Quantitation and composition of cutaneous microbiota in diabetic and nondiabetic men

Journal of Infectious Diseases

Volumn 207, Issue 7, 2013, Pages 1105-1114

  Redel, Henry ^a   Gao, Zhan ^a   Li, Huilin ^a   Alekseyenko, Alexander V ^a   Zhou, Yanjiao ^a   Perez Perez, Guillermo I ^a,b   Weinstock, George ^a   Sodergren, Erica ^a   Blaser, Martin J ^a,b  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b NEW YORK UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

cutaneous; diabetic foot; microbiome; microbiota; Staphylococcus; Staphylococcus aureus

Indexed keywords

ANTIBIOTIC AGENT; HYDROXYMETHYLGLUTARYL COENZYME A REDUCTASE INHIBITOR; NONSTEROID ANTIINFLAMMATORY AGENT; RNA 16S;

ADULT; AGED; ARTICLE; BACTERIAL COUNT; CASE CONTROL STUDY; CLINICAL ARTICLE; CONTROLLED STUDY; DIABETIC FOOT; FUNGUS; HUMAN; HUMAN TISSUE; INFECTION RISK; MALE; MICROBIAL DIVERSITY; OUTPATIENT; PRIORITY JOURNAL; PUBLIC HOSPITAL; QUANTITATIVE ANALYSIS; RNA SEQUENCE; SKIN EXAMINATION; SKIN FLORA; SPECIES COMPOSITION; STAPHYLOCOCCUS AUREUS;

EID: 84874699605     PISSN: 00221899     EISSN: None     Source Type: Journal    
DOI: 10.1093/infdis/jit005     Document Type: Article

References (44)

1. Lipsky BA, Berendt AR, Cornia PB, et al. 2012 Infectious Diseases Society of America clinical practice guideline for the diagnosis and treatment of diabetic foot infections. Clin Infect Dis 2012; 54: e132-73.
2. Ramsey SD, Newton K, Blough D, et al. Incidence, outcomes, and cost of foot ulcers in patients with diabetes. Diabetes Care 1999; 22:382-7. (Pubitemid 29106890)
3. Benfield T, Jensen JS, Nordestgaard BG. Influence of diabetes and hyperglycaemia on infectious disease hospitalisation and outcome. Diabetologia 2007; 50:549-54. (Pubitemid 46215497)
4. Ge Y, MacDonald D, Hait H, Lipsky B, Zasloff M, Holroyd K. Microbiological profile of infected diabetic foot ulcers. Diabet Med 2002; 19:1032-4. (Pubitemid 35471974)
5. Ramakant P, Verma AK, Misra R, et al. Changing microbiological profile of pathogenic bacteria in diabetic foot infections: time for a rethink on which empirical therapy to choose? Diabetologia 2011; 54:58-64.
6. Apelqvist J, Bakker K, van Houtum WH, Schaper NC; International Working Group on the Diabetic Foot (IWGDF) Editorial Board. Practical guidelines on the management and prevention of the diabetic foot: based upon the International Consensus on the Diabetic Foot (2007) Prepared by the International Working Group on the Diabetic Foot. Diabetes Metab Res Rev 2008; 24:S181-7. (Pubitemid 351802788)
7. Gardner SE, Frantz RA. Wound bioburden and infection-related complications in diabetic foot ulcers. Biol Res Nurs 2008; 10:44-53.
8. Dowd SE, Wolcott RD, Sun Y, McKeehan T, Smith E, Rhoads D. Polymicrobial nature of chronic diabetic foot ulcer biofilm infections determined using bacterial tag encoded FLX amplicon pyrosequencing (bTEFAP). PLoS One 2008; 3:e3326.
9. Singh G, Rao DJ. Bacterial flora and the diabetic skin. Indian J Med Res 1975; 63:529-32.
10. Kong HH. Skin microbiome: genomics-based insights into the diversity and role of skin microbes. Trends Mol Med 2011; 17: 320-8.
11. Grice EA, Segre JA. The skin microbiome. Nat Rev Microbiol 2011; 9:244-53.
12. Iwase T, Uehara Y, Shinji H, et al. Staphylococcus epidermidis Esp inhibits Staphylococcus aureus biofilm formation and nasal colonization. Nature 2010; 465:346-9.
13. Gontcharova V, Youn E, Sun Y, Wolcott RD, Dowd SE. A comparison of bacterial composition in diabetic ulcers and contralateral intact skin. Open Microbiol J 2010; 4:8-19.
14. Human Microbiome Consortium. A framework for human microbiome research. Nature 2012; 486:215-21.
15. Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature 2012; 486:207-14.
16. Gao Z, Perez-Perez GI, Chen Y, Blaser MJ. Quantitation of major human cutaneous bacterial and fungal populations. J Clin Microbiol 2010; 48:3575-81.
17. Microbiome Project Data Generation Working Group. Generalized draft form of HMP Data Generation Working Group 16S 454 default protocol. Version 4.2-Pilot Study P.1 (15). Available at: http://www.hmpdacc.org/doc/HMP-MDG-454-16S- Protocol.pdf. Accessed 22 October 2012.
18. Haas BJ, Gevers D, Earl AM, et al.; Human Microbiome Consortium. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res 2011; 21:494-504.
19. Caporaso JG, Kuczynski J, Stombaugh J, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods 2010; 7:335-6.
20. Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 2010; 26:2460-1.
21. 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; 73:5261-7. (Pubitemid 47326658)
22. 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; 26:266-7.
23. Price MN, Dehal PS, Arkin AP. FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS One 2010; 5: e9490.
24. Lozupone C, Knight R. UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 2005; 71: 8228-35. (Pubitemid 41803949)
25. Lozupone C, Lladser ME, Knights D, Stombaugh J, Knight R. UniFrac: an effective distance metric for microbial community comparison. ISME J 2010; 5:169-72.
26. Gentleman RC, Carey VJ, Bates DM, et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 2004; 5:R80.
27. Team RDC. R: a language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing, 2009.
28. Benjamini Y, Hochberg Y. Controlling the False Discovery Rate - a Practical and Powerful Approach to Multiple Testing. J Roy Stat Soc B Met 1995; 57:289-300.
29. Bibel DJ, Aly R, Bayles C, Strauss WG, Shinefield HR, Maibach HI. Competitive adherence as a mechanism of bacterial interference. Can J Microbiol 1983; 29:700-3. (Pubitemid 13050975)
30. Lai Y, Di Nardo A, Nakatsuji T, et al. Commensal bacteria regulate Toll-like receptor 3-dependent inflammation after skin injury. Nat Med 2009; 15:1377-82.
31. Cogen AL, Yamasaki K, Sanchez KM, et al. Selective antimicrobial action is provided by phenol-soluble modulins derived from Staphylococcus epidermidis, a normal resident of the skin. J Invest Dermatol 2010; 130:192-200.
32. Littman DR, Pamer EG. Role of the commensal microbiota in normal and pathogenic host immune responses. Cell Host Microbe 2011; 10:311-23.
33. Kong HH. Skin microbiome: genomics-based insights into the diversity and role of skin microbes. Trends Mol Med 2011; 17:320-8.
34. Markendeya N, Martina V, Mathew A, Srinivas CR. Sweat function in the diabetic foot. Indian J Dermatol Venereol Leprol 2004; 70: 18-19. (Pubitemid 39217019)
35. Rutkove SB, Veves A, Mitsa T, et al. Impaired distal thermoregulation in diabetes and diabetic polyneuropathy. Diabetes Care 2009; 32:671-6.
36. Moyer J, Wilson D, Finkelshtein I, Wong B, Potts R. Correlation between sweat glucose and blood glucose in subjects with diabetes. Diabetes Technol Ther 2012; 14:398-402.
37. Provitera V, Nolano M, Caporaso G, Stancanelli A, Santoro L, Kennedy WR. Evaluation of sudomotor function in diabetes using the dynamic sweat test. Neurology 2010; 74:50-6.
38. Schittek B, Paulmann M, Senyürek I, Steffen H. The role of antimicrobial peptides in human skin and in skin infectious diseases. Infect Disord Drug Targets 2008; 8:135-43.
39. Schittek B, Hipfel R, Sauer B, et al. Dermcidin: a novel human antibiotic peptide secreted by sweat glands. Nat Immunol 2001; 2:1133-7. (Pubitemid 33130147)
40. Shiohara T, Doi T, Hayakawa J. Defective sweating responses in atopic dermatitis. Curr Probl Dermatol 2011; 41:68-79.
41. 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; 326:1694-7.
42. Fierer N, Hamady M, Lauber CL, Knight R. The influence of sex, handedness, and washing on the diversity of hand surface bacteria. Proc Natl Acad Sci U S A 2008; 105:17994-9.
43. Gao Z, Tseng CH, Pei Z, Blaser MJ. Molecular analysis of human forearm superficial skin bacterial biota. Proc Natl Acad Sci U S A 2007; 104:2927-32. (Pubitemid 46327980)
44. 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; 44:2933-41. 1114