Comparing microarrays and next-generation sequencing technologies for microbial ecology research

Trends in Biotechnology

Volumn 28, Issue 6, 2010, Pages 291-299

  Roh, Seong Woon ^a   Abell, Guy C J ^b   Kim, Kyoung Ho ^a   Nam, Young Do ^a   Bae, Jin Woo ^a  

^a Kyung Hee University   (South Korea)

^b CSIRO   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

DNA MICRO-ARRAY; INDIVIDUAL TECHNOLOGY; MICROBIAL ECOLOGY; OPTIMAL APPLICATIONS; POTENTIAL SYNERGIES; SAMPLE NUMBER;

BIOASSAY; BIOCHEMISTRY; BIOCHIPS; MICROBIOLOGY; MOLECULAR BIOLOGY; TECHNOLOGY;

ECOLOGY;

COMPLEMENTARY DNA; RNA 16S;

BIOTECHNOLOGY; COST EFFECTIVENESS ANALYSIS; DNA DNA HYBRIDIZATION; DNA MICROARRAY; ESCHERICHIA COLI; HIGH THROUGHPUT SCREENING; INTERMETHOD COMPARISON; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; MICROBIAL GENETICS; MICROORGANISM; MOLECULAR ECOLOGY; MOLECULAR PHYLOGENY; NONHUMAN; PRIORITY JOURNAL; PROKARYOTE; PYROSEQUENCING; REVIEW; RNA SEQUENCE; SEQUENCE ANALYSIS; SPECIES IDENTIFICATION;

ECOLOGY; ECOSYSTEM; ENVIRONMENTAL MICROBIOLOGY; MICROARRAY ANALYSIS; SEQUENCE ANALYSIS, DNA;

EID: 77953121795     PISSN: 01677799     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tibtech.2010.03.001     Document Type: Review

References (99)

1. Xu J. Microbial ecology in the age of genomics and metagenomics: concepts, tools, and recent advances. Mol. Ecol. 2006, 15:1713-1731.
2. Sogin M.L., et al. Microbial diversity in the deep sea and the underexplored " rare biosphere" Proc. Natl. Acad. Sci. U. S. A. 2006, 103:12115-12120.
3. Schena M., et al. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 1995, 270:467-470.
4. Bodrossy L., Sessitsch A. Oligonucleotide microarrays in microbial diagnostics. Curr. Opin. Microbiol. 2004, 7:245-254.
5. Zhou J. Microarrays for bacterial detection and microbial community analysis. Curr. Opin. Microbiol. 2003, 6:288-294.
6. Bae J.W., Park Y.H. Homogeneous versus heterogeneous probes for microbial ecological microarrays. Trends Biotechnol. 2006, 24:318-323.
7. Wilson K.H., et al. High-density microarray of small-subunit ribosomal DNA probes. Appl. Environ. Microbiol. 2002, 68:2535-2541.
8. Edwards R.A., et al. Using pyrosequencing to shed light on deep mine microbial ecology. BMC Genomics 2006, 7:57.
9. Warnecke F., et al. Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature 2007, 450:560-565.
10. Angly F.E., et al. The marine viromes of four oceanic regions. PLoS Biol. 2006, 4:e368.
11. Brown M.V., et al. Microbial community structure in the North Pacific ocean. ISME J. 2009, 3:1374-1386.
12. Lazarevic V., et al. Metagenomic study of the oral microbiota by Illumina high-throughput sequencing. J. Microbiol. Methods 2009, 79:266-271.
13. Ledford H. The death of microarrays?. Nature 2008, 455:847.
14. Akhras M.S., et al. PathogenMip assay: a multiplex pathogen detection assay. PLoS ONE 2007, 2:e223.
15. Claesson M.J., et al. Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine. PLoS ONE 2009, 4:e6669.
16. Tringe S.G., Hugenholtz P. A renaissance for the pioneering 16S rRNA gene. Curr. Opin. Microbiol. 2008, 11:442-446.
17. Dowd S.E., et al. Polymicrobial nature of chronic diabetic foot ulcer biofilm infections determined using bacterial tag encoded FLX amplicon pyrosequencing (bTEFAP). PLoS ONE 2008, 3:e3326.
18. Huber J.A., et al. Microbial population structures in the deep marine biosphere. Science 2007, 318:97-100.
19. Roesch L.F., et al. Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J. 2007, 1:283-290.
20. Roh S.W., et al. Investigation of archaeal and bacterial diversity in fermented seafood using barcoded pyrosequencing. ISME J. 2010, 4:1-16.
21. Gilbert J.A., et al. Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities. PLoS ONE 2008, 3:e3042.
22. Hewson I., et al. Microbial community gene expression within colonies of the diazotroph, Trichodesmium, from the Southwest Pacific Ocean. ISME J. 2009, 3:1286-1300.
23. Passalacqua K.D., et al. Structure and Complexity of a Bacterial Transcriptome. J. Bacteriol. 2009, 191:3203-3211.
24. Wurtzel O., et al. A single-base resolution map of an archaeal transcriptome. Genome Res. 2010, 20:133-141.
25. Lemarchand K., et al. Molecular biology and DNA microarray technology for microbial quality monitoring of water. Crit. Rev. Microbiol. 2004, 30:145-172.
26. Loy A., et al. Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment. Appl. Environ. Microbiol. 2002, 68:5064-5081.
27. He Z., et al. GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes. ISME J. 2007, 1:67-77.
28. Wang F., 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.
29. Van Nostrand J.D., et al. GeoChip-based analysis of functional microbial communities during the reoxidation of a bioreduced uranium-contaminated aquifer. Environ. Microbiol. 2009, 11:2611-2626.
30. He, S. et al. (2010) Metatranscriptomic array analysis of 'Candidatus Accumulibacter phosphatis'-enriched enhanced biological phosphorus removal sludge. Environ. Microbiol., Epub ahead of print.
31. Vieites J.M., et al. Metagenomics approaches in systems microbiology. FEMS Microbiol. Rev. 2009, 33:236-255.
32. DeAngelis K.M., et al. Selective progressive response of soil microbial community to wild oat roots. ISME J. 2009, 3:168-178.
33. Lauber C.L., et al. Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl. Environ. Microbiol. 2009, 75:5111-5120.
34. Liu Z., et al. Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers. Nucleic Acids Res. 2008, 36:e120.
35. Wang Q., et al. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 2007, 73:5261-5267.
36. Stojanovi M.R., et al. Development and application of the human intestinal tract chip, a phylogenetic microarray: analysis of universally conserved phylotypes in the abundant microbiota of young and elderly adults. Environ. Microbiol. 2009, 11:1736-1751.
37. Brodie E.L., et al. Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation. Appl. Environ. Microbiol. 2006, 72:6288-6298.
38. Loy A., et al. 16S rRNA gene-based oligonucleotide microarray for environmental monitoring of the betaproteobacterial order " Rhodocyclales" Appl. Environ. Microbiol. 2005, 71:1373-1386.
39. Chang H.W., et al. Development of microbial genome-probing microarrays using digital multiple displacement amplification of uncultivated microbial single cells. Environ. Sci. Technol. 2008, 42:6058-6064.
40. Turnbaugh P.J., et al. A core gut microbiome in obese and lean twins. Nature 2009, 457:480-484.
41. Fierer N., et al. The influence of sex, handedness, and washing on the diversity of hand surface bacteria. Proc. Natl. Acad. Sci. U. S. A. 2008, 105:17994-17999.
42. Brose U., et al. Estimating species richness: Sensitivity to sample coverage and insensitivity to spatial patterns. Ecology 2003, 84:2364-2377.
43. Bodrossy L., et al. Development and validation of a diagnostic microbial microarray for methanotrophs. Environ. Microbiol. 2003, 5:566-582.
44. Quince C., et al. Accurate determination of microbial diversity from 454 pyrosequencing data. Nat. Methods 2009, 6:639-641.
45. Gomez-Alvarez V., et al. Systematic artifacts in metagenomes from complex microbial communities. ISME J. 2009, 3:1314-1317.
46. Kunin V., et al. Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environ. Microbiol. 2010, 12:118-123.
47. Margulies M., et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005, 437:376-380.
48. Quinlan A.R., et al. Pyrobayes: an improved base caller for SNP discovery in pyrosequences. Nat. Methods 2008, 5:179-181.
49. Briggs A.W., et al. Patterns of damage in genomic DNA sequences from a Neandertal. Proc. Natl. Acad. Sci. U. S. A. 2007, 104:14616-14621.
50. Reeder J., Knight R. The 'rare biosphere': a reality check. Nat. Methods 2009, 6:636-637.
51. Huse S.M., et al. Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol. 2007, 8:R143.
52. Liu Z., et al. Short pyrosequencing reads suffice for accurate microbial community analysis. Nucleic Acids Res. 2007, 35:e120.
53. Andersson A.F., et al. Comparative analysis of human gut microbiota by barcoded pyrosequencing. PLoS ONE 2008, 3:e2836.
54. Muller S., et al. A novel source of highly specific chromosome painting probes for human karyotype analysis derived from primate homologues. Human Genetics 1997, 101:149-153.
55. Wren J.D., et al. Cross-hybridization on PCR-spotted microarrays. IEEE Eng. Med. Biol. Mag. 2002, 21:71-75.
56. Loy A., Bodrossy L. Highly parallel microbial diagnostics using oligonucleotide microarrays. Clin. Chim. Acta 2006, 363:106-119.
57. Jayaraman A., et al. Computer simulation study of molecular recognition in model DNA microarrays. Biophys. J. 2006, 91:2227-2236.
58. Taroncher-Oldenburg G., et al. Oligonucleotide microarray for the study of functional gene diversity in the nitrogen cycle in the environment. Appl. Environ. Microbiol. 2003, 69:1159-1171.
59. Kane M.D., et al. Assessment of the sensitivity and specificity of oligonucleotide (50mer) microarrays. Nucleic Acids Res. 2000, 28:4552-4557.
60. Wu L., et al. Development and evaluation of functional gene arrays for detection of selected genes in the environment. Appl. Environ. Microbiol. 2001, 67:5780-5790.
61. Zhou X., et al. Fabrication of DNA microarrays on nanoengineered polymeric ultrathin film prepared by self-assembly of polyelectrolyte multilayers. Langmuir 2004, 20:8877-8885.
62. Urakawa H., et al. Optimization of single-base-pair mismatch discrimination in oligonucleotide microarrays. Appl. Environ. Microbiol. 2003, 69:2848-2856.
63. Relogio A., et al. Optimization of oligonucleotide-based DNA microarrays. Nucleic Acids Res. 2002, 30:e51.
64. Liu W.T., et al. Optimization of an oligonucleotide microchip for microbial identification studies: a non-equilibrium dissociation approach. Environ. Microbiol. 2001, 3:619-629.
65. Pozhitkov A.E., et al. Revision of the nonequilibrium thermal dissociation and stringent washing approaches for identification of mixed nucleic acid targets by microarrays. Nucleic Acids Res. 2007, 35:e70.
66. Qiu X., et al. Evaluation of PCR-generated chimeras, mutations, and heteroduplexes with 16S rRNA gene-based cloning. Appl. Environ. Microbiol. 2001, 67:880-887.
67. Polz M.F., Cavanaugh C.M. Bias in template-to-product ratios in multitemplate PCR. Appl. Environ. Microbiol. 1998, 64:3724-3730.
68. Thompson J.R., et al. Heteroduplexes in mixed-template amplifications: formation, consequence and elimination by 'reconditioning PCR'. Nucleic Acids Res. 2002, 30:2083-2088.
69. Acinas S.G., et al. PCR-induced sequence artifacts and bias: insights from comparison of two 16S rRNA clone libraries constructed from the same sample. Appl. Environ. Microbiol. 2005, 71:8966-8969.
70. Hong S., et al. Polymerase chain reaction primers miss half of rRNA microbial diversity. ISME J. 2009, 3:1365-1373.
71. Isenbarger T.A., et al. Miniprimer PCR, a new lens for viewing the microbial world. Appl. Environ. Microbiol. 2008, 74:840-849.
72. Huber T., et al. Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 2004, 20:2317-2319.
73. Ashelford K.E., et al. At least 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies. Appl. Environ. Microbiol. 2005, 71:7724-7736.
74. Tito R.Y., et al. Phylotyping and functional analysis of two ancient human microbiomes. PLoS ONE 2008, 3:e3703.
75. Dinsdale E.A., et al. Microbial ecology of four coral atolls in the Northern Line Islands. PLoS ONE 2008, 3:e1584.
76. Bae J.W., et al. Development and evaluation of genome-probing microarrays for monitoring lactic acid bacteria. Appl. Environ. Microbiol. 2005, 71:8825-8835.
77. Wu L., et al. Development and evaluation of microarray-based whole-genome hybridization for detection of microorganisms within the context of environmental applications. Environ. Sci. Technol. 2004, 38:6775-6782.
78. Small J., et al. Direct detection of 16S rRNA in soil extracts by using oligonucleotide microarrays. Appl. Environ. Microbiol. 2001, 67:4708-4716.
79. Peplies J., et al. Application and validation of DNA microarrays for the 16S rRNA-based analysis of marine bacterioplankton. Environ. Microbiol. 2004, 6:638-645.
80. Huson D.H., et al. MEGAN analysis of metagenomic data. Genome Res. 2007, 17:377-386.
81. von Mering C., et al. Quantitative phylogenetic assessment of microbial communities in diverse environments. Science 2007, 315:1126-1130.
82. Wayne L.G., et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int. J. Syst. Bacteriol. 1987, 37:463-464.
83. Chang H.W., et al. Statistical superiority of genome-probing microarrays as genomic DNA-DNA hybridization in revealing the bacterial phylogenetic relationship compared to conventional methods. J. Microbiol. Methods 2008, 75:523-530.
84. Bally M., et al. Optical microarray biosensing techniques. Surf. Interface Anal. 2006, 38:1442-1458.
85. Marcy Y., et al. Innovative integrated system for real-time measurement of hybridization and melting on standard format microarrays. Biotechniques 2008, 44:913-920.
86. Francois P., et al. Rapid bacterial identification using evanescent-waveguide oligonucleotide microarray classification. J. Microbiol. Methods 2006, 65:390-403.
87. Ferguson J.A., et al. High-density fiber-optic DNA random microsphere array. Anal. Chem. 2000, 72:5618-5624.
88. Blohm D.H., Guiseppi-Elie A. New developments in microarray technology. Curr. Opin. Biotechnol. 2001, 12:41-47.
89. Liu, R.H., and Longiaru, M. (2009) ESensor: An electrochemical detection-based DNA microarray technology enabling sample-to-answer molecular diagnostics. In Proceedings of SPIE - The International Society for Optical Engineering.
90. Binladen J., et al. The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing. PLoS ONE 2007, 2:e197.
91. Parameswaran P., et al. A pyrosequencing-tailored nucleotide barcode design unveils opportunities for large-scale sample multiplexing. Nucleic Acids Res. 2007, 35:e130.
92. Hamady M., et al. Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nat. Methods 2008, 5:235-237.
93. Kjelleberg S. Environmental biotechnology. Curr. Opin. Biotechnol. 2002, 13:199-203.
94. Guschin D.Y., et al. Oligonucleotide microchips as genosensors for determinative and environmental studies in microbiology. Appl. Environ. Microbiol. 1997, 63:2397-2402.
95. Cho J.C., Tiedje J.M. Bacterial species determination from DNA-DNA hybridization by using genome fragments and DNA microarrays. Appl. Environ. Microbiol. 2001, 67:3677-3682.
96. Sebat J.L., et al. Metagenomic profiling: microarray analysis of an environmental genomic library. Appl. Environ. Microbiol. 2003, 69:4927-4934.
97. Park S.J., et al. Metagenome microarray for screening of fosmid clones containing specific genes. FEMS Microbiol. Lett. 2008, 284:28-34.
98. Adamczyk J., et al. The isotope array, a new tool that employs substrate-mediated labeling of rRNA for determination of microbial community structure and function. Appl. Environ. Microbiol. 2003, 69:6875-6887.
99. Hesselsoe M., et al. Isotope array analysis of Rhodocyclales uncovers functional redundancy and versatility in an activated sludge. ISME J. 2009, 3:1349-1364.