Hand bacterial communities vary across two different human populations

Microbiology (United Kingdom)

Volumn 160, Issue PART 6, 2014, Pages 1144-1152

  Hospodsky, Denina ^a   Pickering, Amy J ^b   Julian, Timothy R ^c   Miller, Dana ^a   Gorthala, Sisira ^a   Boehm, Alexandria B ^b   Peccia, Jordan ^a  

^a Yale University   (United States)

^b Stanford University   (United States)

^c JOHNS HOPKINS BLOOMBERG SCHOOL OF PUBLIC HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA 16S;

ACTINOBACTERIA; ADULT; ARTICLE; BACILLACEAE; BACTERIUM IDENTIFICATION; BACTEROIDETES; BRADYRHIZOBIACEAE; BURKHOLDERIALES; COMAMONADACEAE; CONTROLLED STUDY; DNA SEQUENCE; EUROPE; FEMALE; FIRMICUTES; HAND; HUMAN; HUMAN EXPERIMENT; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; MICROBIOME; MICROCOCCACEAE; MOLECULAR LIBRARY; MOUTH; NOCARDIOIDACEAE; NONHUMAN; NORMAL HUMAN; NOSE; PHYLOGENY; POPULATION ABUNDANCE; PRIORITY JOURNAL; PROPIONIBACTERIACEAE; PROTEOBACTERIA; PYROSEQUENCING; RHIZOBIACEAE; RHODOBACTERACEAE; SKIN; SOIL; STAPHYLOCOCCACEAE; STREPTOCOCCACEAE; TANZANIA; UNITED STATES;

EID: 84901720864     PISSN: 13500872     EISSN: 14652080     Source Type: Journal    
DOI: 10.1099/mic.0.075390-0     Document Type: Article

References (40)

1. Aiello, A. E. & Larson, E. L. (2002). What is the evidence for a causal link between hygiene and infections? Lancet Infect Dis 2, 103-110.
2. Blaser, M. J., Dominguez-Bello, M. G., Contreras, M., Magris, M., Hidalgo, G., Estrada, I., Gao, Z., Clemente, J. C., Costello, E. K. & Knight, R. (2013). Distinct cutaneous bacterial assemblages in a sampling of South American Amerindians and US residents. ISME J 7, 85-95.
3. Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., Fierer, N., Peña, A. G., Goodrich, J. K. & other authors (2010). QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7, 335-336.
4. Costello, E. K., Lauber, C. L., Hamady, M., Fierer, N., Gordon, J. I. & Knight, R. (2009). Bacterial community variation in human body habitats across space and time. Science 326, 1694-1697.
5. De Filippo, C., Cavalieri, D., Di Paola, M., Ramazzotti, M., Poullet, J. B., Massart, S., Collini, S., Pieraccini, G. & Lionetti, P. (2010). Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc Natl Acad Sci U S A 107, 14691-14696.
6. DeSantis, T. Z., Hugenholtz, P., Larsen, N., Rojas, M., Brodie, E. L., Keller, K., Huber, T., Dalevi, D., Hu, P. & Andersen, G. L. (2006). Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72, 5069-5072.
7. Eckburg, P. B., Bik, E. M., Bernstein, C. N., Purdom, E., Dethlefsen, L., Sargent, M., Gill, S. R., Nelson, K. E. & Relman, D. A. (2005). Diversity of the human intestinal microbial flora. Science 308, 1635-1638.
8. Fierer, N., Hamady, M., Lauber, C. L. & 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.
9. Flores, G. E., Bates, S. T., Knights, D., Lauber, C. L., Stombaugh, J., Knight, R. & Fierer, N. (2011). Microbial biogeography of public restroom surfaces. PLoS ONE 6, e28132.
10. Garrity, G. M., Bell, J. G. & Lilburn, T. (2001). Taxonomic outline of the Archaea and Bacteria. In Bergey's Manual of Systematic Bacteriology, vol. 1, 2nd edn, pp. 21-217. Edited by D. R. Boone & R. W. Castenholz. New York: Springer.
11. Giacomoni, P. U., Mammone, T. & Teri, M. (2009). Gender-linked differences in human skin. J Dermatol Sci 55, 144-149.
12. Gilbert, J. A., Meyer, F., Antonopoulos, D., Balaji, P., Brown, C. T., Brown, C. T., Desai, N., Eisen, J. A., Evers, D. & other authors (2010). Meeting Report. The terabase metagenomic workshop and the vision of an earth microbiome project. Stand Genomic Sci 3, 3.
13. Grice, E. A., Kong, H. H., Renaud, G., Young, A. C., Bouffard, G. G., Blakesley, R. W., Wolfsberg, T. G., Turner, M. L., Segre, J. A. & NISC Comparative Sequencing Program (2008). A diversity profile of the human skin microbiota. Genome Res 18, 1043-1050.
14. Grice, E. A., Kong, H. H., Conlan, S., Deming, C. B., Davis, J., Young, A. C., Bouffard, G. G., Blakesley, R. W., Murray, P. R. & other authors (2009). Topographical and temporal diversity of the human skin microbiome. Science 324, 1190-1192.
15. Hamady, M., Lozupone, C. & Knight, R. (2010). Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data. ISME J 4, 17-27.
16. Hanski, I., von Hertzen, L., Fyhrquist, N., Koskinen, K., Torppa, K., Laatikainen, T., Karisola, P., Auvinen, P., Paulin, L. & other authors (2012). Environmental biodiversity, human microbiota, and allergy are interrelated. Proc Natl Acad Sci U S A 109, 8334-8339.
17. Hospodsky, D., Qian, J., Nazaroff, W. W., Yamamoto, N., Bibby, K., Rismani-Yazdi, H. & Peccia, J. (2012). Human occupancy as a source of indoor airborne bacteria. PLoS ONE 7, e34867.
18. Hsu, Y. W. & Yu, C. Y. (2010). Hand surface area estimation formula using 3D anthropometry. J Occup Environ Hyg 7, 633-639.
19. Kembel, S. W., Jones, E., Kline, J., Northcutt, D., Stenson, J., Womack, A. M., Bohannan, B. J. M., Brown, G. Z. & Green, J. L. (2012). Architectural design influences the diversity and structure of the built environment microbiome. ISME J 6, 1469-1479.
20. Kong, H. H. (2011). Skin microbiome: genomics-based insights into the diversity and role of skin microbes. Trends Mol Med 17, 320-328.
21. Kuykendall, L. D., Young, J. M., Martinez-Romero, E., Kerr, A. & Sawada, H. (2001). Genus Rhizobium. In Bergey's Manual of Systematic Bacteriology, vol. 2, 2nd edn, pp. 325-339. Edited by J. T. Staley, D. J. Brenner & N. R. Kreig. New York: Springer.
22. Lauber, C. L., Hamady, M., Knight, R. & Fierer, N. (2009). Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl Environ Microbiol 75, 5111-5120.
23. Lazarevic, V., Whiteson, K., Hernandez, D., Francois, P. & Schrenzel, J. (2010). Study of inter-and intra-individual variations in the salivary microbiota. BMC Genomics 11, 523.
24. Lee, Z. M.-P., Bussema, C.,& Schmidt, T. M. (2009). rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea. Nucleic Acids Res 37 (Database), D489-D493.
25. Leyden, J. J., McGinley, K. J., Nordstrom, K. M. & Webster, G. F. (1987). Skin microflora. J Invest Dermatol 88 (Suppl), 65s-72s.
26. Liu, Z., Lozupone, C., Hamady, M., Bushman, F. D. & Knight, R. (2007). Short pyrosequencing reads suffice for accurate microbial community analysis. Nucleic Acids Res 35, e120.
27. Logan, N. A. & DeVos, P. (2001). Genus Bacillus. In Bergey's Manual of Systematic Bacteriology, vol. 3, pp. 21-127. Edited by P. Vos, G. M. Garrity, D. Jones, N. R. Kreig, W. Ludwig, F. Rainey, K.-H. Schleifer & W. B. Whitman. New York: Springer.
28. Luby, S. P., Agboatwalla, M., Feikin, D. R., Painter, J., Billhimer, W., Altaf, A. & Hoekstra, R. M. (2005). Effect of handwashing on child health: a randomised controlled trial. Lancet 366, 225-233.
29. Marples, M. J. (1965). The Ecology of the Human Skin. Springfield, IL: Charles C Thomas.
30. Nasidze, I., Li, J., Quinque, D., Tang, K. & Stoneking, M. (2009). Global diversity in the human salivary microbiome. Genome Res 19, 636-643.
31. Nasidze, I., Li, J., Schroeder, R., Creasey, J. L., Li, M. & Stoneking, M. (2011). High diversity of the saliva microbiome in Batwa Pygmies. PLoS ONE 6, e23352.
32. Pickering, A. J., Boehm, A. B., Mwanjali, M. & Davis, J. (2010). Efficacy of waterless hand hygiene compared with handwashing with soap: a field study in Dar es Salaam, Tanzania. Am J TropMed Hyg 82, 270-278.
33. Pickering, A. J., Julian, T. R., Mamuya, S., Boehm, A. B. & Davis, J. (2011). Bacterial hand contamination among Tanzanian mothers varies temporally and following household activities. Trop Med Int Health 16, 233-239.
34. Price, P. B. (1938). The bacteriology of normal skin; a new quantitative test applied to a study of the bacterial flora and the disinfectant action of mechanical cleansing. J Infect Dis 63, 301-318.
35. Qian, J., Hospodsky, D., Yamamoto, N., Nazaroff, W. W. & Peccia, J. (2012). Size-resolved emission rates of airborne bacteria and fungi in an occupied classroom. Indoor Air 22, 339-351.
36. Quince, C., Lanzén, A., Curtis, T. P., Davenport, R. J., Hall, N., Head, I. M., Read, L. F. & Sloan, W. T. (2009). Accurate determination of microbial diversity from 454 pyrosequencing data. Nat Methods 6, 639-641.
37. Quince, C., Lanzen, A., Davenport, R. J. & Turnbaugh, P. J. (2011). Removing noise from pyrosequenced amplicons. BMC Bioinformatics 12, 38.
38. Sickbert-Bennett, E. E., Weber, D. J., Gergen-Teague, M. F., Sobsey, M. D., Samsa, G. P. & Rutala, W. A. (2005). Comparative efficacy of hand hygiene agents in the reduction of bacteria and viruses. Am J Infect Control 33, 67-77.
39. Wang, Q., Garrity, G. M., Tiedje, J. M. & Cole, J. R. (2007). Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73, 5261-5267.
40. Yamamoto, N., Bibby, K., Qian, J., Hospodsky, D., Rismani-Yazdi, H., Nazaroff, W. W. & Peccia, J. (2012). Particle-size distributions and seasonal diversity of allergenic and pathogenic fungi in outdoor air. ISME J 6, 1801-1811.