Development of functional gene microarrays for microbial community analysis

Current Opinion in Biotechnology

Volumn 23, Issue 1, 2012, Pages 49-55

  He, Zhili ^a   Deng, Ye ^a   Zhou, Jizhong ^a  

^a UNIVERSITY OF OKLAHOMA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBIOTIC RESISTANCE; BIOGEOCHEMICAL CYCLING; ENVIRONMENTAL CONTAMINANT; EXTREME ENVIRONMENT; FUNCTIONAL GENES; MICROBIAL COMMUNITIES; MICROBIAL COMMUNITY ANALYSIS; QUANTITATIVE TOOL; RAPID ANALYSIS; STRESS RESPONSE;

ANALYTICAL GEOCHEMISTRY; BIODEGRADATION; MICROORGANISMS; PHOSPHORUS; SULFUR;

GENES;

AMOA GENE; FUNCTIONAL GENE ARRAY; GENE PRODUCT; GENE SEQUENCE; GENE TARGETING; GENE TECHNOLOGY; MICROARRAY ANALYSIS; MICROBIAL COMMUNITY; NIRK GENE; NIRS GENE; NONHUMAN; OLIGONUCLEOTIDE PROBE; PMOA GENE; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; REVIEW; SENSITIVITY AND SPECIFICITY; VALIDATION PROCESS;

BACTERIA; BIODEGRADATION, ENVIRONMENTAL; ECOSYSTEM; ENVIRONMENTAL MICROBIOLOGY; HUMANS; METAGENOME; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OLIGONUCLEOTIDE PROBES; SENSITIVITY AND SPECIFICITY;

EID: 84856484915     PISSN: 09581669     EISSN: 18790429     Source Type: Journal    
DOI: 10.1016/j.copbio.2011.11.001     Document Type: Review

References (53)

1. Zhou J., Thompson D.K. Challenges in applying microarrays to environmental studies. Curr Opin Biotechnol 2002, 13:204-207.
2. Zhou J. Microarrays for bacterial detection and microbial community analysis. Curr Opin Microbiol 2003, 6:288-294.
3. Zhou J., He Q., Hemme C.L., Mukhopadhyay A., Hillesland K., Zhou A., He Z., Van Nostrand J.D., Hazen T.C., Stahl D.A., et al. How sulphate-reducing microorganisms cope with stress: lessons from systems biology. Nat Rev Microbiol 2011, 9:452-466.
4. Huber J.A., Mark Welch D.B., Morrison H.G., Huse S.M., Neal P.R., Butterfield D.A., Sogin M.L. Microbial population structures in the deep marine biosphere. Science 2007, 318:97-100.
5. Iwai S., Chai B., Sul W.J., Cole J.R., Hashsham S.A., Tiedje J.M. Gene-targeted-metagenomics reveals extensive diversity of aromatic dioxygenase genes in the environment. ISME J 2009, 4:279-285.
6. Qin J., Li R., Raes J., Arumugam M., Burgdorf K.S., Manichanh C., Nielsen T., Pons N., Levenez F., Yamada T., et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010, 464:59-65.
7. He Z., Gentry T.J., Schadt C.W., Wu L., Liebich J., Chong S.C., Huang Z., Wu W., Gu B., Jardine P., et al. GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes. ISME J 2007, 1:67-77.
8. He Z., Deng Y., Van Nostrand J.D., Tu Q., Xu M., Hemme C.L., Li X., Wu L., Gentry T.J., Yin Y., et al. GeoChip 3.0 as a high-throughput tool for analyzing microbial community composition, structure and functional activity. ISME J 2010, 4:1167-1179.
9. Hazen T.C., Dubinsky E.A., DeSantis T.Z., Andersen G.L., Piceno Y.M., Singh N., Jansson J.K., Probst A., Borglin S.E., Fortney J.L., et al. Deep-sea oil plume enriches indigenous oil-degrading bacteria. Science 2010, 330:204-208.
10. Lu Z, Deng Y, Van Nostrand JD, He Z, Voordeckers J, Zhou A, Lee YJ, Mason OU, Dubinsky EA, Chavarria KL, et al.: Microbial gene functions enriched in the deepwater horizon deep-sea oil plume. ISME J 2011, doi:10.1038/ismej.2011.91.
11. Wu L., Thompson D.K., Li G., Hurt R.A., Tiedje J.M., Zhou J. Development and evaluation of functional gene arrays for detection of selected genes in the environment. Appl Environ Microbiol 2001, 67:5780-5790.
12. Tiquia S.M., Wu L., Chong S.C., Passovets S., Xu D., Xu Y., Zhou J. Evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in environmental samples. Biotechniques 2004, 36:664-670.
13. Rhee S.-K., Liu X., Wu L., Chong S.C., Wan X., Zhou J. Detection of genes involved in biodegradation and biotransformation in microbial communities by using 50-mer oligonucleotide microarrays. Appl Environ Microbiol 2004, 70:4303-4317.
14. Wu L., Liu X., Schadt C.W., Zhou J. Microarray-based analysis of subnanogram quantities of microbial community DNAs by using whole-community genome amplification. Appl Environ Microbiol 2006, 72:4931-4941.
15. Van Nostrand J.D., Wu W.-M., Wu L., Deng Y., Carley J., Carroll S., He Z., Gu B., Luo J., Criddle C.S., et al. GeoChip-based analysis of functional microbial communities during the reoxidation of a bioreduced uranium-contaminated aquifer. Environ Microbiol 2009, 11:2611-2626.
16. Kimes N.E., Van Nostrand J.D., Weil E., Zhou J., Morris P.J. Microbial functional structure of Montastraea faveolata, an important Caribbean reef-building coral, differs between healthy and yellow-band diseased colonies. Environ Microbiol 2010, 12:541-556.
17. Xu M., Wu W.-M., Wu L., He Z., Van Nostrand J.D., Deng Y., Luo J., Carley J., Ginder-Vogel M., Gentry T.J., et al. Responses of microbial community functional structures to pilot-scale uranium in situ bioremediation. ISME J 2010, 4:1060-1070.
18. Yergeau E., Kang S., He Z., Zhou J., Kowalchuk G.A. Functional microarray analysis of nitrogen and carbon cycling genes across an Antarctic latitudinal transect. ISME J 2007, 1:163-179.
19. Zhou J., Kang S., Schadt C.W., Garten C.T. Spatial scaling of functional gene diversity across various microbial taxa. Proc Natl Acad Sci U S A 2008, 105:7768-7773.
20. 2. Ecol Lett 2010, 13:564-575.
21. Wang F., Zhou H., Meng J., Peng X., Jiang L., Sun P., Zhang C., Van Nostrand J.D., Deng Y., He Z., et al. GeoChip-based analysis of metabolic diversity of microbial communities at the Juan de Fuca Ridge hydrothermal vent. Proc Natl Acad Sci U S A 2009, 106:4840-4845.
22. Xie J., He Z., Liu X., Liu X., Van Nostrand J.D., Deng Y., Wu L., Qiu G., Zhou J. GeoChip-based analysis of the functional gene diversity and metabolic potential of microbial communities in acid mine drainage. Appl Environ Microbiol 2011, 77:991-999.
23. Liu W., Wang A., Cheng S., Logan B.E., Yu H., Deng Y., Van Nostrand J.D., Wu L., He Z., Zhou J. Geochip-based functional gene analysis of anodophilic communities in microbial electrolysis cells under different operational modes. Environ Sci Technol 2010, 44:7729-7735.
24. Liang Y., Van Nostrand J.D., Deng Y., He Z., Wu L., Zhang X., Li G., Zhou J. Functional gene diversity of soil microbial communities from five oil-contaminated fields in China. ISME J 2011, 5:403-413.
25. Taroncher-Oldenburg G., Griner E.M., Francis C.A., Ward B.B. Oligonucleotide microarray for the study of functional gene diversity in the nitrogen cycle in the environment. Appl Environ Microbiol 2003, 69:1159-1171.
26. Steward G.F., Jenkins B.D., Ward B.B., Zehr J.P. Development and testing of a DNA macroarray to assess nitrogenase (nifH) gene diversity. Appl Environ Microbiol 2004, 70:1455-1465.
27. Bontemps C., Golfier G., Gris-Liebe C., Carrere S., Talini L., Boivin-Masson C. Microarray-based detection and typing of the Rhizobium nodulation gene nodC: potential of DNA arrays to diagnose biological functions of interest. Appl Environ Microbiol 2005, 71:8042-8048.
28. Zhang L., Hurek T., Reinhold-Hurek B. A nifH-based oligonucleotide microarray for functional diagnostics of nitrogen-fixing microorganisms. Microb Ecol 2007, 53:456-470.
29. Bodrossy L., Stralis-Pavese N., Murrell J.C., Radajewski S., Weilharter A., Sessitsch A. Development and validation of a diagnostic microbial microarray for methanotrophs. Environ Microbiol 2003, 5:566-582.
30. Bodrossy L., Stralis-Pavese N., Konrad-Koszler M., Weilharter A., Reichenauer T.G., Schofer D., Sessitsch A. mRNA-based parallel detection of active methanotroph populations by use of a diagnostic microarray. Appl Environ Microbiol 2006, 72:1672-1676.
31. Call D.R., Bakko M.K., Krug M.J., Roberts M.C. Identifying antimicrobial resistance genes with DNA microarrays. Antimicrob Agents Chemother 2003, 47:3290-3295.
32. Kostic T., Weilharter A., Sessitsch A., Bodrossy L. High-sensitivity, polymerase chain reaction-free detection of microorganisms and their functional genes using 70-mer oligonucleotide diagnostic microarray. Anal Biochem 2005, 346:333-335.
33. Cleven B.E.E., Palka-Santini M., Gielen J., Meembor S., Kronke M., Krut O. Identification and characterization of bacterial pathogens causing bloodstream infections by DNA microarray. J Clin Microbiol 2006, 44:2389-2397.
34. Jaing C., Gardner S., McLoughlin K., Mulakken N., Alegria-Hartman M., Banda P., Williams P., Gu P., Wagner M., Manohar C., et al. A functional gene array for detection of bacterial virulence elements. PLoS ONE 2008, 3:e2163.
35. Miller S.M., Tourlousse D.M., Stedtfeld R.D., Baushke S.W., Herzog A.B., Wick L.M., Rouillard J.M., Gulari E., Tiedje J.M., Hashsham S.A. In situ-synthesized virulence and marker gene biochip for detection of bacterial pathogens in water. Appl Environ Microbiol 2008, 74:2200-2209.
36. Palka-Santini M., Cleven B., Eichinger L., Kronke M., Krut O. Large scale multiplex PCR improves pathogen detection by DNA microarrays. BMC Microbiol 2009, 9:1.
37. Yin H., Cao L., Qiu G., Wang D., Kellogg L., Zhou J., Dai Z., Liu X. Development and evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in acid mine drainages and bioleaching systems. J Microbiol Methods 2007, 70:165-178.
38. McGrath K.C., Mondav R., Sintrajaya R., Slattery B., Schmidt S., Schenk P.M. Development of an environmental functional gene microarray for soil microbial communities. Appl Environ Microbiol 2010, 76:7161-7170.
39. Liang Y., He Z., Wu L., Deng Y., Li G., Zhou J. Development of a common oligo reference standard (CORS) for microarray data normalization and comparison across different microbial communities. Appl Environ Microbiol 2010, 76:1088-1094.
40. Eddy S.R. Profile hidden Markov models. Bioinformatics 1998, 14:755-763.
41. Li X., He Z., Zhou J. Selection of optimal oligonucleotide probes for microarrays using multiple criteria, global alignment and parameter estimation. Nucleic Acids Res 2005, 33:6114-6123.
42. He Z., Wu L., Fields M.W., Zhou J. Use of microarrays with different probe sizes for monitoring gene expression. Appl Environ Microbiol 2005, 71:5154-5162.
43. Liebich J., Schadt C.W., Chong S.C., He Z., Rhee S.K., Zhou J. Improvement of oligonucleotide probe design criteria for functional gene microarrays in environmental applications. Appl Environ Microbiol 2006, 72:1688-1691.
44. He Z., Wu L., Li X., Fields M.W., Zhou J. Empirical establishment of oligonucleotide probe design criteria. Appl Environ Microbiol 2005, 71:3753-3760.
45. Chung W.-H., Rhee S.-K., Wan X.-F., Bae J.-W., Quan Z.-X., Park Y.-H. Design of long oligonucleotide probes for functional gene detection in a microbial community. Bioinformatics 2005, 21:4092-4100.
46. Feng S., Tillier E.R.M. A fast and flexible approach to oligonucleotide probe design for genomes and gene families. Bioinformatics 2007, 23:1195-1202.
47. Dugat-Bony E., Missaoui M., Peyretaillade E., Biderre-Petit C., Bouzid O., Gouinaud C., Hill D., Peyret P. HiSpOD: probe design for functional DNA microarrays. Bioinformatics 2011, 27:641-648.
48. He Z., Zhou J. Empirical evaluation of a new method for calculating signal-to-noise ratio for microarray data analysis. Appl Environ Microbiol 2008, 74:2957-2966.
49. Deng Y., He Z., Van Nostrand J., Zhou J. Design and analysis of mismatch probes for long oligonucleotide microarrays. BMC Genomics 2008, 9:491.
50. Chen Q., Yin H., Luo H., Xie M., Qiu G., Liu X. Micro-array based whole-genome hybridization for detection of microorganisms in acid mine drainage and bioleaching systems. Hydrometallurgy 2009, 95:96-103.
51. Gao H., Yang Z.K., Gentry T.J., Wu L., Schadt C.W., Zhou J. Microarray-based analysis of microbial community RNAs by whole-community RNA amplification. Appl Environ Microbiol 2007, 73:563-571.
52. Denef V.J., Park J., Rodrigues J.L.M., Tsoi T.V., Hashsham S.A., Tiedje J.M. Validation of a more sensitive method for using spotted oligonucleotide DNA microarrays for functional genomics studies on bacterial communities. Environ Microbiol 2003, 5:933-943.
53. Zhou J., He Z., Van Nostrand J.D., Wu L., Deng Y. Applying GeoChip analysis to disparate microbial communities. Microbe 2010, 5:60-65.