Lineage-dependent ecological coherence in bacteria

FEMS Microbiology Ecology

Volumn 81, Issue 3, 2012, Pages 574-582

  Koeppel, Alexander F ^a   Wu, Martin ^a  

^a UNIVERSITY OF VIRGINIA   (United States)

Author keywords

Ecological coherence; Human microbiota; Taxonomic hierarchy

Indexed keywords

RNA 16S;

BACTERIUM; HIERARCHICAL SYSTEM; HYPOTHESIS TESTING; MICROBIAL COMMUNITY; PHYLOGENETICS; RELATIVE ABUNDANCE; SKIN; SPECIES DIVERSITY; TAXONOMY;

ACTINOBACTERIA; ARTICLE; BACTERIUM; CLASSIFICATION; ECOSYSTEM; GASTROINTESTINAL TRACT; GENETICS; HUMAN; ISOLATION AND PURIFICATION; METAGENOME; MICROBIOLOGY; OBESITY; PHYLOGENY; PROTEOBACTERIA; SKIN;

ACTINOBACTERIA; BACTERIA; ECOSYSTEM; GASTROINTESTINAL TRACT; HUMANS; METAGENOME; OBESITY; PHYLOGENY; PROTEOBACTERIA; RNA, RIBOSOMAL, 16S; SKIN;

BACTERIA (MICROORGANISMS);

EID: 84864582440     PISSN: 01686496     EISSN: 15746941     Source Type: Journal    
DOI: 10.1111/j.1574-6941.2012.01387.x     Document Type: Article

References (53)

1. Auguet J, Barberan A & Casamayor EO (2010) Global ecological patterns in uncultured Archaea. ISME J 4: 182-190.
2. Barberán A, Bates ST, Casamayor EO & Fierer N (2012) Using network analysis to explore co-occurrence patterns in soil microbial communities. ISME J 6: 343-351.
3. Bryant JA, Lamanna C, Morlon H, Kerkhoff AJ, Enquist BJ & Green JL (2008) Colloquium paper: microbes on mountainsides: contrasting elevational patterns of bacterial and plant diversity. P Natl Acad Sci USA 105 (suppl 1): 11505-11511.
4. Cani PD, Amar J, Iglesias MA et al. (2007) Metabolic endotoxemia initiates obesity and insulin resistance. Diabetes 56: 1761-1772.
5. Cardenas E, Wu WM, Leigh MB et al. (2010) A combined massively parallel sequencing - indicator species approach revealed significant association between sulfate-reducing bacteria and uranium-reducing microbial communities. Appl Environ Microbiol 76: 6778-6786.
6. Cavender-Bares J, Keen A & Miles B (2006) Phylogenetic structure of Floridian plant communities depends on taxonomic and spatial scale. Ecology 87: 109-122.
7. Cavender-Bares J, Ackerly DD, Baum DA & Bazzaz FA (2004) Phylogenetic overdispersion in Floridian oak communities. Am Nat 163: 823-843.
8. Cohan FM & Koeppel AF (2008) The origins of ecological diversity in prokaryotes. Curr Biol 18: R1024-R1034.
9. Connor N, Sikorski J, Rooney AP et al. (2010) Ecology of speciation in the genus Bacillus. Appl Environ Microbiol 76: 1349-1358.
10. Danon M, Franke-Whittle IH, Insam H, Chen Y & Hadar Y (2008) Molecular analysis of bacterial community succession during prolonged compost curing. FEMS Microbiol Ecol 65: 133-144.
11. Dominguez-Bello MG, Costello EK, Contreras M, Magris M, Hidalgo G, Fierer N & Knight R (2010) Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. P Natl Acad Sci USA 107: 11971-11975.
12. Dufrene M & Legendre P (1997) Species assemblages and indicator species: the need for a flexible asymmetrical approach. Ecol Monogr 67: 345.
13. Ettema TJ & Andersson SG (2009) The alpha-proteobacteria: the Darwin finches of the bacterial world. Biol Lett 5: 429-432.
14. Fierer N, Bradford MA & Jackson RB (2007) Toward an ecological classification of soil bacteria. Ecology 88: 1354-1364.
15. Fierer N, Hamady M, Lauber CL & Knight R (2008) The influence of sex, handedness, and washing on the diversity of hand surface bacteria. P Natl Acad Sci USA 105: 17994-17999.
16. Fulthorpe RR, Roesch LF, Riva A & Triplett EW (2008) Distantly sampled soils carry few species in common. ISME J 2: 901-910.
17. Giongo A, Gano KA, Crabb DB et al. (2011) Toward defining the autoimmune microbiome for type 1 diabetes. ISME J 5: 82-91.
18. Giovannoni SJ & Stingl U (2005) Molecular diversity and ecology of microbial plankton. Nature 437: 343-348.
19. Goris J, Konstantinidis K, Klappenbach J, Coenye T, Vandamme P & Tiedje J (2007) DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57: 81-91.
20. Grice EA & Segre JA (2011) The skin microbiome. Nat Rev Microbiol 9: 244-253.
21. Grice EA, Kong HH, Conlan S et al. (2009) Topographical and temporal diversity of the human skin microbiome. Science 324: 1190-1192.
22. Hackl E, Zechmeister-Boltenstern S, Bodrossy L & Sessitsch A (2004) Comparison of diversities and compositions of bacterial populations inhabiting natural forest soils. Appl Environ Microbiol 70: 5057-5065.
23. Hamady M & Knight R (2009) Microbial community profiling for human microbiome projects: tools, techniques, and challenges. Genome Res 19: 1141-1152.
24. Hartman AL, Lough DM, Barupal DK, Fiehn O, Fishbein T, Zasloff M & Eisen JA (2009) Human gut microbiome adopts an alternative state following small bowel transplantation. P Natl Acad Sci USA 106: 17187-17192.
25. Hartmann M, Lee S, Hallam SJ & Mohn WW (2009) Bacterial, archaeal and eukaryal community structures throughout soil horizons of harvested and naturally disturbed forest stands. Environ Microbiol 11: 3045-3062.
26. Horner-Devine MC & Bohannan BJM (2006) Phylogenetic clustering and overdispersion in bacterial communities. Ecology 87: 100-108.
27. Hunt DE, David LA, Gevers D, Preheim SP, Alm EJ & Polz MF (2008) Resource partitioning and sympatric differentiation among closely related bacterioplankton. Science 320: 1081-1085.
28. Jones RT, Robeson MS, Lauber CL, Hamady M, Knight R & Fierer N (2009) A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses. ISME J 3: 442-453.
29. Keddy PA & Weiher E (1999) Introduction: the scope and goals of research on assembly rules. (Keddy PA & Weiher E, eds). Ecological Assembly Rules: Perspectives, Advances, Retreats. Cambridge University Press, Cambridge, UK, pp. 1-22.
30. Koeppel A, Perry EB, Sikorski J et al. (2008) Identifying the fundamental units of bacterial diversity: a paradigm shift to incorporate ecology into bacterial systematics. P Natl Acad Sci USA 105: 2504-2509.
31. Kuczynski J, Elizabeth CK, Nemergut DR et al. (2010) Direct sequencing of the human microbiome readily reveals community differences. Genome Biol 11: 210.
32. Ley RE (2005) Obesity alters gut microbial ecology. P Natl Acad Sci USA 102: 11070-11075.
33. Ley RE, Turnbaugh PJ, Klein S & Gordon JI (2006) Microbial ecology: human gut microbes associated with obesity. Nature 444: 1022-1023.
34. Lozupone C & Knight R (2005) UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71: 8228-8235.
35. Lozupone CA & Knight R (2007) Global patterns in bacterial diversity. P Natl Acad Sci USA 104: 11436-11440.
36. Martiny AC, Tai APK, Veneziano D, Primeau F & Chisholm SW (2009) Taxonomic resolution, ecotypes and the biogeography of Prochlorococcus. Environ Microbiol 11: 823-832.
37. Newton RJ, Jones SE, Helmus MR & McMahon KD (2007) Phylogenetic ecology of the freshwater Actinobacteria acI lineage. Appl Environ Microbiol 73: 7169-7176.
38. Ordovas JM & Mooser V (2006) Metagenomics: the role of the microbiome in cardiovascular diseases. Curr Opin Lipidol 17: 157-161.
39. Philippot L, Bru D, Saby NPA, Čuhel J, Arrouays D, Šimek M & Hallin S (2009) Spatial patterns of bacterial taxa in nature reflect ecological traits of deep branches of the 16S rRNA bacterial tree. Environ Microbiol 11: 3096-3104.
40. Philippot L, Andersson SG, Battin TJ, Prosser JI, Schimel JP, Whitman WB & Hallin S (2010) The ecological coherence of high bacterial taxonomic ranks. Nat Rev Microbiol 8: 523-529.
41. Pointing SB, Chan Y, Lacap DC, Lau MC, Jurgens JA & Farrell RL (2009) Highly specialized microbial diversity in hyper-arid polar desert. P Natl Acad Sci USA 106: 19964-19969.
42. Schloss PD, Westcott SL, Ryabin T et al. (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75: 7537-7541.
43. Silvertown J, Dodd M & Gowing D (2001) Phylogeny and the niche structure of meadow plant communities. J Ecol 89: 428-435.
44. Silvertown J, Dodd M, Gowing D, Lawson C & McConway K (2006) Phylogeny and the hierarchical organization of plant diversity. Ecology 87: 39-49.
45. Stackebrandt E & Ebers J (2006) Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 33: 152-155.
46. Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R & Gordon JI (2007) The human microbiome project. Nature 449: 804-810.
47. Turnbaugh PJ, Hamady M, Yatsunenko T et al. (2009) A core gut microbiome in obese and lean twins. Nature 457: 480-484.
48. Vogel TM, Simonet P, Jansson JK, Hirsch PR, Tiedje JM, van Elsas JD, Bailey MJ, Nalin R & Philippot L (2009) TerraGenome: a consortium for the sequencing of a soil metagenome. Nat Rev Microbiol 7: 252.
49. von Mering C, Hugenholtz P, Raes J, Tringe SG, Doerks T, Jensen LJ, Ward N & Bork P (2007) Quantitative phylogenetic assessment of microbial communities in diverse environments. Science 315: 1126-1130.
50. Wang Q, Garrity GM, Tiedje JM & Cole JR (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73: 5261-5267.
51. Ward DM, Bateson MM, Ferris MJ, Kuhl M, Wieland A, Koeppel A & Cohan FM (2006) Cyanobacterial ecotypes in the microbial mat community of Mushroom Spring (Yellowstone National Park, Wyoming) as species-like units linking microbial community composition, structure and function. Philos Trans R Soc Lond B Biol Sci 361: 1997-2008.
52. Webb CO, Ackerly DD, McPeek MA & Donoghue MJ (2002) Phylogenies and community ecology. Annu Rev Ecol Syst 33: 475-505.
53. Weiher E & Keddy PA (1995) The assembly of experimental wetland plant communities. Oikos 73: 323.