donnell AG, Bailey MJ, (2000) Rapid method for coextraction of DNA and RNA from natural environments for analysis of ribosomal DNA-and rRNA-based microbial community composition. Applied and Environmental Microbiology 66: 5488.
10. Li W, Godzik A, (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22: 1658-1659 doi:10.1093/bioinformatics/btl158.
11. Meyer F, Paarmann D, D'Souza M, Olson R, Glass E, et al. (2008) The metagenomics RAST server- a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9: 386 doi:10.1186/1471-2105-9-386.
12. Huson DH, Auch AF, Qi J, Schuster SC, (2007) MEGAN analysis of metagenomic data. Genome Res 17: 377-386 doi:10.1101/gr.5969107.
13. Delmont TO, Malandain C, Prestat E, Larose C, Monier J-M, et al. (2011) Metagenomic mining for microbiologists. ISME J 5: 1837-1843.
14. Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang H-Y, et al. (2005) The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res 33: 5691-5702 doi:10.1093/nar/gki866.
15. Wilson M (2004) Microbial Inhabitants Of Humans: Their Ecology And Role In Health And Disease. Cambridge University Press. 476 p.
16. Radner FP, Grond S, Haemmerle G, Lass A, Zechner R, (2011) Fat in the skin. Dermatoendocrinol 3: 77-83 doi:10.4161/derm.3.2.15472.
17. Casiano-Colon A, Marquis RE, (1988) Role of the arginine deiminase system in protecting oral bacteria and an enzymatic basis for acid tolerance. Appl Environ Microbiol 54: 1318-1324.