A Jungle in There: Bacteria in Belly Buttons are Highly Diverse, but Predictable

PLoS ONE

Volumn 7, Issue 11, 2012, Pages

  Hulcr, Jiri ^a,b   Latimer, Andrew M ^c   Henley, Jessica B ^d   Rountree, Nina R ^b   Fierer, Noah ^d   Lucky, Andrea ^a,b   Lowman, Margaret D ^a,e   Dunn, Robert R ^b  

^a UNIVERSITY OF FLORIDA   (United States)

^b NORTH CAROLINA STATE UNIVERSITY   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d UNIVERSITY OF COLORADO   (United States)

^e NORTH CAROLINA MUSEUM OF NATURAL SCIENCES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA 16S;

ARCHAEON; ARTICLE; BACTERIUM; EVOLUTION; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; NONHUMAN; PHYLOGENY; PYROSEQUENCING; UMBILICUS;

ARCHAEA; BACTERIA; HUMANS; MOLECULAR TYPING; PHYLOGENY; RNA, ARCHAEAL; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; UMBILICUS;

ARCHAEA; BACTERIA (MICROORGANISMS);

EID: 84868704705     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0047712     Document Type: Article

References (31)

1. Grice EA, Segre JA, (2011) The skin microbiome. Nature Reviews Microbiology 9: 244-253.
2. Fraser C, Alm EJ, Polz MF, Spratt BG, Hanage WP, (2009) The Bacterial Species Challenge: Making Sense of Genetic and Ecological Diversity. Science 323: 741-746.
3. Grice EA, Kong HH, Conlan S, Deming CB, Davis J, et al. (2009) Topographical and Temporal Diversity of the Human Skin Microbiome. Science 324: 1190-1192.
4. Costello EK, Lauber CL, Hamady M, Fierer N, Gordon JI, et al. (2009) Bacterial variation in human body habitats across space and time. Science 326: 1694-1697.
5. Hubbell SP (2001) The Unified Neutral Theory of Biodiversity and Biogeography: Princeton University Press. 448 p.
6. Pitman NCA, Terborgh JW, Silman MR, Nunez P, Neill DA, et al. (2001) Dominance and distribution of tree species in upper Amazonian terra firme forests. Ecology 82: 2101-2117.
7. Magurran AE, Henderson PA, (2003) Explaining the excess of rare species in natural species abundance distributions. Nature 422: 714-716.
8. ter Steege H, Pitman NCA, Phillips OL, Chave J, Sabatier D, et al. (2006) Continental-scale patterns of canopy tree composition and function across Amazonia. Nature 443: 444-447.
9. Preston FW, (1948) The Commonness, and Rarity, of Species. Ecology 29: 254-283.
10. Fisher RA, Corbet AS, Williams CB, (1943) The relation between the number of species and the number of individuals in a random sample of an animal population. Journal of Animal Ecology 12: 42-58.
11. Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, et al. (2009) A core gut microbiome in obese and lean twins. Nature 457: 480-U487.
12. Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, et al. (2007) The Human Microbiome Project. Nature 449: 804.
13. Shade A, Handelsman J, (2011) Beyond the Venn diagram: the hunt for a core microbiome. Environmental Microbiology 14: 4-12.
14. Losos JB, (2008) Phylogenetic niche conservatism, phylogenetic signal and the relationship between phylogenetic relatedness and ecological similarity among species. Ecology Letters 11: 995-1003.
15. Webb CO, Ackerly DD, McPeek MA, Donoghue MJ, (2002) Phylogenies and community ecology. Annual Review of Ecology and Systematics 33: 475-505.
16. Kembel SW, Hubbell SP, (2006) The phylogenetic structure of a neotropical forest tree community. Ecology 87: S86-S99.
17. Lauber CL, Zhou N, Gordon JI, Knight R, Fierer N, (2009) Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples. FEMS Microbiology Letters 307: 80-86.
18. Bates ST, Berg-Lyons D, Caporaso JG, Walters WA, Knight R, et al. (2011) Examining the global distribution of dominant archaeal populations in soil. ISME J 5: 908.
19. Bergmann GT, Bates ST, Eilers KG, Lauber CL, Caporaso JG, et al. (2011) The under-recognized dominance of Verrucomicrobia in soil bacterial communities. Soil Biology and Biochemistry 43: 1450-1455.
20. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, et al. (2010) QIIME allows analysis of high-throughput community sequencing data. Nature Methods 7: 335-336.
21. Caporaso JG, Bittinger K, Bushman FD, DeSantis TZ, Andersen GL, et al. (2010) PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics 26: 266-267.
22. Wang Q, Garrity GM, Tiedje JM, Cole JR, (2007) Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy. Applied And Environmental Microbiology 73: 5261-5267.
23. Tamura K, Dudley J, Nei M, Kumar S, (2007) MEGA4: Molecular Evolutionary Genetics Analysis, software version 4.0 Molacular Biology and Evolution. 24: 1596-1599.
24. Ornithologists UA (1998) Check-list: Available: http://www.aou.org/checklist/north/.American Ornithologists Union. Accessed: September 3, 2012.
25. Fisher BL, Cover SP (2007) Ants of North America: A Guide to the Genera: University of California Press. 216 p.
26. Kloos WE, Musselwhite mS, (1975) Distribution and persistence of Staphylococcus and Micrococcus species and other aerobic bacteria on human skin. Applied Microbiology 30: 381-395.
27. Dridi B, Raoult D, Drancourt M, (2011) Archaea as emerging organisms in complex human microbiomes. Anaerobe 17: 56.
28. Hanski I, von Hertzen L, Fyhrquist N, Koskinen K, Torppa K, et al. (2012) Environmental biodiversity, human microbiota, and allergy are interrelated. Proceedings of the National Academy of Sciences online early.
29. Naik S, Bouladoux N, Wilhelm C, Molloy M J, Salcedo R, et al. (2012) Compartmentalized Control of Skin Immunity by Resident Commensals. Science, online early, DOI: 10.1126/science.1225152.
30. Bojar R, Holland K, (2002) Review: the human cutaneous microflora and factors controlling colonisation. World Journal of Microbiology & Biotechnology 18: 889-903.
31. Hamady M, Knight R, (2009) Microbial community profiling for human microbiome projects: Tools, techniques, and challenges. Genome Research 19: 1141-1152.