title: Predicting prokaryotic ecological niches using genome sequence analysis.
abstract: Automated DNA sequencing technology is so rapid that analysis has become the rate-limiting step. Hundreds of prokaryotic genome sequences are publicly available, with new genomes uploaded at the rate of approximately 20 per month. As a result, this growing body of genome sequences will include microorganisms not previously identified, isolated, or observed. We hypothesize that evolutionary pressure exerted by an ecological niche selects for a similar genetic repertoire in those prokaryotes that occupy the same niche, and that this is due to both vertical and horizontal transmission. To test this, we have developed a novel method to classify prokaryotes, by calculating their Pfam protein domain distributions and clustering them with all other sequenced prokaryotic species. Clusters of organisms are visualized in two dimensions as 'mountains' on a topological map. When compared to a phylogenetic map constructed using 16S rRNA, this map more accurately clusters prokaryotes according to functional and environmental attributes. We demonstrate the ability of this map, which we term a "niche map", to cluster according to ecological niche both quantitatively and qualitatively, and propose that this method be used to associate uncharacterized prokaryotes with their ecological niche as a means of predicting their functional role directly from their genome sequence.
authors: Department of Biology, Syracuse University, Syracuse, New York, United States of America.
authors: Garret
authors: G
authors: Suen
authors: Barry S
authors: BS
authors: Goldman
authors: Roy D
authors: RD
authors: Welch
mesh_terms: D001483:Base Sequence; D005075:Biological Evolution; D016000:Cluster Analysis; D004463:Ecology; D017753:Ecosystem; D020563:Gammaproteobacteria / Q000145:classification / Q000235:genetics; D016678:Genome; D006801:Humans; D008969:Molecular Sequence Data; D010802:Phylogeny; D011387:Prokaryotic Cells / Q000145:classification / Q000502:physiology*; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D012336:RNA, Ribosomal, 16S
references: Nature. 2000 May 18;405(6784):299-304
references: 10830951
references: PLoS Comput Biol. 2005 Jul;1(2):106-12
references: 16110337
references: Genome Biol. 2002;3(2):REVIEWS0003
references: 11864374
references: Science. 2001 May 11;292(5519):1096-9
references: 11352062
references: PLoS Biol. 2005 May;3(5):e130
references: 15799709
references: Cell. 2006 Aug 11;126(3):453-65
references: 16901780
references: Proc Natl Acad Sci U S A. 2005 May 3;102 Suppl 1:6608-13
references: 15851667
references: Nucleic Acids Res. 2006 Jan 1;34(Database issue):D344-8
references: 16381883
references: Annu Rev Biochem. 2005;74:867-900
references: 15954844
references: Microbiology. 2001 Dec;147(Pt 12):3249-62
references: 11739757
references: Proc Natl Acad Sci U S A. 2005 Jan 11;102(2):373-8
references: 15630082
references: Annu Rev Genet. 2003;37:283-328
references: 14616063
references: Theor Popul Biol. 2002 Jun;61(4):423-34
references: 12167362
references: Science. 2006 Mar 3;311(5765):1283-7
references: 16513982
references: Int J Syst Evol Microbiol. 2005 May;55(Pt 3):1021-6
references: 15879228
references: Nat Genet. 1999 Jan;21(1):108-10
references: 9916801
references: Genome Res. 2000 Jun;10(6):808-18
references: 10854412
references: Microbiol Rev. 1987 Jun;51(2):221-71
references: 2439888
references: J Bacteriol. 2005 Sep;187(18):6258-64
references: 16159757
references: Nucleic Acids Res. 2006 Jan 1;34(Database issue):D247-51
references: 16381856
references: Annu Rev Genet. 2004;38:615-43
references: 15568988
references: Nat Rev Microbiol. 2006 Feb;4(2):102-12
references: 16415926
references: Nature. 2007 Jan 25;445(7126):369
references: 17251963
references: Nucleic Acids Res. 2007 Jan;35(Database issue):D169-72
references: 17090583
references: Mol Biol Evol. 2002 Dec;19(12):2226-38
references: 12446813
references: J Mol Biol. 2001 Jul 6;310(2):311-25
references: 11428892
references: PLoS Comput Biol. 2005 Dec;1(7):e75
references: 16362074
references: Nucleic Acids Res. 2004;32(5):1792-7
references: 15034147
references: Microbiology. 2007 Apr;153(Pt 4):917-23
references: 17379702
references: Cell. 2002 Mar 8;108(5):583-6
references: 11893328
references: Nucleic Acids Res. 2007 Jan;35(Database issue):D237-40
references: 17135202
references: Nature. 1997 Dec 11;390(6660):580-6
references: 9403685
references: Science. 2003 Jun 13;300(5626):1701-3
references: 12805536
references: Proc Natl Acad Sci U S A. 2005 May 3;102 Suppl 1:6595-9
references: 15851673
references: PLoS Biol. 2003 Oct;1(1):E19
references: 12975657
references: Annu Rev Genet. 2004;38:525-52
references: 15568985
references: Nature. 2000 Feb 10;403(6770):601-3
references: 10688178
references: Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
references: 9254694
references: Proc Natl Acad Sci U S A. 1990 Jun;87(12):4576-9
references: 2112744
references: Microbiol Immunol. 1992;36(12):1251-75
references: 1283774