Omics for understanding microbial functional dynamics

Environmental Microbiology

Volumn 14, Issue 1, 2012, Pages 1-3

  Jansson, Janet K ^a   Neufeld, Josh D ^b   Moran, Mary Ann ^c   Gilbert, Jack A ^d,e  

^a LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^b UNIVERSITY OF WATERLOO   (Canada)

^c UNIVERSITY OF GEORGIA   (United States)

^d ARGONNE NATIONAL LABORATORY   (United States)

^e UNIVERSITY OF CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGY; DNA SEQUENCE; ECOLOGY; GENE EXPRESSION PROFILING; GENOMICS; LETTER; METABOLOMICS; METHODOLOGY; MICROBIOLOGICAL PHENOMENA AND FUNCTIONS; PROTEOMICS; SEQUENCE ANALYSIS;

COMPUTATIONAL BIOLOGY; ECOLOGY; GENE EXPRESSION PROFILING; GENOMICS; METABOLOMICS; MICROBIOLOGICAL PHENOMENA; PROTEOMICS; SEQUENCE ANALYSIS, DNA; SEQUENCE ANALYSIS, RNA;

EID: 84855285090     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/j.1462-2920.2011.02518.x     Document Type: Letter

References (14)

1. Chourey, K., Jansson, J., VerBerkmoes, N., Shah, M., Chavarria, K.L., Tom, L.M., etal. (2010) Direct cellular lysis/protein extraction protocol for soil metaproteomics. J Proteome Res 9: 6615-6622.
2. Dumont, M.G., Pommerenke, B., Casper, P., and Conrad, R. (2011) DNA-, rRNA- and mRNA-based stable isotope probing of aerobic methanotrophs in lake sediment. Environ Microbiol 13: 1153-1167.
3. Edlund, A., and Jansson, J.K. (2008) Use of bromodeoxyuridine immunocapture to identify psychrotolerant phenanthrene-degrading bacteria in phenanthrene-enriched polluted Baltic Sea sediments. FEMS Microbiol Ecol 65: 513-525.
4. Jansson, J., Willing, B., Lucio, M., Fekete, A., Dicksved, J., Halfvarson, J., etal. (2009) Metabolomics reveals metabolic biomarkers of Crohn's disease. PLoS ONE 4: e6386.
5. Larsen, P.E., Collart, F., Field, D., McGrath, J., Quinn, J., Gilbert, J.A., etal. (2011). Predicted Relative Metabolomic Turnover (PRMT): determining metabolic turnover from a coastal marine metagenomic dataset. Conference proceedings for BIOSTEC 2011; Meta2011, Metagenomic Sequence Data Analysis.
6. Morris, R.M., Nunn, B.L., Frazar, C., Goodlett, D.R., Ting, Y.S., and Rocap, G. (2010) Comparative metaproteomics reveals ocean-scale shifts in microbial nutrient utilization and energy transduction. ISME J 4: 673-685.
7. Mou, X., Sun, S., etal. (2008) Bacterial carbon processing by generalist species in the coastal ocean. Nature 451: 708-711.
8. Neufeld, J.D., Vohra, J., Dumont, M.G., Lueders, T., Manefield, M., Friedrich, M.W., and Murrell, J.C. (2007) DNA stable-isotope probing. Nat Protoc 2: 860-866.
9. Passalacqua, K.D., Varadarajan, A., Ondov, B.D., Okou, D.T., Zwick, M.E., and Bergman, N.H. (2009) Structure and complexity of a bacterial transcriptome. J Bacteriol 191: 3203-3211.
10. Ram, R.J., Verberkmoes, N.C., Thelen, M.P., Tyson, G.W., Baker, B.J., Blake, R.C., 2nd, etal. (2005) Community proteomics of a natural microbial biofilm. Science 308: 1915-1920.
11. Rehman, A., Lepage, P., Nolte, A., Hellmig, S., Schreiber, S., Ott, S.J. (2010) Transcriptional activity of the dominant gut mucosal microbiota in chronic inflammatory bowel disease patients. J Med Microbiol 59: 1114-1122.
12. Tao, H., Bausch, C., Richmond, C., Blattner, F.R., and Conway, T. (1999) Functional genomics: expression analysis of Escherichia coli growing on minimal and rich media. J Bacteriol 181: 6425-6440.
13. Urich, T., Lanzen, A., Qi, J., Huson, D.H., Schleper, C., and Schuster, S.C. (2008) Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome. PLoS ONE 3: e2527.
14. Verberkmoes, N.C., Russell, A.L., Shah, M., Godzik, A., Rosenquist, M., Halfvarson, J., etal. (2009) Shotgun metaproteomics of the human distal gut microbiota. ISME J 3: 179-189.