Nestle FO, Kaplan DH, Barker J: Psoriasis. N Engl J Med. 2009, 361: 496-509. 10.1056/NEJMra0804595.
Article
CAS
PubMed
Google Scholar
Fahlen A, Engstrand L, Baker BS, Powles A, Fry L: Comparison of bacterial microbiota in skin biopsies from normal and psoriatic skin. Arch Dermatol Res. 2012, 304: 15-22. 10.1007/s00403-011-1189-x.
Article
CAS
PubMed
Google Scholar
Paulino LC, Tseng CH, Strober BE, Blaser MJ: Molecular analysis of fungal microbiota in samples from healthy human skin and psoriatic lesions. J Clin Microbiol. 2006, 44: 2933-2941. 10.1128/JCM.00785-06.
Article
PubMed Central
CAS
PubMed
Google Scholar
Paulino LC, Tseng CH, Blaser MJ: Analysis of Malassezia microbiota in healthy superficial human skin and in psoriatic lesions by multiplex real-time PCR. FEMS Yeast Res. 2008, 8: 460-471. 10.1111/j.1567-1364.2008.00359.x.
Article
CAS
PubMed
Google Scholar
Gao Z, Tseng CH, Strober BE, Pei Z, Blaser MJ: Substantial alterations of the cutaneous bacterial biota in psoriatic lesions. PLoS One. 2008, 3: e2719-10.1371/journal.pone.0002719.
Article
PubMed Central
PubMed
Google Scholar
Costello EK, Lauber CL, Hamady M, Fierer N, Gordon JI, Knight R: Bacterial community variation in human body habitats across space and time. Science. 2009, 326: 1694-1697. 10.1126/science.1177486.
Article
PubMed Central
CAS
PubMed
Google Scholar
Grice EA, Segre JA: The human microbiome: our second genome. Annu Rev Genomics Hum Genet. 2012, 13: 151-170. 10.1146/annurev-genom-090711-163814.
Article
PubMed Central
CAS
PubMed
Google Scholar
Grice EA, Kong HH, Conlan S, Deming CB, Davis J, Young AC, Bouffard GG, Blakesley RW, Murray PR, Green ED, Turner ML, Segre JA, NISC Comparative Sequencing Program: Topographical and temporal diversity of the human skin microbiome. Science. 2009, 324: 1190-1192. 10.1126/science.1171700.
Article
PubMed Central
CAS
PubMed
Google Scholar
Blaser MJ, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Estrada I, Gao Z, Clemente JC, Costello EK, Knight R: Distinct cutaneous bacterial assemblages in a sampling of south American Amerindians and US residents. ISME J. 2013, 7: 85-95. 10.1038/ismej.2012.81.
Article
PubMed Central
CAS
PubMed
Google Scholar
Fierer N, Lauber CL, Zhou N, McDonald D, Costello EK, Knight R: Forensic identification using skin bacterial communities. Proc Natl Acad Sci USA. 2010, 107: 6477-6481. 10.1073/pnas.1000162107.
Article
PubMed Central
CAS
PubMed
Google Scholar
Dominguez-Bello MG, Costello EK, Contreras M, Magris M, Hidalgo G, Fierer N, Knight R: Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc Natl Acad Sci USA. 2010, 107: 11971-11975. 10.1073/pnas.1002601107.
Article
PubMed Central
PubMed
Google Scholar
Redel H, Gao Z, Li H, Alekseyenko AV, Zhou Y, Perez-Perez GI, Weinstock G, Sodergren E, Blaser MJ: Quantitation and composition of cutaneous microbiota in diabetic and nondiabetic men. J Infect Dis. 2013, 207: 1105-1114. 10.1093/infdis/jit005.
Article
PubMed Central
CAS
PubMed
Google Scholar
Gardner SE, Hillis SL, Heilmann K, Segre JA, Grice EA: The neuropathic diabetic foot ulcer microbiome is associated with clinical factors. Diabetes. 2013, 62: 923-930. 10.2337/db12-0771.
Article
PubMed Central
CAS
PubMed
Google Scholar
Kong HH, Oh J, Deming C, Conlan S, Grice EA, Beatson MA, Nomicos E, Polley EC, Komarow HD, Murray PR, Turner ML, Segre JA, NISC Comparative Sequence Program: Temporal shifts in the skin microbiome associated with disease flares and treatment in children with atopic dermatitis. Genome Res. 2012, 22: 850-859. 10.1101/gr.131029.111.
Article
PubMed Central
CAS
PubMed
Google Scholar
Grice EA, Segre JA: Interaction of the microbiome with the innate immune response in chronic wounds. Adv Exp Med Biol. 2012, 946: 55-68. 10.1007/978-1-4614-0106-3_4.
Article
PubMed Central
CAS
PubMed
Google Scholar
Li K, Bihan M, Yooseph S, Methe BA: Analyses of the microbial diversity across the human microbiome. PLoS One. 2012, 7: e32118-10.1371/journal.pone.0032118.
Article
PubMed Central
CAS
PubMed
Google Scholar
Fitz-Gibbon S, Tomida S, Chiu BH, Nguyen L, Du C, Liu M, Elashoff D, Erfe MC, Loncaric A, Kim J, Modlin RL, Miller JF, Sodergren E, Craft N, Weinstock GM, Li H: Propionibacterium acnes strain populations in the human skin microbiome associated with acne. J Invest Dermatol. 2013, 133: 2152-2160. 10.1038/jid.2013.21.
Article
PubMed Central
CAS
PubMed
Google Scholar
The Human Microbiome Project Consortium: A framework for human microbiome research. Nature. 2012, 486: 215-221. 10.1038/nature11209.
Article
Google Scholar
The Human Microbiome Project Consortium: Structure, function and diversity of the healthy human microbiome. Nature. 2012, 486: 207-214. 10.1038/nature11234.
Article
PubMed Central
Google Scholar
Gao Z, Perez-Perez GI, Chen Y, Blaser MJ: Quantitation of major human cutaneous bacterial and fungal populations. J Clin Microbiol. 2010, 48: 3575-3581. 10.1128/JCM.00597-10.
Article
PubMed Central
CAS
PubMed
Google Scholar
Jumpstart Consortium Human Microbiome Project Data Generation Working Group: Evaluation of 16S rDNA-based community profiling for human microbiome research. PLoS One. 2012, 7: e39315-10.1371/journal.pone.0039315.
Article
PubMed Central
Google Scholar
Gao Z, Tseng CH, Pei Z, Blaser MJ: Molecular analysis of human forearm superficial skin bacterial biota. Proc Natl Acad Sci USA. 2007, 104: 2927-2932. 10.1073/pnas.0607077104.
Article
PubMed Central
CAS
PubMed
Google Scholar
Li K, Venter E, Yooseph S, Stockwell TB, Eckerle LD, Denison MR, Spiro DJ, Methe BA: ANDES: statistical tools for the ANalyses of DEep sequencing. BMC Res Notes. 2010, 3: 199-10.1186/1756-0500-3-199.
Article
PubMed Central
PubMed
Google Scholar
Li K, Brownley A, Stockwell TB, Beeson K, McIntosh TC, Busam D, Ferriera S, Murphy S, Levy S: Novel computational methods for increasing PCR primer design effectiveness in directed sequencing. BMC Bioinforma. 2008, 9: 191-10.1186/1471-2105-9-191.
Article
Google Scholar
Grice EA, Kong HH, Renaud G, Young AC, Bouffard GG, Blakesley RW, Wolfsberg TG, Turner ML, Segre JA: A diversity profile of the human skin microbiota. Genome Res. 2008, 18: 1043-1050. 10.1101/gr.075549.107.
Article
PubMed Central
CAS
PubMed
Google Scholar
Cho I, Yamanishi S, Cox L, Methé BA, Zavadil J, Li K, Gao Z, Mahana D, Raju K, Teitler I, Li H, Alekseyenko AV, Blaser MJ: Antibiotics in early life alter the murine colonic microbiome and adiposity. Nature. 2012, 488: 621-626. 10.1038/nature11400.
Article
PubMed Central
CAS
PubMed
Google Scholar
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R: QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010, 7: 335-336. 10.1038/nmeth.f.303.
Article
PubMed Central
CAS
PubMed
Google Scholar
Edgar RC: Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010, 26: 2460-2461. 10.1093/bioinformatics/btq461.
Article
CAS
PubMed
Google Scholar
Wang Q, Garrity GM, Tiedje JM, Cole JR: Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol. 2007, 73: 5261-5267. 10.1128/AEM.00062-07.
Article
PubMed Central
CAS
PubMed
Google Scholar
Caporaso JG, Bittinger K, Bushman FD, DeSantis TZ, Andersen GL, Knight R: PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics. 2010, 26: 266-267. 10.1093/bioinformatics/btp636.
Article
PubMed Central
CAS
PubMed
Google Scholar
Price MN, Dehal PS, Arkin AP: FastTree 2–approximately maximum-likelihood trees for large alignments. PLoS One. 2010, 5: e9490-10.1371/journal.pone.0009490.
Article
PubMed Central
PubMed
Google Scholar
Lozupone C, Knight R: UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol. 2005, 71: 8228-8235. 10.1128/AEM.71.12.8228-8235.2005.
Article
PubMed Central
CAS
PubMed
Google Scholar
R Development Core Team: R: A Language and Environment for Statistical Computing. 2012, Vienna, Austria: R Foundation for Statistical Computing
Google Scholar
Haas BJ, Gevers D, Earl AM, Feldgarden M, Ward DV, Giannoukos G, Ciulla D, Tabbaa D, Highlander SK, Sodergren E, Methé B, DeSantis TZ, Petrosino JF, Knight R, Birren BW, Human Microbiome Consortium: Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res. 2011, 21: 494-504. 10.1101/gr.112730.110.
Article
PubMed Central
CAS
PubMed
Google Scholar
Dray S, Dufour A-B: The ade4 package: implementing the duality diagram for ecologists. J Stat Softw. 2007, 22: 1-20.
Article
Google Scholar
Cailliez F: The analytical solution of the additive constant problem. Psychometrika. 1983, 48: 305-310. 10.1007/BF02294026.
Article
Google Scholar
Benjamini Y, Hochberg Y: Controlling the false discovery rate - a practical and powerful approach to multiple testing. J R Stat Soc Ser B. 1995, 57: 289-300.
Google Scholar
Sing T, Sander O, Beerenwinkel N, Lengauer T: ROCR: visualizing classifier performance in R. Bioinformatics. 2005, 21: 3940-3941. 10.1093/bioinformatics/bti623.
Article
CAS
PubMed
Google Scholar
Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, Hansen T, Hattori M, Hayashi T, Kleerebezem M, Kurokawa K, Leclerc M, Levenez F, Manichanh C, Nielsen HB, Nielsen T, Pons N, Poulain J, Qin J, Sicheritz-Ponten T, Tims S: Enterotypes of the human gut microbiome. Nature. 2011, 473: 174-180. 10.1038/nature09944.
Article
PubMed Central
CAS
PubMed
Google Scholar
Reynolds A, Richards G, de la Iglesia B, Rayward-Smith V: Clustering rules: a comparison of partitioning and hierarchical clustering algorithms. J Math Model Algorithm. 1992, 5: 475-504.
Article
Google Scholar
Calinski R, Harabasz J: A dendrite method for cluster analysis. Comm Stat. 1974, 3: 1-27.
Article
Google Scholar
Tibshirani R, Walther G, Hastie T: Estimating the number of clusters in a data set via the gap statistic. J R Stat Soc Ser B. 2001, 63: 411-423. 10.1111/1467-9868.00293.
Article
Google Scholar
Anderson MJ: A new method for non-parametric multivariate analysis of variance. Austral Ecol. 2001, 26: 32-46.
Google Scholar
Oksanen J, Kindt R, Legendre P, O’Hara B, Stevens MHH, Oksanen MJ, Suggests M: The vegan package. Community ecology package. [http://r-forge.r-project.org/projects/vegan/]
Nam RK, Toi A, Klotz LH, Trachtenberg J, Jewett MA, Appu S, Loblaw DA, Sugar L, Narod SA, Kattan MW: Assessing individual risk for prostate cancer. J Clin Oncol. 2007, 25: 3582-3588. 10.1200/JCO.2007.10.6450.
Article
CAS
PubMed
Google Scholar
Statnikov A, Alekseyenko AV, Li Z, Henaff M, Perez-Perez GI, Blaser MJ, Aliferis CF: Microbiomic signatures of psoriasis: feasibility and methodology comparison. Sci Rep. 2013, 3: 2620-
Article
PubMed Central
PubMed
Google Scholar
Lozupone C, Lladser ME, Knights D, Stombaugh J, Knight R: UniFrac: an effective distance metric for microbial community comparison. ISME J. 2011, 5: 169-172. 10.1038/ismej.2010.133.
Article
PubMed Central
PubMed
Google Scholar
Reid NM, Carstens BC: Phylogenetic estimation error can decrease the accuracy of species delimitation: a Bayesian implementation of the general mixed Yule-coalescent model. BMC Evol Biol. 2012, 12: 196-10.1186/1471-2148-12-196.
Article
PubMed Central
PubMed
Google Scholar
Ikeda S, Takahashi H, Suga Y, Eto H, Etoh T, Okuma K, Takahashi K, Kanbara T, Seishima M, Morita A, Imai Y, Kanekura T: Therapeutic depletion of myeloid lineage leukocytes in patients with generalized pustular psoriasis indicates a major role for neutrophils in the immunopathogenesis of psoriasis. J Am Acad Dermatol. 2013, 68: 609-617. 10.1016/j.jaad.2012.09.037.
Article
CAS
PubMed
Google Scholar
Nickoloff BJ, Nestle FO: Recent insights into the immunopathogenesis of psoriasis provide new therapeutic opportunities. J Clin Invest. 2004, 113: 1664-1675.
Article
PubMed Central
CAS
PubMed
Google Scholar
Mak RK, Hundhausen C, Nestle FO: Progress in understanding the immunopathogenesis of psoriasis. Actas Dermosifiliogr. 2009, 100 (Suppl 2): 2-13.
Article
PubMed Central
PubMed
Google Scholar
Loffredo S, Ayala F, Marone G, Delfino G, Stranges S, Marone G: Immunopathogenesis of psoriasis and pharmacological perspectives. J Rheumatol Suppl. 2009, 83: 9-11. 10.3899/jrheum.090210.
Article
CAS
PubMed
Google Scholar
Di Cesare A, Di Meglio P, Nestle FO: The IL-23/Th17 axis in the immunopathogenesis of psoriasis. J Invest Dermatol. 2009, 129: 1339-1350. 10.1038/jid.2009.59.
Article
CAS
PubMed
Google Scholar