Metabolic classification of microbial genomes using functional probes

BMC Genomics

Volumn 13, Issue 1, 2012, Pages

  Lee, Chi Ching ^a   Lo, Wei Cheng ^b   Lai, Szu Ming ^a   Chen, Yi Ping P ^c   Tang, Chuan Y ^a,d,e   Lyu, Ping Chiang ^a,e  

^a NATIONAL TSING HUA UNIVERSITY   (Taiwan)

^b NATIONAL CHIAO TUNG UNIVERSITY   (Taiwan)

^c LA TROBE UNIVERSITY   (Australia)

^d PROVIDENCE UNIVERSITY   (Taiwan)

^e CHINA MEDICAL UNIVERSITY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEOME;

AMINO ACID SEQUENCE; ARCHAEAL GENOME; ARTICLE; BACTERIAL GENOME; COMPUTER MODEL; GENOME ANALYSIS; MICROBIAL METABOLISM; MICROBIOLOGICAL EXAMINATION; MOLECULAR PROBE; NONHUMAN; PHENOTYPIC VARIATION; PHYLOGENETIC TREE; PROCESS DEVELOPMENT; SENSITIVITY ANALYSIS; SPECIES DIFFERENCE; TAXONOMIC IDENTIFICATION; TAXONOMY; BACTERIUM; GENETICS; GENOMICS; HORIZONTAL GENE TRANSFER; METABOLISM; METHODOLOGY; PHYLOGENY; PROTEOMICS;

BACTERIA; GENE TRANSFER, HORIZONTAL; GENOMICS; PHYLOGENY; PROTEOMICS;

EID: 84860219745     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-13-157     Document Type: Article

References (53)

1. Cardenas E, Tiedje JM. New tools for discovering and characterizing microbial diversity. Curr Opin Biotechnol 2008, 19(6):544-549. 10.1016/j.copbio.2008.10.010, 18984052.
2. Brodie EL, DeSantis TZ, Joyner DC, Baek SM, Larsen JT, Andersen GL, Hazen TC, Richardson PM, Herman DJ, Tokunaga TK, et al. Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation. Appl Environ Microbiol 2006, 72(9):6288-6298. 10.1128/AEM.00246-06, 1563607, 16957256.
3. Hugenholtz P, Tyson GW, Blackall LL. Design and evaluation of 16S rRNA-targeted oligonucleotide probes for fluorescence in situ hybridization. Methods Mol Biol 2002, 179:29-42.
4. Pace NR, Stahl DA, Lane DJ, Olsen GJ. The analysis of natural microbial-populations by Ribosomal-Rna sequences. Adv Microb Ecol 1986, 9:1-55.
5. Sogin ML, Morrison HG, Huber JA, Mark Welch D, Huse SM, Neal PR, Arrieta JM, Herndl GJ. Microbial diversity in the deep sea and the underexplored "rare biosphere". Proc Natl Acad Sci USA 2006, 103(32):12115-12120. 10.1073/pnas.0605127103, 1524930, 16880384.
6. Symonds J. Bergey Manual of Systematic Bacteriology, Krieg, Nr, Holt, Jg. Lancet 1984, 2(8411):1075-1076.
7. Woese CR. Bacterial evolution. Microbiol Rev 1987, 51(2):221-271. 373105, 2439888.
8. Woese CR, Fox GE. Phylogenetic structure of prokaryotic domain - primary kingdoms. Proc Natl Acad Sci USA 1977, 74(11):5088-5090. 10.1073/pnas.74.11.5088, 432104, 270744.
9. Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms - proposal for the domains archaea, bacteria, and eucarya. Proc Natl Acad Sci USA 1990, 87(12):4576-4579. 10.1073/pnas.87.12.4576, 54159, 2112744.
10. Lin J, Gerstein M. Whole-genome trees based on the occurrence of folds and orthologs: implications for comparing genomes on different levels. Genome Res 2000, 10(6):808-818. 10.1101/gr.10.6.808, 310900, 10854412.
11. Qi J, Wang B, Hao BI. Whole proteome prokaryote phylogeny without sequence alignment: A K-string composition approach. J Mol Evol 2004, 58(1):1-11. 10.1007/s00239-003-2493-7, 14743310.
12. Mazurie A, Bonchev D, Schwikowski B, Buck GA. Phylogenetic distances are encoded in networks of interacting pathways. Bioinformatics 2008, 24(22):2579-2585. 10.1093/bioinformatics/btn503, 2579716, 18820265.
13. Chang CW, Lyu PC, Arita M. Reconstructing phylogeny from metabolic substrate-product relationships. BMC Bioinformatics 2011, 12(Suppl 1):S27. 10.1186/1471-2105-12-S1-S27, 3044282, 21342557.
14. Borenstein E, Kupiec M, Feldman MW, Ruppin E. Large-scale reconstruction and phylogenetic analysis of metabolic environments. Proc Natl Acad Sci USA 2008, 105(38):14482-14487. 10.1073/pnas.0806162105, 2567166, 18787117.
15. Clemente JC, Satou K, Valiente G. Reconstruction of phylogenetic relationships from metabolic pathways based on the enzyme hierarchy and the gene ontology. Genome Inform 2005, 16(2):45-55.
16. Clemente JC, Satou K, Valiente G. Phylogenetic reconstruction from non-genomic data. Bioinformatics 2007, 23(2):E110-E115. 10.1093/bioinformatics/btl307, 17237077.
17. Forst CV, Schulten K. Phylogenetic analysis of metabolic pathways. J Mol Evol 2001, 52(6):471-489.
18. Shigenobu S, Watanabe H, Hattori M, Sakaki Y, Ishikawa H. Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp APS. Nature 2000, 407(6800):81-86. 10.1038/35024074, 10993077.
19. Stephens RS, Kalman S, Lammel C, Fan J, Marathe R, Aravind L, Mitchell W, Olinger L, Tatusov RL, Zhao QX, et al. Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis. Science 1998, 282(5389):754-759.
20. Durot M, Bourguignon PY, Schachter V. Genome-scale models of bacterial metabolism: reconstruction and applications. FEMS Microbiol Rev 2009, 33(1):164-190. 10.1111/j.1574-6976.2008.00146.x, 2704943, 19067749.
21. Cash P. Proteomics in the study of the molecular taxonomy and epidemiology of bacterial pathogens. Electrophoresis 2009, 30(Suppl 1):S133-S141.
22. Jabbour RE, Deshpande SV, Stanford MF, Wick CH, Zulich AW, Snyder AP. A protein processing filter method for bacterial identification by mass spectrometry-based proteomics. J Proteome Res 2011, 10(2):907-912. 10.1021/pr101086a, 21126090.
23. Trost B, Haakensen M, Pittet V, Ziola B, Kusalik A. Analysis and comparison of the pan-genomic properties of sixteen well-characterized bacterial genera. BMC Microbiol 2010, 10:258. 10.1186/1471-2180-10-258, 3020658, 20942950.
24. Turse JE, Marshall MJ, Fredrickson JK, Lipton MS, Callister SJ. An empirical strategy for characterizing bacterial proteomes across species in the absence of genomic sequences. PLoS One 2010, 5(11):e13968. 10.1371/journal.pone.0013968, 2980473, 21103051.
25. Ciccarelli FD. Toward automatic reconstruction of a highly resolved tree of life. Science 2006, 311(5765):1283-1287. 10.1126/science.1123061, 16513982.
26. Marchler-Bauer A, Lu SN, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR, et al. CDD: a Conserved Domain Database for the functional annotation of proteins. Nucleic Acids Res 2011, 39:D225-D229. 10.1093/nar/gkq1189, 3013737, 21109532.
27. Bernal A, Ear U, Kyrpides N. Genomes OnLine Database (GOLD): a monitor of genome projects world-wide. Nucleic Acids Res 2001, 29(1):126-127. 10.1093/nar/29.1.126, 29859, 11125068.
28. Pruitt KD, Tatusova T, Maglott DR. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 2007, (35 Database):D61-D65.
29. Boore JL, Brown WM. Big trees from little genomes: mitochondrial gene order as a phylogenetic tool. Curr Opin Genet Dev 1998, 8(6):668-674. 10.1016/S0959-437X(98)80035-X, 9914213.
30. Brown JR, Douady CJ, Italia MJ, Marshall WE, Stanhope MJ. Universal trees based on large combined protein sequence data sets. Nat Genet 2001, 28(3):281-285. 10.1038/90129, 11431701.
31. Li W, Fang W, Ling L, Wang J, Xuan Z, Chen R. Phylogeny based on whole genome as inferred from complete information set analysis. J Biol Phys 2002, 28(3):439-447.
32. Snel B, Bork P, Huynen MA. Genome phylogeny based on gene content. Nat Genet 1999, 21(1):108-110. 10.1038/5052, 9916801.
33. McHardy AC, Rigoutsos I. What's in the mix: phylogenetic classification of metagenome sequence samples. Curr Opin Microbiol 2007, 10(5):499-503. 10.1016/j.mib.2007.08.004, 17933580.
34. Hansen AK, Moran NA. Aphid genome expression reveals host-symbiont cooperation in the production of amino acids. Proc Natl Acad Sci USA 2011, 108(7):2849-2854. 10.1073/pnas.1013465108, 3041126, 21282658.
35. Wilson ACC, Ashton PD, Calevro F, Charles H, Colella S, Febvay G, Jander G, Kushlan PF, Macdonald SJ, Schwartz JF, et al. Genomic insight into the amino acid relations of the pea aphid, Acyrthosiphon pisum, with its symbiotic bacterium Buchnera aphidicola. Insect Mol Biol 2010, 19:249-258.
36. Zientz E, Dandekar T, Gross R. Metabolic interdependence of obligate intracellular bacteria and their insect hosts. Microbiology and Molecular Biology Reviews 2004, 68(4):745-770. 10.1128/MMBR.68.4.745-770.2004, 539007, 15590782.
37. Kisand V, Wikner J. Limited resolution of 16S rDNA DGGE caused by melting properties and closely related DNA sequences. J Microbiol Methods 2003, 54(2):183-191. 10.1016/S0167-7012(03)00038-1, 12782374.
38. Vandamme P, Pot B, Gillis M, DeVos P, Kersters K, Swings J. Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiological Reviews 1996, 60(2):407-438. 239450, 8801440.
39. Kyrpides NC. Genomes OnLine Database (GOLD 1.0): a monitor of complete and ongoing genome projects world-wide. Bioinformatics 1999, 15(9):773-774. 10.1093/bioinformatics/15.9.773, 10498782.
40. Stiles ME, Holzapfel WH. Lactic acid bacteria of foods and their current taxonomy. Int J Food Microbiol 1997, 36(1):1-29. 10.1016/S0168-1605(96)01233-0, 9168311.
41. Boussau B, Gueguen L, Gouy M. Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of Bacteria. BMC Evolutionary Biology 2008, 8:272. 10.1186/1471-2148-8-272, 2584045, 18834516.
42. Dutta C, Pan A. Horizontal gene transfer and bacterial diversity. J Biosci 2002, 27(1):27-33. 10.1007/BF02703681, 11927775.
43. Kanhere A, Vingron M. Horizontal Gene Transfers in prokaryotes show differential preferences for metabolic and translational genes. BMC Evolutionary Biology 2009, 9:9. 10.1186/1471-2148-9-9, 2651853, 19134215.
44. Garcia-Vallve S, Guzman E, Montero MA, Romeu A. HGT-DB: a database of putative horizontally transferred genes in prokaryotic complete genomes. Nucleic Acids Res 2003, 31(1):187-189. 10.1093/nar/gkg004, 165451, 12519978.
45. Coram NJ, Rawlings DE. Molecular relationship between two groups of the genus Leptospirillum and the finding that Leptosphillum ferriphilum sp nov dominates South African commercial biooxidation tanks that operate at 40 degrees C. Appl Environ Microbiol 2002, 68(2):838-845. 10.1128/AEM.68.2.838-845.2002, 126727, 11823226.
46. Tyson GW, Lo I, Baker BJ, Allen EE, Hugenholtz P, Banfield JF. Genome-directed isolation of the key nitrogen fixer Leptospirillum ferrodiazotrophum sp nov from an acidophilic microbial community. Appl Environ Microbiol 2005, 71(10):6319-6324. 10.1128/AEM.71.10.6319-6324.2005, 1266007, 16204553.
47. Sekiguchi Y, Muramatsu M, Imachi H, Narihiro T, Ohashi A, Harada H, Hanada S, Kamagata Y. Thermodesulfovibrio aggregans sp nov and Thermodesulfovibrio thiophilus sp nov., anaerobic, thermophilic, sulfate-reducing bacteria isolated from thermophilic methanogenic sludge, and emended description of the genus Thermodesulfovibrio. Int J Syst Evol Micr 2008, 58:2541-2548.
48. Dopson M, Baker-Austin C, Bond PL. First use of two-dimensional polyacrylamide gel electrophoresis to determine phylogenetic relationships. J Microbiol Meth 2004, 58(3):297-302.
49. Delcher AL, Kasif S, Fleischmann RD, Peterson J, White O, Salzberg SL. Alignment of whole genomes. Nucleic Acids Res 1999, 27(11):2369-2376. 10.1093/nar/27.11.2369, 148804, 10325427.
50. Lu CL, Huang YL, Huang CC, Tang CY. SoRT(2): a tool for sorting genomes and reconstructing phylogenetic trees by reversals, generalized transpositions and translocations. Nucleic Acids Res 2010, 38:W221-W227. 10.1093/nar/gkq520, 2896082, 20538651.
51. Colwell RR. Polyphasic Taxonomy of Genus Vibrio - Numerical Taxonomy of Vibrio-Cholerae, Vibrio-Parahaemolyticus, and Related Vibrio Species. Journal of Bacteriology 1970, 104(1):410-433. 248227, 5473901.
52. Repoila F, Darfeuille F. Small regulatory non-coding RNAs in bacteria: physiology and mechanistic aspects. Biol Cell 2009, 101(2):117-131. 10.1042/BC20070137, 19076068.
53. Aho AV, Hopcroft JE, Ullman JD. On finding lowest common ancestors in trees. Proceedings of the fifth annual ACM symposium on Theory of computing 1973, 253-265. Austin: ACM.