Ecological succession and viability of human-associated microbiota on restroom surfaces

Applied and Environmental Microbiology

Volumn 81, Issue 2, 2015, Pages 765-773

  Gibbons, Sean M ^a,b   Schwartz, Tara ^c   Fouquier, Jennifer ^c,d   Mitchell, Michelle ^c   Sangwan, Naseer ^b   Gilbert, Jack A ^a,b,e,f   Kelley, Scott T ^c  

^a UNIVERSITY OF CHICAGO   (United States)

^b ARGONNE NATIONAL LABORATORY   (United States)

^c SAN DIEGO STATE UNIVERSITY   (United States)

^d SAN DIEGO STATE UNIVERSITY   (United States)

^e MARINE BIOLOGICAL LABORATORY   (United States)

^f ZHEJIANG UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ECOLOGY; FLOORS; VIRUSES;

ASSOCIATED BACTERIA; BACTERIAL ABUNDANCE; BACTERIAL COMMUNITY; BUILT ENVIRONMENT; CULTIVABLE BACTERIA; ECOLOGICAL SUCCESSIONS; HUMAN PAPILLOMA VIRUS; METHICILLIN-RESISTANT STAPHYLOCOCCUS AUREUS;

BACTERIA;

EXCLUSION EXPERIMENT; FLOOR; GENOME; HOST; MICROBIAL COMMUNITY; PRIMATE; PUBLIC HEALTH; SUCCESSION; VIABILITY; VIRULENCE; VIRUS;

BACTERIA (MICROORGANISMS); HUMAN PAPILLOMAVIRUS; METHICILLIN RESISTANT STAPHYLOCOCCUS AUREUS; STAPHYLOCOCCUS;

BACTERIUM; BIOTA; CLASSIFICATION; HUMAN; ISOLATION AND PURIFICATION; MICROBIAL VIABILITY; MICROBIOLOGY; VIRUS;

BACTERIA; BIOTA; ENVIRONMENTAL MICROBIOLOGY; HUMANS; MICROBIAL VIABILITY; VIRUSES;

EID: 84920721220     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.03117-14     Document Type: Article

References (39)

1. Custovic A, Taggart S, Woodcock A. 1994. House dust mite and cat allergen in different indoor environments. Clin Exp Allergy 24:1164. http: //dx.doi.org/10.1111/j.1365-2222.1994.tb03323.x.
2. Kelley ST, Gilbert JA. 2013. Studying the microbiology of the indoor environment. Genome Biol 14:202. http://dx.doi.org/10.1186/gb-2013-14 -2-202.
3. Kembel SW, Jones E, Kline J, Northcutt D, Stenson J, Womack AM, Bohannan BJ, Brown G, Green JL. 2012. Architectural design influences the diversity and structure of the built environment microbiome. ISME J 6:1469-1479. http://dx.doi.org/10.1038/ismej.2011.211.
4. Flores GE, Bates ST, Knights D, Lauber CL, Stombaugh J, Knight R, Fierer N. 2011. Microbial biogeography of public restroom surfaces. PLoS One 6:e28132. http://dx.doi.org/10.1371/journal.pone.0028132.
5. Rintala H, Pitkäranta M, Toivola M, Paulin L, Nevalainen A. 2008. Diversity and seasonal dynamics of bacterial community in indoor environment. BMC Microbiol 8:56. http://dx.doi.org/10.1186/1471 -2180-8-56.
6. Angenent LT, Kelley ST, Amand AS, Pace NR, Hernandez MT. 2005. Molecular identification of potential pathogens in water and air of a hospital therapy pool. Proc Natl Acad SciUSA102:4860-4865. http://dx.doi.org/10.1073/pnas.0501235102.
7. Knights D, Kuczynski J, Charlson ES, Zaneveld J, Mozer MC, Collman RG, Bushman FD, Knight R, Kelley ST. 2011. Bayesian community-wide culture-independent microbial source tracking. Nat Methods 8:761-763. http://dx.doi.org/10.1038/nmeth.1650.
8. Hewitt KM, Gerba CP, Maxwell SL, Kelley ST. 2012. Office space bacterial abundance and diversity in three metropolitan areas. PLoS One 7:e37849. http://dx.doi.org/10.1371/journal.pone.0037849.
9. Knight R, Jansson J, Field D, Fierer N, Desai N, Fuhrman JA, Hugenholtz P, van der Lelie D, Meyer F, Stevens R. 2012. Unlocking the potential of metagenomics through replicated experimental design. Nat Biotechnol 30:513-520. http://dx.doi.org/10.1038/nbt.2235.
10. Sano E, Carlson S, Wegley L, Rohwer F. 2004. Movement of viruses between biomes. Appl Environ Microbiol 70:5842-5846. http://dx.doi.org /10.1128/AEM.70.10.5842-5846.2004.
11. Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N, Owens SM, Betley J, Fraser L, Bauer M, Gormley N, Gilbert JA, Smith G, Knight R. 2012. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J 6:1621-1624. http://dx.doi.org/10.1038/ismej.2012.8.
12. Glass EM, Meyer F. 2011. The metagenomics RAST server: a public resource for the automatic phylogenetic and functional analysis of metagenomes, p 325-331. In de Bruijn FJ (ed), Handbook of molecular microbial ecology I: metagenomics and complementary approaches. John Wiley & Sons, Inc, Hoboken, NJ.
13. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena 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. 2010. QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7:335-336. http://dx.doi.org/10.1038/nmeth.f.303.
14. Rideout JR, He Y, Navas-Molina JA, Walters WA, Ursell LK, Gibbons SM, Chase J, McDonald D, Gonzalez A, Robbins-Pianka A. 2014. Subsampled open-reference clustering creates consistent, comprehensive OTUdefinitions and scales to billions of sequences. PeerJ 2:e545. http://dx.doi.org/10.7717/peerj.545.
15. McDonald D, Price MN, Goodrich J, Nawrocki EP, DeSantis TZ, Probst A, Andersen GL, Knight R, Hugenholtz P. 2012. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J 6:610-618. http://dx.doi.org/10.1038 /ismej.2011.139.
16. Caporaso JG, Bittinger K, Bushman FD, DeSantis TZ, Andersen GL, Knight R. 2010. PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics 26:266-267. http://dx.doi.org/10.1093 /bioinformatics/btp636.
17. Price MN, Dehal PS, Arkin AP. 2010. FastTree 2-approximately maximum- likelihood trees for large alignments. PLoS One 5:e9490. http://dx.doi.org/10.1371/journal.pone.0009490.
18. Lozupone C, Knight R. 2005. UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71:8228- 8235. http://dx.doi.org/10.1128/AEM.71.12.8228-8235.2005.
19. R Core Development Team. 2008. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.
20. Hunter JD. 2007. Matplotlib: a 2D graphics environment. Comput Sci Eng 9:90-95. http://dx.doi.org/10.1109/MCSE.2007.55.
21. Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821-829. http://dx.doi.org/10.1101/gr.074492.107.
22. Haft DH, Tovchigrechko A. 2012. High-speed microbial community profiling. Nat Methods 9:793-794. http://dx.doi.org/10.1038/nmeth.2080.
23. Suzuki R, Shimodaira H. 2006. Pvclust: an R package for assessing the uncertainty in hierarchical clustering. Bioinformatics 22:1540-1542. http: //dx.doi.org/10.1093/bioinformatics/btl117.
24. Wu M, Scott AJ. 2012. Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2. Bioinformatics 28:1033-1034. http://dx.doi.org/10.1093/bioinformatics/bts079.
25. Ruby JG, Bellare P, DeRisi JL. 2013. PRICE: software for the targeted assembly of components of (meta) genomic sequence data. G3 3:865-880. http://dx.doi.org/10.1534/g3.113.005967.
26. International Working Group on the Classification of Staphylococcal Cassette Chromosome Elements (IWG-SCC). 2009. Classification of staphylococcal cassette chromosome mec (SCCmec): guidelines for reporting novel SCCmec elements. Antimicrob Agents Chemother 53:4961- 4967. http://dx.doi.org/10.1128/AAC.00579-09.
27. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M. 2008. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9:75. http://dx.doi.org/10.1186/1471-2164-9-75.
28. Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M. 2007. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 35:W182-W185. http://dx.doi.org/10.1093/nar/gkm321.
29. Segata N, Börnigen D, Morgan XC, Huttenhower C. 2013. PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes. Nat Commun 4:2304. http://dx.doi.org/10.1038/ncomms3304.
30. Kelley ST, Dobler S. 2011. Comparative analysis of microbial diversity in Longitarsus flea beetles (Coleoptera: Chrysomelidae). Genetica 139:541- 550. http://dx.doi.org/10.1007/s10709-010-9498-0.
31. Vásquez A, Jakobsson T, Ahrné S, Forsum U, Molin G. 2002. Vaginal Lactobacillus flora of healthy Swedish women. J Clin Microbiol 40:2746- 2749. http://dx.doi.org/10.1128/JCM.40.8.2746-2749.2002.
32. Ma B, Forney LJ, Ravel J. 2012. Vaginal microbiome: rethinking health and disease. Annu Rev Microbiol 66:371-389. http://dx.doi.org/10.1146 /annurev-micro-092611-150157.
33. Ravel J, Gajer P, Abdo Z, Schneider GM, Koenig SS, McCulle SL, Karlebach S, Gorle R, Russell J, Tacket CO. 2011. Vaginal microbiome of reproductive-age women. Proc Natl Acad Sci U S A 108:4680-4687. http://dx.doi.org/10.1073/pnas.1002611107.
34. LeBlanc DM, Reece EM, Horton JB, Janis JE. 2007. Increasing incidence of methicillin-resistant Staphylococcus aureus in hand infections: a 3-year county hospital experience. Plast Reconstr Surg 119:935-940. http://dx.doi.org/10.1097/01.prs.0000252270.84195.41.
35. 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. http://dx.doi.org/10.1126 /science.1177486.
36. Weinbauer MG. 2004. Ecology of prokaryotic viruses. FEMS Microbiol Rev 28:127-181. http://dx.doi.org/10.1016/j.femsre.2003.08.001.
37. Lewis K. 2010. Persister cells. Annu Rev Microbiol 64:357-372. http://dx.doi.org/10.1146/annurev.micro.112408.134306.
38. Davison AJ, Eberle R, Ehlers B, Hayward GS, McGeoch DJ, Minson AC, Pellett PE, Roizman B, Studdert MJ, Thiry E. 2009. The order Herpesvirales. Arch Virol 154:171-177. http://dx.doi.org/10.1007/s00705-008 -0278-4.
39. Walboomers JM, Jacobs MV, Manos MM, Bosch FX, Kummer JA, Shah KV, Snijders PJ, Peto J, Meijer CJ, Munoz N. 1999. Human papillomavirus is a necessary cause of invasive cervical cancer worldwide. J Pathol 189:12-19. http://dx.doi.org/10.1002/(SICI)1096-9896(199909)189:1<1 2::AID-PATH431>3.0.CO;2-F.