An application of statistics to comparative metagenomics

BMC Bioinformatics

Volumn 7, Issue , 2006, Pages

  Rodriguez Brito, Beltran ^a   Rohwer, Forest ^a   Edwards, Robert A ^a,b  

^a SAN DIEGO STATE UNIVERSITY   (United States)

^b Fellowship for Interpretation of Genomes   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACID MINE DRAINAGE; GENOMIC DNA; METAGENOMES; METAGENOMICS; MODEL COMMUNITIES; NON-REDUNDANT; SEQUENCE ANALYSIS;

ECOSYSTEMS; PHYSIOLOGY;

METABOLISM;

GENOMIC DNA; NUCLEIC ACID; PHOSPHATE; PROTEOME;

ARTICLE; CONTROLLED STUDY; DATA BASE; DNA ISOLATION; DNA SEQUENCE; ECOLOGY; ECOSYSTEM; ENVIRONMENTAL FACTOR; GENOMICS; HYPOTHESIS; METAGENOMICS; METHODOLOGY; MICROBIAL METABOLISM; NONHUMAN; PHYSIOLOGY; PREDICTION; SEQUENCE ANALYSIS; STATISTICAL ANALYSIS; ALGORITHM; BIOLOGICAL MODEL; COMPARATIVE STUDY; COMPUTER SIMULATION; METABOLISM; PROCEDURES; SIGNAL TRANSDUCTION; STATISTICAL MODEL;

ALGORITHMS; COMPUTER SIMULATION; DATA INTERPRETATION, STATISTICAL; GENOMICS; MODELS, BIOLOGICAL; MODELS, STATISTICAL; PROTEOME; SEQUENCE ANALYSIS, DNA; SIGNAL TRANSDUCTION;

EID: 33744784298     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-7-162     Document Type: Article

References (29)

1. Riesenfeld CS, Schloss PD, Handelsman J: Metagenomics: genomic analysis of microbial communities. Annu Rev Genet 2004, 38:525-552.
2. Breitbart M, Felts B, Kelley S, Mahaffy JM, Nulton J, Salamon P, Rohwer F: Diversity and population structure of a near-shore marine-sediment viral community. Proc R Soc Lond B Biol Sci 2004, 271(1539):565-574.
3. Breitbart M, Hewson I, Felts B, Mahaffy JM, Nulton J, Salamon P, Rohwer F: Metagenomic analyses of an uncultured viral community from human feces. J Bacteriol 2003, 185(20):6220-6223.
4. Breitbart M, Salamon P, Andresen B, Mahaffy JM, Segall AM, Mead D, Azam F, Rohwer F: Genomic analysis of uncultured marine viral communities. Proc Natl Acad Sci U S A 2002, 99(22):14250-14255.
5. Cann AJ, Fandrich SE, Heaphy S: Analysis of the virus population present in equine faeces indicates the presence of hundreds of uncharacterized virus genomes. Virus Genes 2005, 30(2):151-156.
6. Tringe SG, von Mering C, Kobayashi A, Salamov AA, Chen K, Chang HW, Podar M, Short JM, Mathur EJ, Detter JC, Bork P, Hugenholtz P, Rubin EM: Comparative metagenomics of microbial communities. Science 2005, 308(5721):554-557.
7. Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers YH, Smith HO: Environmental genome shotgun sequencing of the Sargasso Sea. Science 2004, 304(5667):66-74.
8. Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS, Banfield JF: Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 2004, 428(6978):37-43.
9. Overbeek R, Begley T, Butler R, Choudhuri J, Chuang H, Cohoon M, de Crécy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank E, Gerdes S, Glass E, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy A, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, Pusch G, Rodionov D, Rückert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y, Zagnitko O, Vonstein V: The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res 2005.
10. Keil RG, Kirchman DL: Utilization of dissolved protein and amino acids in the northern Sargasso Sea. Aquatic Microbial Ecology 1999, 18(3):293-300.
11. Suttle CA, Chan AM, Fuhrman JA: Dissolved free amino-acids in the Sargasso Sea - uptake and respiration rates, turnover times, and concentrations. Marine Ecology-Progress Series 1991, 70(2):189-199.
12. Oren A: Diversity of halophilic microorganisms: Environments, phylogeny, physiology, and applications. Journal Of Industrial Microbiology & Biotechnology 2002, 28(1):56-63.
13. Roesser M, Muller V: Osmoadaptation in bacteria and archaea: common principles and differences. Environ Microbiol 2001, 3(12):743-754.
14. Sleator RD, Hill C: Bacterial osmoadaptation: the role of osmolytes in bacterial stress and virulence. Fems Microbiology Reviews 2002, 26(1):49-71.
15. Yancey PH, Clark ME, Hand SC, Bowlus RD, Somero GN: Living with water stress: evolution of osmolyte systems. Science 1982, 217(4566):1214-1222.
16. Galinski EA: Osmoadaptation in bacteria. Adv Microb Physiol 1995, 37:272-328.
17. Mackay MA, Norton RS, Borowitzka LJ: Organic osmoregulatory solutes In cyanobacteria. Journal Of General Microbiology 1984, 130(SEP):2177-2191.
18. Deiwick J, Nikolaus T, Erdogan S, Hensel M: Environmental regulation of Salmonella pathogenicity island 2 gene expression. Mol Microbiol 1999, 31(6):1759-1773.
19. Wu JF, Sunda W, Boyle EA, Karl DM: Phosphate depletion in the western North Atlantic Ocean. Science 2000, 289(5480):759-762.
20. Grossart HP, Riemann L, Azam F: Bacterial motility in the sea and its ecological implications. Aquatic Microbial Ecology 2001, 25(3):247-258.
21. Mitchell JG, Pearson L, Bonazinga A, Dillon S, Khouri H, Paxinos R: Long lag times and high velocities in the motility of natural assemblages of marine-bacteria. Applied And Environmental Microbiology 1995, 61(3):877-882.
22. McCarren J, Heuser J, Roth R, Yamada N, Martone M, Brahamsha B: Inactivation of swmA results in the loss of an outer cell layer in a swimming synechococcus strain. J Bacteriol 2005, 187(1):224-230.
23. Waterbury JB, Willey JM, Franks DG, Valois FW, Watson SW: A cyanobacterium capable of swimming motility. Science 1985, 230(4721):74-76.
24. Henrichsen J: The occurrence of twitching motility among gram-negative bacteria. Acta Pathol Microbiol Scand [B] 1975, 83(3):171-178.
25. Supplemental Data on the String Website [http:string.embl.de/metagenome_comp_suppl/ keggmap.detection.frequencies.txt]
26. Oremland RS, Capone DG, Stolz JF, Fuhrman J: Whither or wither geomicrobiology in the era of 'community metagenomics'. Nat Rev Microbiol 2005, 3(7):572-578.
27. The SEED [http://theseed.uchicago.edu/FIG/index.cgi]
28. Meyer F, Goesmann A, McHardy AC, Bartels D, Bekel T, Clausen J, Kalinowski J, Linke B, Rupp O, Giegerich R, Puhler A: GenDB - an open source genome annotation system for prokaryote genomes. Nucleic Acids Res 2003, 31(8):2187-2195.
29. DeLong EF: Microbial community genomics in the ocean. Nat Rev Microbiol 2005, 3(6):459-469.