Global phenotypic characterization of bacteria

FEMS Microbiology Reviews

Volumn 33, Issue 1, 2009, Pages 191-205

  Bochner, Barry R ^a  

^a Biolog Inc   (United States)

Author keywords

Cell phenotypes; Metabolomics; Phenomics; Phenotypic analysis; Phenotypic characterization; Phenotyping

Indexed keywords

BACTERIAL GROWTH; BACTERIAL METABOLISM; BACTERIUM CULTURE; BACTERIUM IDENTIFICATION; BIOLOGICAL MODEL; BIOPROCESS; CARBON METABOLISM; CELL TRANSFORMATION; GENE FUNCTION; GENOMICS; METABOLOMICS; MICROBIAL RESPIRATION; MICROMORPHOLOGY; NITROGEN METABOLISM; NONHUMAN; PATHOGENICITY; PHENOTYPE; PROTEOMICS; REVIEW; TAXONOMY;

BACTERIA; INDUSTRIAL MICROBIOLOGY; METABOLIC NETWORKS AND PATHWAYS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHENOTYPE; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY;

EID: 57649123534     PISSN: 01686445     EISSN: 15746976     Source Type: Journal    
DOI: 10.1111/j.1574-6976.2008.00149.x     Document Type: Review

References (92)

1. Baba T, Huan HC, Datsenko K, Wanner BL Mori H (2008) The applications of systematic in-frame, single-gene knockout mutant collection of Escherichia coli K-12. Method Mol Biol 416 : 183 194.
2. Bailey AM, Paulsen IT Piddock LJ (2008) RamA confers multidrug resistance in Salmonella enterica via increased expression of acrB, which is inhibited by chlorpromazine. Antimicrob Agents Ch 52 : 3604 3611.
3. Bibb MJ (2005) Regulation of secondary metabolism in streptomycetes. Curr Opin Microbiol 8 : 208 215.
4. Biswas S Biswas I (2005) Role of HtrA in surface protein expression and biofilm formation by Streptococcus mutants. Infect Immun 73 : 6923 6934.
5. Bochner B (1992) Methods for detection, identification and speciation of Listerias. US Patent 5,134,063.
6. Bochner BR (2003) New technologies to assess genotype-phenotype relationships. Nat Rev Genet 4 : 309 314.
7. Bochner BR Savageau MA (1977) Generalized indicator plate for genetic, metabolic, and taxonomic studies with microorganisms. Appl Environ Microb 33 : 434 444.
8. Bochner BR, Gadzinski P Panomitros E (2001) Phenotype MicroArrays for high-throughput phenotypic testing and assay of gene function. Genome Res 11 : 1246 1255.
9. Bochner BR, Giovannetti L Viti C (2008) Important discoveries from analysing bacterial phenotypes. Mol Microbiol 70 : 274 280.
10. Chavira M, Cao N, Le K, Riar T, Moradshahi N, McBride M, Lux R Shi W (2007) β-d-Allose inhibits fruiting body formation and sporulation in Myxococcus xanthus. J Bacteriol 189 : 169 178.
11. Chen S, Cui S, McDermott PF, Zhao S, White DG, Paulsen I Meng J (2007) Contribution of target gene mutations and efflux to decreased susceptibility of Salmonella enterica Serovar Typhimurium to fluoroquinolones and other antimicrobials. Antimicrob Agents Ch 51 : 535 542.
12. Chico-Calero I, Suarez M, Gonzalez-Zorn B, Scortti M, Slaghuis J, Goebel W, The European Listeria Genome Consortium Vazquez-Boland JA (2002) Hpt, a bacterial homolog of the microsomal glucose-6-phosphate translocase, mediates rapid intracellular proliferation in Listeria. P Natl Acad Sci USA 99 : 431 436.
13. Chouikha I, Germon P, Brée A, Gilot P, Moulin-Schouleur M Schouler C (2006) A selC-associated genomic island of the extraintestinal avian pathogenic Escherichia coli strain BEN2908 is involved in carbohydrate uptake and virulence. J Bacteriol 188 : 977 987.
14. Cooper VS Lenski RE (2000) The population genetics of ecological specialization in evolving Escherichia coli populations. Nature 407 : 736 739.
15. Covert MW, Knight EM, Reed JL, Herrgard MJ Palsson BO (2004) Integrating high-throughput and computational data elucidates bacterial networks. Nature 429 : 92 96.
16. Dalebroux ZD, Edwards RL Swanson MS (2008) SpoT governs Legionella pneumophila differentiation in host macrophages. Mol Microbiol, in press.
17. Datsenko KA Wanner BL (2000) One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. P Natl Acad Sci USA 97 : 6640 6645.
18. Datta A, Carter L Burall L (2008) Comparative phenotypic microarray analysis of Listeria monocytogenes strains involved in invasive and gastroenteritis listeriosis outbreaks (abstract). Florence Conference on Phenotype MicroArray Analysis of Microorganisms: The Environment, Agriculture, and Human Health, Florence, Italy.
19. den Dooren de Jong LE (1926) Bijdrage tot de kennis van het mineralsatieproces. Dissertation, Rotterdam.
20. Druzhinina IS, Schmoll M, Seiboth B Kubicek CP (2006) Global carbon utilization profiles of wild-type, mutant, and transformant strains of Hypocrea jecorina. Appl Environ Microb 72 : 2126 2133.
21. Durso LM, Smith D Hutkins RW (2004) Measurements of fitness and competition in commensal Escherichia coli and E. coli O157:H7 strains. Appl Environ Microb 70 : 6466 6472.
22. Edwards RL, Dalebroux ZD Swanson MS (2008) Legionella pneumophila couples fatty acid flux to microbial differentiation and virulence. Mol Microbiol, in press.
23. Erol I, Jeong K-C, Baumler DJ, Vykhodets B, Choi SH Kaspar CW (2006) H-NS controls metabolism and stress tolerance in Escherichia coli O157:H7 that influence mouse passage. BMC Microbiol 6 : 72 83.
24. Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V Palsson BØ (2007) A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol Syst Biol 3 : 121 138.
25. Fodor SA, Rava RP, Huang XC, Pease AC, Holmes CP Adams CL (1993) Multiplexed biochemical assays with biological chips. Nature 364 : 555 556.
26. Franco-Buff A, Gomez V, Olender E, Gadzinski G Bochner B (2008) Development of a new test panel for identification of both Gram-negative and Gram-positive bacteria (abstract). ECCMID 2008, Barcelona.
27. Fraser CM, Gocayne JD, White O et al 1995) The minimal gene complement of Mycoplasma genitalium. Science 270 : 397 403.
28. Friedl MA, Kubicek CP Druzhinina IS (2008a) Carbon source dependence and photostimulation of conidiation in Hypocrea atroviridis. Appl Environ Microb 74 : 245 250.
29. Friedl MA, Schmoll M, Kubicek CP Druzhinina IS (2008b) Photostimulation of Hypocrea atroviridis growth occurs due to a cross-talk of carbon metabolism, blue light receptors and response to oxidative stress. Microbiology 154 : 1229 1241.
30. Funchain P, Yeung A, Stewart JL, Lin R, Slupska MM Miller JH (2000) The consequences of growth of a mutator strain of Escherichia coli as measured by loss of function among multiple gene targets and loss of fitness. Genetics 154 : 959 970.
31. Gale CA, Bendel CM, McClellan M, Hauser M, Becker JM, Berman J Hostetter MK (1998) Linkage of adhesion, filamentous growth, and virulence in Candida albicans to a single gene, INT1. Science 279 : 1355 1358.
32. 2+ as an extracellular signal: environmental regulation of Salmonella virulence. Cell 84 : 165 174.
33. Gorman C (2003) Fast tracking bioprocessing development and optimization. Drug Plus Int 2 : 6 9.
34. Guard-Bouldin J, Gast RK, Humphrey TJ, Henzler DJ, Morales C Coles K (2004) Subpopulation characteristics of egg-contaminating Salmonella enterica serovar Enteritidis as defined by the lipopolysaccharide O chain. Appl Environ Microb 70 : 2756 2763.
35. Haoping L (2001) Transcriptional control of dimorphism in Candida albicans. Curr Opin Microbiol 4 : 728 735.
36. Hauser NC, Fellenberg K Rupp S (2002) How to discover pathogenic mechanisms - new evaluation tools towards drug discovery. Screening 3 : 28 31.
37. Holtz AE, Fodor IK, Fitch JP McCutchen-Maloney SL (2004) Metabolic differences in Yersinia pestis as a function of temperature and calcium detected by phenotype arrays (abstract). 44th Annual Meeting of the American Society for Cell Biology. Washington, DC.
38. Ishii N, Nakahigashi K, Baba T, et al 2007) Multiple high-throughput analyses monitor the response of E. coli to perturbations. Science 316 : 593 597.
39. Iversen C, Lehner A, Mullane N, Bidlas E, Cleenwerck I, Marugg J, Fanning S, Stephan R Joosten H (2007) The taxonomy of Enterobacter sakazakii: proposal of a new genus Cronobacter gen. nov. and descriptions of Cronobacter sakazakii comb. nov. Cronobacter sakazakii subsp. sakazakii, comb. nov., Cronobacter sakazakii subsp. malonaticus subsp. nov., Cronobacter turicensis sp. nov., Cronobacter muytjensii sp. nov., Cronobacter dublinensis sp. nov. and Cronobacter genomospecies 1. BMC Evol Biol 7 : 64 74.
40. Johnson DA, Tetu SG, Phillippy K, Chen J, Ren Q Paulsen IT (2008) High throughput phenotypic characterization of Pseudomonas aeruginosa membrane transport genes. PLoS Genet 4 : 1 11.
41. Jones J, Studholme DJ, Knight CG Preston GM (2007) Integrated bioinformatic and phenotypic analysis of RpoN-dependent traits in the plant growth-promoting bacterium Pseudomonas fluorescens SBW25. Environ Microbiol 9 : 3046 3064.
42. Kapatral V, Campbell JW, Minnich SA, Thomson NR, Matsumura P Pruess BM (2004) Gene array analysis of Yersinia enterocolitica FlhD and FlhC: regulation of enzymes affecting synthesis and degradation of carbamoylphosphate. Microbiology 150 : 2289 2300.
43. Keymer DP, Miller MC, Schoolnik GK Bohm AB (2007) Genomic and phenotypic diversity of coastal Vibrio cholerae strains is linked to environmental factors. Appl Environ Microb 73 : 3705 3714.
44. Koo BM, Yoon MJ, Lee CR, Nam TW, Choe YJ, Jaffe H, Peterkofsky A Seok YJ (2004) A Novel fermentation/respiration switch protein regulated by enzyme IIAGlc in Escherichia coli. J Biol Chem 279 : 31613 31621.
45. ® Microbial Identification System. Encyclopedia of Rapid Microbiological Methods, Vol. 3 (Miller MJ, ed), pp. 1 56. DHI Publishing, LLC, River Grove, IL.
46. Lee C-R, Koo B-M, Cho S-H, Kim Y-J, Yoon M-J, Peterkofsky A Seok Y-J (2005) Requirements of the dephospho-form of enzyme IIANtr for derepression of Escherichia coli K-12 ilvBN expression. Mol Microbiol 58 : 334 344.
47. Lee C-R, Cho S-H, Yoon M-J, Peterkofsky A Seok Y-J (2007) Escherichia coli enzyme IIANtr regulates the K+ transporter TrkA. P Natl Acad Sci USA 104 : 4124 4129.
48. Lei X-H Bochner B (2008) Phenotype MicroArray analysis of the metabolism of Helicobacter pylori (abstract). Spring Meeting, Society for General Microbiology, Edinburgh.
49. Li W Lu C-D (2007) Regulation of carbon and nitrogen utilization by CbrAB and NtrBC two-component systems in Pseudomonas aeruginosa. J Bacteriol 189 : 5413 5420.
50. Lifland BD (1997) Identification of Francisella tularensis using Biolog GN MicroPlate with visual plate reading (abstract). 40th Meeting, American Association of Veterinary Laboratory Diagnosticians, Louisville, KY.
51. Liu H (2001) Transcriptional control of dimorphism in Candida albicans. Curr Opin Microbiol 4 : 728 735.
52. Llama-Palacios A, Lopez-Solanilla E Rodriguez-Palenzuela P (2005) Role of the PhoP-PhoQ system in the virulence of Erwinia chrysanthemi strain 3937: involvement in sensitivity to plant antimicrobial peptides, survival at acid pH, and regulation of pectolytic enzymes. J Bacteriol 187 : 2157 2162.
53. Loh KD, Gyaneshwar P, Papadimitriou EM, Fong R, Kim K-S, Parales R, Zhou Z, Inwood W Kustu S (2006) A previously undescribed pathway for pyrimidine catabolism. P Natl Acad Sci USA 103 : 5114 5119.
54. MacLean RC Bell G (2002) Experimental adaptive radiation in Pseudomonas. Am Nat 160 : 569 581.
55. MacLean RC Bell G (2003) Divergent evolution during an adaptive radiation. Proc Roy Soc B - Biol Sci 270 : 1645 1650.
56. Maheswaran M Forchhammer K (2003) Carbon-source-dependent nitrogen regulation in Escherichia coli is mediated through glutamine-dependent GlnB signalling. Microbiology 149 : 2163 2172.
57. Mascher T, Hachmann A-B Helmann J D (2007) Regulatory overlap and functional redundancy among Bacillus subtilis extracytoplasmic function σ factors. J Bacteriol 189 : 7500 7511.
58. Mekalanos JJ (1992) Environmental signals controlling expression of virulence determinants in bacteria. J Bacteriol 174 : 1 7.
59. Mols M, de Been M, Zwietering MH, Moezelaar R Abee T (2007) Metabolic capacity of Bacillus cereus strains ATCC 14579 and ATCC 10987 interlinked with comparative genomics. Environ Microbiol 9 : 2933 2944.
60. Morales CA, Porwollik S, Frye JG, Kinde H, McClelland M Guard-Bouldin J (2005) Correlation of phenotype with the genotype of egg-contaminating Salmonella enterica serovar Enteritidis. Appl Environ Microb 71 : 4388 4399.
61. Morales CA, Gast R Guard-Bouldin J (2006) Linkage of avian and reproductive tract tropism with sequence divergence adjacent to the 5S ribosomal subunit rrfH of Salmonella enterica. FEMS Microbiol Lett 264 : 48 58.
62. Mukherjee A, Jackson SA, LeClerc JE Cebula TA (2006) Exploring genotypic and phenotypic diversity of microbes using microarray approaches. Toxicol Mech Method 16 : 121 128.
63. Mukherjee A, Mammel MK, LeClerc JE Cebula TA (2008) Altered utilization of N-acetyl-d-galactosamine by Escherichia coli O157:H7 from the 2006 spinach outbreak. J Bacteriol 190 : 1710 1717.
64. Munoz-Elias EJ McKinney JD (2006) Carbon metabolism of intracellular bacteria. Cell Microbiol 8 : 10 22.
65. Nagy V, Seidl V, Szakacs G, Komoñ-Zelazowska M, Kubicek CP Druzhinina IS (2007) Application of DNA bar codes for screening of industrially important fungi: the haplotype of Trichoderma harzianum sensu stricto indicates superior chitinase formation. Appl Environ Microb 73 : 7048 7058.
66. Neidhardt FC, Vaughn V, Phillips TA Bloch PL (1983) Gene-protein index of Escherichia coli K-12. Microbiol Rev 2 : 231 284.
67. Oberhardt MA, Puchałka J, Fryer KE, Martins dos Santos VA Papin JA (2008) Genome-scale metabolic network analysis of the opportunistic pathogen Pseudomonas aeruginosa PAO1. J Bacteriol 190 : 2790 2803.
68. O'Farrell PH (1975) High resolution two-dimensional electrophoresis of proteins. J Biol Chem 250 : 4007 4021.
69. Oh YK, Palsson BO, Park SM, Schilling CH Mahadevan R (2007) Genome-scale reconstruction of metabolic network in Bacillus subtilis based on high-throughput phenotyping and gene essentiality data. J Biol Chem 282 : 28791 28799.
70. Perkins AE Nicholson WL (2008) Uncovering new metabolic capabilities of Bacillus subtilis using phenotype profiling of rifampin-resistant rpoB mutants. J Bacteriol 190 : 807 814.
71. Pruess BM, Campbell JW, Van Dyk TK, Zhu C, Kogan Y Matsumura P (2003) FlhD/FlhC is a regulator of anaerobic respiration and the Entner-Doudoroff pathway through induction of the methyl-accepting chemotaxis protein aer. J Bacteriol 185 : 534 543.
72. Rico A Preston GM (2008) Pseudomonas syringae pv. tomato DC3000 uses constitutive and apoplast-induced nutrient assimilation pathways to catabolize nutrients that are abundant in the tomato apoplast. Mol Plant Microbe In 21 : 269 282.
73. Ripio MT, Brehm K, Lara M, Suarez M Vazquez-Boland JA (1997) Glucose-1-phosphate utilization by Listeria monocytogenes is PrfA dependent and coordinately expressed with virulence factors. J Bacteriol 179 : 7174 7180.
74. Sauer JD, Bachman MA Swanson MS (2005) The phagosomal transporter A couples threonine acquisition to differentiation and replication of Legionella pneumophila in macrophages. P Natl Acad Sci USA 102 : 9924 9929.
75. Schmid AK, Reiss DJ, Kaur A, Pan M, King N, Van PT, Hohmann L, Martin DB Baliga N (2007) The anatomy of microbial cell state transitions in response to oxygen. Genome Res 17 : 1399 1413.
76. Schnupf P, Hofmann J, Norseen J, Glomski IJ, Schwartzstein H Decatur AL (2006) Regulated translation of listeriolysin O controls virulence of Listeria monocytogenes. Mol Microbiol 61 : 999 1012.
77. Scortti M, Monzo HJ, Lacharme-Lora L, Lewis DA Vazquez-Boland JA (2007) The PrfA virulence regulon. Microbes Infect 9 : 1196 1207.
78. Seidl V, Druzhinina IS Kubicek CP (2006) A screening system for C-sources enhancing beta-N-acetylglucosaminidase formation in Hypocrea atroviridis (Trichoderma atroviride). Microbiology 152 : 2003 2012.
79. Shakarji L, Mikael LG, Srikumar R, Kobisch M, Coulton JW Jacques M (2006) FhuA and HgbA, outer membrane proteins of Actinobacillus pleuropneumoniae: their role as virulence determinants. Can J Microbiol 52 : 391 396.
80. Stephens JC, Artz SW Adams BN (1975) Guanosine 5′-diphosphate 3′-diphosphate (ppGpp): positive effector for histidine operon transcription and general signal for amino-acid deficiency. P Nat Acad Sci USA 72 : 4389 4393.
81. Tohsato Y Mori H (2008) Phenotype profiling of single gene deletion mutants of E. coli using Biolog technology. Proceedings of the 19th International Conference on Genome Informatics (GIW 2008), Gold Coast, Australia, pp. 1 11.
82. Tracy BS, Edwards KK Eisenstark A (2002) Carbon and nitrogen substrate utilization by archival Salmonella typhimurium LT2 Cells. BMC Evol Biol 2 : 1 6.
83. Upadhyay B, Fielder MD Wheeler PR (2008) Adapting Biolog Phenotype MicroArray technology to reveal the metabolomics of Mycobacterium tuberculosis and Mycobacterium bovis, slow-growing pathogens with d=0.03 to 0.05/h (abstract). Florence Conference on Phenotype MicroArray Analysis of Microorganisms: The Environment, Agriculture, and Human Health, Florence, Italy.
84. VanBogelen RA, Schiller EE, Thomas JD Neidhardt FC (1999) Diagnosis of cellular states of microbial organisms using proteomics. Electrophoresis 11 : 2149 2159.
85. Van Dyk TK, Templeton LJ, Cantera KA, Sharpe PL Sariaslani FS (2004) Characterization of the Escherichia coli AaeAB efflux pump: a metabolic relief valve? J Bacteriol 186 : 7196 7204.
86. Vazquez-Boland JA, Kuhn M, Berche P, Chakraborty T, Dominguez-Bernal G, Goebel W, Gonzalez-Zorn B, Wehland J Kreft J (2001) Listeria pathogenesis and molecular virulence determinants. Clin Microbiol Rev 14 : 584 640.
87. * proteins and structure-function of the virulence regulator PrfA. Mol Microbiol 52 : 1553 1565.
88. Venail PA, MacLean RC, Bouvier T, Brockhurst MA, Hochberg ME Mouquet N (2008) Diversity and productivity peak at intermediate dispersal rate in evolving metacommunities. Nature 452 : 210 214.
89. Viti C, Decorosi F, Tatti E Giovannetti L (2007) Characterization of chromate-resistant and -reducing bacteria by traditional means and by a high-throughput phenomic technique for bioremediation purposes. Biotechnol Progr 23 : 553 559.
90. von Eiff C, McNamara P, Becker K, Bates D, Lei X-H, Ziman M, Bochner BR, Peters G Proctor RA (2006) Phenotype MicroArray profiling of Staphylococcus aureus menD and hemB mutants with the small-colony-variant phenotype. J Bacteriol 188 : 687 693.
91. Zhang X-X Rainey PB (2008) Dual Involvement of CbrAB and NtrBC in the regulation of histidine utilization in Pseudomonas fluorescens SBW25. Genetics 178 : 185 195.
92. Zhou L, Lei X-H, Bochner BR Wanner BL (2003) Phenotype MicroArray analysis of Escherichia coli K-12 mutants with deletions of all two-component systems. J Bacteriol 185 : 4956 4972.