The intersection of microbiome and host at the skin interface: Genomic- and metagenomic-based insights

Genome Research

Volumn 25, Issue 10, 2015, Pages 1514-1520

  Grice, Elizabeth A ^a  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIINFECTIVE AGENT; COSMETIC;

DIAGNOSTIC TEST; ECOLOGY; HOST; HUMAN; HYGIENE PRODUCT; METABOLOMICS; METAGENOMICS; MICROBIAL COMMUNITY; MICROBIOME; MICROORGANISM; NONHUMAN; PRIORITY JOURNAL; REVIEW; SKIN; SKIN DISEASE; ANIMAL; BACTERIAL SKIN DISEASE; FORECASTING; GENOMICS; MICROBIOLOGY; MICROFLORA; VIROLOGY;

ANIMALS; FORECASTING; GENOMICS; HUMANS; METAGENOMICS; MICROBIOTA; SKIN; SKIN DISEASES, BACTERIAL;

EID: 84942934681     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.191320.115     Document Type: Review

References (48)

1. Amber K, McLeodMP, Nouri K. 2013. The Merkel cell polyomavirus and its involvement in Merkel cell carcinoma. Dermatol Surg 39: 232-238.
2. Angly F, Rodriguez-Brito B, Bangor D, McNairnie P, Breitbart M, Salamon P, Felts B, Nulton J, Mahaffy J, Rohwer F. 2005. PHACCS, an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information. BMC Bioinformatics 6: 41.
3. Arron ST, Dimon MT, Li Z, Johnson ME, A Wood T, Feeney L, G Angeles J, Lafyatis R, Whitfield ML. 2014. High Rhodotorula sequences in skin transcriptome of patients with diffuse systemic sclerosis. J Invest Dermatol 134: 2138-2145.
4. Austin M, Mellow M, Tierney WM. 2014. Fecal microbiota transplantation in the treatment of Clostridium difficile infections. Am J Med 127: 479-483.
5. Bouslimani A, Porto C, Rath CM, Wang M, Guo Y, Gonzalez A, Berg-Lyon D, Ackermann G, Moeller Christensen GJ, Nakatsuji T, et al. 2015. Molecular cartography of the human skin surface in 3D. Proc Natl Acad Sci 112: E2120-E2129.
6. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI, et al. 2010. QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7: 335-336.
7. Chehoud C, Rafail S, Tyldsley AS, Seykora JT, Lambris JD, Grice EA. 2013. Complement modulates the cutaneous microbiome and inflammatory milieu. Proc Natl Acad Sci 110: 15061-15066.
8. Costello EK, Lauber CL, Hamady M, Fierer N, Gordon JI, Knight R. 2009. Bacterial community variation in human body habitats across space and time. Science 326: 1694-1697.
9. Dimon MT, Wood HM, Rabbitts PH, LiaoW, Cho RJ, Arron ST. 2014. No evidence for integrated viral DNA in the genome sequence of cutaneous squamous cell carcinoma. J Invest Dermatol 134: 2055-2057.
10. Eishi Y. 2013. Etiologic aspect of sarcoidosis as an allergic endogenous infection caused by Propionibacterium acnes. BioMed Res Int 2013: 935289.
11. Feng H, Shuda M, Chang Y, Moore PS. 2008. Clonal integration of a polyomavirus in human Merkel cell carcinoma. Science 319: 1096-1100.
12. Findley K, Oh J, Yang J, Conlan S, Deming C, Meyer JA, Schoenfeld D, Nomicos E, Park M, Becker J, et al. 2013. Topographic diversity of fungal and bacterial communities in human skin. Nature 498: 367-370.
13. Fitz-Gibbon S, Tomida S, Chiu BH, Nguyen L, Du C, Liu M, Elashoff D, Erfe MC, Loncaric A, Kim J, et al. 2013. Propionibacterium acnes strain populations in the human skin microbiome associated with acne. J Invest Dermatol 133: 2152-2160.
14. Flores GE, Caporaso JG, Henley JB, Rideout JR, Domogala D, Chase J, Leff JW, Vazquez-Baeza Y, Gonzalez A, Knight R, et al. 2014. Temporal variability is a personalized feature of the human microbiome. Genome Biol 15: 531.
15. Foulongne V, Sauvage V, Hebert C, Dereure O, Cheval J, Gouilh MA, Pariente K, Segondy M, Burguiere A, Manuguerra JC, et al. 2012. Human skin microbiota: high diversity of DNA viruses identified on the human skin by high throughput sequencing. PLoS One 7: e38499.
16. Furukawa A, Uchida K, Ishige Y, Ishige I, Kobayashi I, Takemura T, Yokoyama T, Iwai K, Watanabe K, Shimizu S, et al. 2009. Characterization of Propionibacterium acnes isolates from sarcoid and non-sarcoid tissues with special reference to cell invasiveness, serotype, and trigger factor gene polymorphism. Microb Pathog 46: 80-87.
17. Gao Z, Tseng CH, Pei Z, Blaser MJ. 2007. Molecular analysis of human forearm superficial skin bacterial biota. Proc Natl Acad Sci 104: 2927-2932.
18. Gribbon EM, Cunliffe WJ, Holland KT. 1993. Interaction of Propionibacterium acnes with skin lipids in vitro. J Gen Microbiol 139: 1745-1751.
19. Grice EA, Segre JA. 2011. The skin microbiome. Nat Rev Microbiol 9: 244-253.
20. Grice EA, Kong HH, Conlan S, Deming CB, Davis J, Young AC, Bouffard GG, BlakesleyRW, Murray PR, Green ED, et al. 2009. Topographical and temporal diversity of the human skin microbiome. Science 324: 1190-1192.
21. Grice EA, Snitkin ES, Yockey LJ, Bermudez DM, Liechty KW, Segre JA. 2010. Longitudinal shift in diabetic wound microbiota correlates with prolonged skin defense response. Proc Natl Acad Sci 107: 14799-14804.
22. Holmfeldt K, Solonenko N, Shah M, Corrier K, Riemann L, Verberkmoes NC, Sullivan MB. 2013. Twelve previously unknown phage genera are ubiquitous in global oceans. Proc Natl Acad Sci 110: 12798-12803.
23. The Human Microbiome Project Consortium. 2012. Structure, function and diversity of the healthy human microbiome. Nature 486: 207-214.
24. Kobayashi T, Glatz M, Horiuchi K, Kawasaki H, Akiyama H, Kaplan DH, Kong HH, Amagai M, Nagao K. 2015. Dysbiosis and Staphylococcus aureus colonization drives inflammation in atopic dermatitis. Immunity 42: 756-766.
25. Kong HH, Oh J, Deming C, Conlan S, Grice EA, Beatson MA, Nomicos E, Polley EC, Komarow HD, Murray PR, et al. 2012. Temporal shifts in the skin microbiome associated with disease flares and treatment in children with atopic dermatitis. Genome Res 22: 850-859.
26. Lane DJ, Pace B, Olsen GJ, Stahl DA, Sogin ML, Pace NR. 1985. Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc Natl Acad Sci 82: 6955-6959.
27. Leyden JJ, Marples RR, Mills OH Jr, Kligman AM. 1973. Gram-negative folliculitis: a complication of antibiotic therapy in acne vulgaris. Br J Dermatol 88: 533-538.
28. Maurice CF, Haiser HJ, Turnbaugh PJ. 2013. Xenobiotics shape the physiology and gene expression of the active human gut microbiome. Cell 152: 39-50.
29. Minot S, Sinha R, Chen J, Li H, Keilbaugh SA, Wu GD, Lewis JD, Bushman FD. 2011. The human gut virome: inter-individual variation and dynamic response to diet. Genome Res 21: 1616-1625.
30. Minot S, Grunberg S, Wu GD, Lewis JD, Bushman FD. 2012. Hypervariable loci in the human gut virome. Proc Natl Acad Sci 109: 3962-3966.
31. Naik S, Bouladoux N, Wilhelm C, Molloy MJ, Salcedo R, Kastenmuller W, Deming C, Quinones M, Koo L, Conlan S, et al. 2012. Compartmentalized control of skin immunity by resident commensals. Science 337: 1115-1119.
32. Naik S, Bouladoux N, Linehan JL, Han SJ, Harrison OJ, Wilhelm C, Conlan S, Himmelfarb S, Byrd AL, Deming C, et al. 2015. Commensal-dendriticcell interaction specifies a unique protective skin immune signature. Nature 520: 104-108.
33. Nakatsuji T, Chiang HI, Jiang SB, Nagarajan H, Zengler K, Gallo RL. 2013. The microbiome extends to subepidermal compartments of normal skin. Nat Commun 4: 1431.
34. Nikkari T. 1974. Comparative chemistry of sebum. J Invest Dermatol 62: 257-267.
35. Oh J, Freeman AF, Park M, Sokolic R, Candotti F, Holland SM, Segre JA, Kong HH. 2013. The altered landscape of the human skin microbiome in patients with primary immunodeficiencies. Genome Res 23: 2103-2114.
36. Oh J, Byrd AL, Deming C, Conlan S, Program NCS, Kong HH, Segre JA, Program NCS. 2014. Biogeography and individuality shape function in the human skin metagenome. Nature 514: 59-64.
37. Palm NW,deZoeteMR,CullenTW,BarryNA,Stefanowski J,HaoL,DegnanPH, Hu J, Peter I, ZhangW, et al. 2014. Immunoglobulin A coating identifies colitogenic bacteria in inflammatory bowel disease. Cell 158: 1000-1010.
38. Pillsbury DM, Kligman AM. 1954. Some current problems in cutaneous bacteriology. In Modern trends in dermatology (ed. MacKenna RMB), pp. 187-213. Butterworth, London.
39. Reyes A, Haynes M, Hanson N, Angly FE, Heath AC, Rohwer F, Gordon JI. 2010. Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature 466: 334-338.
40. Ridky TW, Chow JM, Wong DJ, Khavari PA. 2010. Invasive three-dimensional organotypic neoplasia from multiple normal human epithelia. Nat Med 16: 1450-1455.
41. Saidha S, Sotirchos ES, Eckstein C. 2012. Etiology of sarcoidosis: does infection play a role? Yale J Biol Med 85: 133-141.
42. Saunders CW, Scheynius A, Heitman J. 2012. Malassezia fungi are specialized to live on skin and associated with dandruff, eczema, and other skin diseases. PLoS Pathog 8: e1002701.
43. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, et al. 2009. Introducing mothur: open-source, platform-independent, community- supported software for describing and comparing microbial communities. Appl Environ Microbiol 75: 7537-7541.
44. Seok J, Warren HS, Cuenca AG, Mindrinos MN, Baker HV, Xu W, Richards DR, McDonald-Smith GP, Gao H, Hennessy L, et al. 2013. Genomic responses in mouse models poorly mimic human inflammatory diseases. Proc Natl Acad Sci 110: 3507-3512.
45. Sood RF, Gu H, Djukovic D, Deng L, Ga M, Muffley LA, Raftery D, Hocking AM. 2015. Targeted metabolic profiling of wounds in diabetic and nondiabetic mice. Wound Repair Regen 23: 423-434.
46. van der Zee HH, Laman JD, Boer J, Prens EP. 2012. Hidradenitis suppurativa: viewpoint on clinical phenotyping, pathogenesis and novel treatments. Exp Dermatol 21: 735-739.
47. Weide B, Walz T, Garbe C. 2000. Is morphoea caused by Borrelia burgdorferi? A review. Br J Dermatol 142: 636-644.
48. Wylie KM, Mihindukulasuriya KA, Zhou Y, Sodergren E, Storch GA, Weinstock GM. 2014. Metagenomic analysis of double-stranded DNA viruses in healthy adults. BMC Biol 12: 71.