The future of skin metagenomics

Research in Microbiology

Volumn 165, Issue 2, 2014, Pages 69-76

  Mathieu, Alban ^a,b   Vogel, Timothy M ^a   Simonet, Pascal ^a  

^a ECOLE CENTRALE DE LYON   (France)

^b LibraGen   (France)

Author keywords

Metagenomics; Skin microbial ecology; Skin microbiome

Indexed keywords

ARTICLE; BACTERIUM CULTURE; COSMETIC INDUSTRY; DENSITY; METAGENOMICS; MICROBIAL COMMUNITY; MICROBIOME; NONHUMAN; PRIORITY JOURNAL; SKIN; TAXONOMY;

BACTERIA (MICROORGANISMS);

METAGENOMICS; SKIN MICROBIAL ECOLOGY; SKIN MICROBIOME;

HUMANS; METAGENOMICS; MICROBIOTA; SKIN;

EID: 84896040879     PISSN: 09232508     EISSN: 17697123     Source Type: Journal    
DOI: 10.1016/j.resmic.2013.12.002     Document Type: Article

References (46)

1. Abubucker S., Segata N., Goll J., Schubert A.M., Izard J., Cantarel B.L., et al. Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS Comput Biol 2012, 8:e1002358.
2. Amann R., Ludwig W., Schleifer K. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Mol Biol Rev 1995, 59:143-169.
3. Binga E.K., Lasken R.S., Neufeld J.D. Something from (almost) nothing: the impact of multiple displacement amplification on microbial ecology. ISME J 2008, 2:233-241.
4. Blaser M.J., Dominguez-Bello M.G., Contreras M., Magris M., Hidalgo G., Estrada I., et al. Distinct cutaneous bacterial assemblages in a sampling of South American Amerindians and US residents. ISME J 2013, 7:85-95.
5. Capone K.A., Dowd S.E., Stamatas G.N., Nikolovski J. Diversity of the human skin microbiome early in life. J Invest Dermatol 2011, 131:2026-2032.
6. Casiano-Colon A., Marquis R.E. Role of the arginine deiminase system in protecting oral bacteria and an enzymatic basis for acid tolerance. Appl Environ Microbiol 1988, 54:1318-1324.
7. Chen K., Pachter L. Bioinformatics for whole-genome shotgun sequencing of microbial communities. PLoS Comput Biol 2005, 1:e24.
8. Chen Y.E., Tsao H. The skin microbiome: current perspectives and future challenges. J Am Acad Dermatol 2013, 69:143-155. e3.
9. Chiller K., Selkin B.A., Murakawa G.J. Skin microflora and bacterial infections of the skin. J Investig Dermatol Symp 2001, 6:170-174.
10. Claesson M.J., Jeffery I.B., Conde S., Power S.E., O'Connor E.M., Cusack S., et al. Gut microbiota composition correlates with diet and health in the elderly. Nature 2012, 488:178-184.
11. Cogen A.L., Yamasaki K., Muto J., Sanchez K.M., Crotty Alexander L., Tanios J., et al. Staphylococcus epidermidis antimicrobial δ-toxin (phenol-soluble modulin-γ) cooperates with host antimicrobial peptides to kill group a streptococcus. PLoS One 2010, 5:e8557.
12. Delmont T.O., Malandain C., Prestat E., Larose C., Monier J.-M., Simonet P., et al. Metagenomic mining for microbiologists. ISME J 2011, 5:1837-1843.
13. Dessinioti C., Katsambas A.D. The role of Propionibacterium acnes in acne pathogenesis: facts and controversies. Clin Dermatol 2010, 28:2-7.
14. Dominguez-Bello M.G., Costello E.K., Contreras M., Magris M., Hidalgo G., Fierer N., et al. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc Natl Acad Sci U S A 2010.
15. Eisen J.A. Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbes. PLoS Biol 2007, 5:e82.
16. Fierer N., Hamady M., Lauber C.L., Knight R. The influence of sex, handedness, and washing on the diversity of hand surface bacteria. Proc Natl Acad Sci U S A 2008, 105:17994-17999.
17. Fierer N., Lauber C.L., Zhou N., McDonald D., Costello E.K., Knight R. Forensic identification using skin bacterial communities. Proc Natl Acad Sci U S A 2010, 107:6477-6481.
18. Fitz-Gibbon S., Tomida S., Chiu B.-H., Nguyen L., Du C., Liu M., et al. Propionibacterium acnes strain populations in the human skin microbiome associated with acne. J Invest Dermatol 2013.
19. Fluhr J.W., Behne M.J., Brown B.E., Moskowitz D.G., Selden C., Mao-Qiang M., et al. Stratum corneum acidification in neonatal skin: secretory phospholipase A2 and the sodium/hydrogen antiporter-1 acidify neonatal rat stratum corneum. J Invest Dermatol 2004, 320-329.
20. Foulongne V., Sauvage V., Hebert C., Dereure O., Cheval J., Gouilh M.A., et al. Human skin microbiota: high diversity of DNA viruses identified on the human skin by high throughput sequencing. PloS One 2012, 7:e38499.
21. Fredricks D.N. Microbial ecology of human skin in health and disease. J Investig Dermatol Symp Proc 2001, 6:167-169.
22. Gao Q., Garcia-Pichel F. Microbial ultraviolet sunscreens. Nat Rev Microbiol 2011, 791-802.
23. Gao Z., Tseng C., Pei Z., Blaser M.J. Molecular analysis of human forearm superficial skin bacterial biota. Proc Natl Acad Sci U S A 2007, 104:2927-2932.
24. Gao Z., Tseng C., Strober B.E., Pei Z., Blaser M.J. Substantial alterations of the cutaneous bacterial biota in psoriatic lesions. PLoS One 2008, 3:e2719.
25. 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 2009, 324:1190-1192.
26. Grice E.A., Kong H.H., Renaud G., Young A.C., Bouffard G.G., Blakesley R.W., et al. A diversity profile of the human skin microbiota. Genome Res 2008, 18:1043-1050.
27. Grice E.A., Segre J.A. The skin microbiome. Nat Rev Microbiol 2011, 9:244-253.
28. Handelsman J., Rondon M.R., Brady S.F., Clardy J., Goodman R.M. Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem Biol 1998, 5:R245-R249.
29. Kong H.H. Skin microbiome: genomics-based insights into the diversity and role of skin microbes. Trends Mol Med 2011, 17:320-328.
30. Kong H.H., Oh J., Deming C., Conlan S., Grice E.A., Beatson M., et al. Temporal shifts in the skin microbiome associated with atopic dermatitis disease flares and treatment. Genome Res 2012, 22:850-859.
31. Kuczynski J., Lauber C.L., Walters W.A., Parfrey L.W., Clemente J.C., Gevers D., et al. Experimental and analytical tools for studying the human microbiome. Nat Rev Genet 2011, 13:47-58.
32. Mathieu A., Delmont T.O., Vogel T.M., Robe P., Nalin R., Simonet P. Life on human surfaces: skin metagenomics. PLoS One 2013, 8:e65288.
33. Meadow J.F., Bateman A.C., Herkert K.M., O'Connor T.K., Green J.L. Significant changes in the skin microbiome mediated by the sport of roller derby. PeerJ 2013, 1:e53.
34. Olsen G.J., Lane D.J., Giovannoni S.J., Pace N.R., Stahl D.A. Microbial ecology and evolution: a ribosomal RNA approach. Annu Rev Microbiol 1986, 40:337-365.
35. Paulino L.C., Tseng C.-H., Strober B.E., Blaser M.J. Molecular analysis of fungal microbiota in samples from healthy human skin and psoriatic lesions. J Clin Microbiol 2006, 44:2933-2941.
36. Peterson J., Garges S., Giovanni M., McInnes P., Wang L., Schloss J.A., et al. The NIH human microbiome project. Genome Res 2009, 19:2317-2323.
37. Radner F.P., Grond S., Haemmerle G., Lass A., Zechner R. Fat in the skin. Dermato-endocrinology 2011, 3:77-83.
38. Sokol H., Pigneur B., Watterlot L., Lakhdari O., Bermúdez-Humarán L.G., Gratadoux J.-J., et al. Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. Proc Natl Acad Sci U S A 2008, 105:16731-16736.
39. Sommer M.O.A., Dantas G. Antibiotics and the resistant microbiome. Curr Opin Microbiol 2011, 14:556-563.
40. Staudinger T., Pipal A., Redl B. Molecular analysis of the prevalent microbiota of human male and female forehead skin compared to forearm skin and the influence of make-up. J Appl Microbiol 2011, 110:1381-1389.
41. Structure, function and diversity of the healthy human microbiome. Nature 2012, 486:207-214. The Human Microbiome Project Consortium.
42. Thomas W.R., Smith W.-A., Hales B.J. The allergenic specificities of the house dust mite. Chang Gung Med J 2004, 27:563-569.
43. Wilson M. Microbial Inhabitants of Humans: Their Ecology and Role in Health and Disease 2004, Cambridge University Press.
44. Yilmaz S., Allgaier M., Hugenholtz P. Multiple displacement amplification compromises quantitative analysis of metagenomes. Nat Meth 2010, 7:943-944.
45. Zeeuwen P.L., Boekhorst J., Bogaard E.H.van den, Koning H.D.de, Kerkhof P.M.van de, Saulnier D.M., et al. Microbiome dynamics of human epidermis following skin barrier disruption. Genome Biol 2012, 13:R101.
46. Zhu B., Wang X., Li L. Human gut microbiome: the second genome of human body. Protein Cell 2010, 1:718-725.