Bacterial Genomes: Habitat Specificity and Uncharted Organisms

Microbial Ecology

Volumn 64, Issue 1, 2012, Pages 1-7

  Dini Andreote, Francisco ^a,c   Andreote, Fernando Dini ^a   Araújo, Welington Luiz ^a   Trevors, Jack T ^b   van Elsas, Jan Dirk ^c  

^a UNIVERSITY OF SÃO PAULO   (Brazil)

^b UNIVERSITY OF GUELPH   (Canada)

^c UNIVERSITY OF GRONINGEN   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL; BACTERIAL GENOME; BACTERIUM; CLASSIFICATION; ECOSYSTEM; GENETICS; HUMAN; ISOLATION AND PURIFICATION; MICROBIOLOGY; PHYLOGENY; REVIEW;

ANIMALS; BACTERIA; ECOSYSTEM; ENVIRONMENTAL MICROBIOLOGY; GENOME, BACTERIAL; HUMANS; PHYLOGENY;

BACTERIA (MICROORGANISMS);

EID: 84857679945     PISSN: 00953628     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00248-012-0017-y     Document Type: Review

References (28)

1. Abby S, Daubin V (2007) Comparative genomics and the evolution of prokaryotes. Trends Microbiol 15: 135-141.
2. Angly FE, Willner D, Prieto-Davó A, Edwards RA et al (2009) The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes. PLoS Comput Biol 5(12): e1000593.
3. Barrick JE, Yu DS, Yoon SH, Jeong H et al (2009) Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature 461: 1243-1249.
4. Bernal A, Ear U, Kyrpides N (2001) Genomes OnLine Database (GOLD): a monitor of genome projects world-wide. Nucleic Acids Res 29: 126-127.
5. Burke GR, Moran NA (2011) Massive genomic decay in Serratia symbiotica, a recently evolved symbiont of Aphids. Genome Biol Evol 3: 195-208.
6. Dinsdale EA, Edwards RA, Hall D, Angly F et al (2008) Functional metagenomic profiling of nine biomes. Nature 452: 629-633.
7. Gilbert JA, Meyer F, Bailey MJ (2011) The future of microbial metagenomics (or is ignorance bliss?). ISME J 5: 777-779.
8. Harris JK, Kelley ST, Pace NR (2004) New perspective on uncultured bacterial phylogenetic division OP11. Appl Environ Microbiol 70: 845-849.
9. Ishoey T, Woyke T, Stepanauskas R, Novotny M et al (2008) Genomic sequencing of single microbial cells from environmental samples. Curr Opin Microbiol 11: 198-204.
10. Jones RT, Robeson MS, Lauber CL, Hamady M et al (2009) A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses. ISME J 3: 442-453.
11. Lapierre P, Gogarten JP (2009) Estimating the size of the bacterial pan-genome. Trends Genet 25: 107-110.
12. Lee PKH, Cheng D, Hu P, West KA et al (2011) Comparative genomics of two newly isolated Dehalococcoides strains and an enrichment using a genus microarray. ISME J 5: 1014-1024.
13. Oksana L, Wassenaar TM, Ussery DW (2010) Comparison of 61 sequenced Escherichia coli genomes. Microb Ecol 60: 708-720.
14. Pace NR (2009) Mapping the tree of life: progress and prospects. Microbiol Mol Biol Rev 73: 565-576.
15. Pedrós-Alió C (2007) Dipping into the rare biosphere. Science 315: 192.
16. Philippot L, Andersson SGE, Battin T, Prosser JI et al (2010) The ecological coherence of high bacterial taxonomic ranks. Nat Rev Microbiol 8: 523-529.
17. Raes J, Korbel JO, Lercher MJ, von Mering C, Bork P (2007) Prediction of effective genome size in metagenomic samples. Genome Biol 8: R10.
18. Ranea JAG, Buchan DWA, Thornton JM, Orengo CA (2004) Evolution of protein superfamilies and bacterial genome size. J Mol Biol 336: 871-887.
19. Sogin ML, Morrison HG, Huber JA, Welch DM et al (2006) Microbial diversity in the deep sea and the underexplored "rare biosphere". Proc Natl Acad Sci USA 103: 12115-12120.
20. Toh H, Weiss BL, Perkin SAH, Yamashita A et al (2006) Massive genome erosion and functional adaptations provide insights into the symbiotic lifestyle of Sodalis glossinidius in the tsetse host. Genome Res 16: 149-156.
21. Touchon M, Hoede C, Tenaillon O, Barbe V et al (2009) Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genet 5(1): e1000344.
22. Trevors JT, Masson L (2010) Microbial DNA technologies: what's next applied to microbiology research? Antonie van Leeuwenhoek 98: 249-262, Erratum 2011: 99: 431.
23. Tringe SG, von Mering C, Kobayashi A, Salamov AA et al (2005) Comparative metagenomics of microbial communities. Science 308: 554-557.
24. Vogel TM, Simonet P, Jansson JK, Hirsch PR et al (2009) TerraGenome: a consortium for the sequencing of a soil metagenome. Nature 7: 252.
25. Wagner M (2009) Single-cell ecophysiology of microbes as revealed by Raman microspectroscopy or secondary ion mass spectrometry imaging. Annu Rev Microbiol 63: 411-429.
26. Woyke T, Tighe D, Mavromatis K, Clum A et al (2010) One bacterial cell, one complete genome. PLoS One 5(4): e10314.
27. Wu D, Hugenholtz P, Mavromatis K, Pukall R et al (2009) A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 462: 1056-1060.
28. Yilmaz P, Gilbert JA, Knight R, Amaral-Zettler L et al (2011) The genomic standards consortium: bringing standards to life for microbial ecology. ISME J 5: 1565-1567.