High-throughput metagenomic technologies for complex microbial community analysis. Open and closed formats

Zhou, Jizhong; He, Zhili; Yang, Yunfeng; Deng, Ye; Tringe, Susannah G.; Alvarez-Cohen, Lisa

doi:10.1128/mBio.02288-14

Title: High-throughput metagenomic technologies for complex microbial community analysis. Open and closed formats

Journal Article · Tue Jan 27 00:00:00 EST 2015 · mBio (Online)

DOI:https://doi.org/10.1128/mBio.02288-14· OSTI ID:1215655

Zhou, Jizhong ^[1]; He, Zhili ^[2]; Yang, Yunfeng ^[3]; Deng, Ye ^[4]; Tringe, Susannah G. ^[5]; Alvarez-Cohen, Lisa ^[6]

Univ. of Oklahoma, Norman, OK (United States); Tsinghua Univ., Beijing (China); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Univ. of Oklahoma, Norman, OK (United States)
Tsinghua Univ., Beijing (China)
Univ. of Oklahoma, Norman, OK (United States); Chinese Academy of Sciences, Beijing (China)
Dept. of Energy Joint Genome Institute, Walnut Creek, CA (United States)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States)

Understanding the structure, functions, activities and dynamics of microbial communities in natural environments is one of the grand challenges of 21st century science. To address this challenge, over the past decade, numerous technologies have been developed for interrogating microbial communities, of which some are amenable to exploratory work (e.g., high-throughput sequencing and phenotypic screening) and others depend on reference genes or genomes (e.g., phylogenetic and functional gene arrays). Here, we provide a critical review and synthesis of the most commonly applied “open-format” and “closed-format” detection technologies. We discuss their characteristics, advantages, and disadvantages within the context of environmental applications and focus on analysis of complex microbial systems, such as those in soils, in which diversity is high and reference genomes are few. In addition, we discuss crucial issues and considerations associated with applying complementary high-throughput molecular technologies to address important ecological questions.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1215655

Alternate ID(s):: OSTI ID: 1512158

Journal Information:: mBio (Online), Vol. 6, Issue 1; ISSN 2150-7511

Publisher:: American Society for MicrobiologyCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 254 works

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References (158)

Replicate or lie: The need for replication Prosser, James I. Environmental Microbiology, Vol. 12, Issue 7 https://doi.org/10.1111/j.1462-2920.2010.02201.x	journal	March 2010
Microbial interactions: from networks to models Faust, Karoline; Raes, Jeroen Nature Reviews Microbiology, Vol. 10, Issue 8 https://doi.org/10.1038/nrmicro2832	journal	July 2012
Stochastic Assembly Leads to Alternative Communities with Distinct Functions in a Bioreactor Microbial Community Zhou, Jizhong; Liu, Wenzong; Deng, Ye mBio, Vol. 4, Issue 2 https://doi.org/10.1128/mBio.00584-12	journal	March 2013
A Molecular View of Microbial Diversity and the Biosphere Pace, N. R. Science, Vol. 276, Issue 5313, p. 734-740 https://doi.org/10.1126/science.276.5313.734	journal	May 1997
Microbial diversity in the deep sea and the underexplored "rare biosphere" Sogin, M. L.; Morrison, H. G.; Huber, J. A. Proceedings of the National Academy of Sciences, Vol. 103, Issue 32 https://doi.org/10.1073/pnas.0605127103	journal	July 2006
Development and applications of functional gene microarrays in the analysis of the functional diversity, composition, and structure of microbial communities He, Zhili; Van Nostrand, Joy D.; Deng, Ye Frontiers of Environmental Science & Engineering in China, Vol. 5, Issue 1 https://doi.org/10.1007/s11783-011-0301-y	journal	January 2011
High-Throughput Quantitative Analysis of the Human Intestinal Microbiota with a Phylogenetic Microarray Paliy, O.; Kenche, H.; Abernathy, F. Applied and Environmental Microbiology, Vol. 75, Issue 11 https://doi.org/10.1128/AEM.02764-08	journal	April 2009
Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Muyzer, G.; de Waal, E. C.; Uitterlinden, A. G. Applied and Environmental Microbiology, Vol. 59, Issue 3 https://doi.org/10.1128/AEM.59.3.695-700.1993	journal	January 1993
Evaluation of PCR-Generated Chimeras, Mutations, and Heteroduplexes with 16S rRNA Gene-Based Cloning Qiu, X.; Wu, L.; Huang, H. Applied and Environmental Microbiology, Vol. 67, Issue 2 https://doi.org/10.1128/AEM.67.2.880-887.2001	journal	February 2001
Metagenomic Analysis of Streptomyces lividans Reveals Host-Dependent Functional Expression McMahon, Matthew D.; Guan, Changhui; Handelsman, Jo Applied and Environmental Microbiology, Vol. 78, Issue 10 https://doi.org/10.1128/AEM.00044-12	journal	March 2012
Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization Sharon, I.; Morowitz, M. J.; Thomas, B. C. Genome Research, Vol. 23, Issue 1 https://doi.org/10.1101/gr.142315.112	journal	August 2012
Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla Wrighton, K. C.; Thomas, B. C.; Sharon, I. Science, Vol. 337, Issue 6102 https://doi.org/10.1126/science.1224041	journal	September 2012
Microbial gene functions enriched in the Deepwater Horizon deep-sea oil plume Lu, Zhenmei; Deng, Ye; Van Nostrand, Joy D. The ISME Journal, Vol. 6, Issue 2 https://doi.org/10.1038/ismej.2011.91	journal	August 2011
Succession of endophytic fungi and arbuscular mycorrhizal fungi associated with the growth of plant and their correlation with secondary metabolites in the roots of plants Dang, Hanli; Zhang, Tao; Wang, Zhongke BMC Plant Biology, Vol. 21, Issue 1 https://doi.org/10.1186/s12870-021-02942-6	journal	April 2021
Contrasting denitrifier communities relate to contrasting N2O emission patterns from acidic peat soils in arctic tundra Palmer, Katharina; Biasi, Christina; Horn, Marcus A. The ISME Journal, Vol. 6, Issue 5 https://doi.org/10.1038/ismej.2011.172	journal	December 2011
Selection of optimal oligonucleotide probes for microarrays using multiple criteria, global alignment and parameter estimation Li, X. Nucleic Acids Research, Vol. 33, Issue 19 https://doi.org/10.1093/nar/gki914	journal	October 2005
Practical innovations for high-throughput amplicon sequencing Lundberg, Derek S.; Yourstone, Scott; Mieczkowski, Piotr Nature Methods, Vol. 10, Issue 10 https://doi.org/10.1038/nmeth.2634	journal	September 2013
Metabolite identification via the Madison Metabolomics Consortium Database Cui, Qiu; Lewis, Ian A.; Hegeman, Adrian D. Nature Biotechnology, Vol. 26, Issue 2 https://doi.org/10.1038/nbt0208-162	journal	February 2008
Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes Giannoukos, Georgia; Ciulla, Dawn M.; Huang, Katherine Genome Biology, Vol. 13, Issue 3 https://doi.org/10.1186/gb-2012-13-3-r23	journal	January 2012
Extraction of inhibitor-free metagenomic DNA from polluted sediments, compatible with molecular diversity analysis using adsorption and ion-exchange treatments Desai, C.; Madamwar, D. Bioresource Technology, Vol. 98, Issue 4 https://doi.org/10.1016/j.biortech.2006.04.004	journal	March 2007
Wide Variation in Antibiotic Resistance Proteins Identified by Functional Metagenomic Screening of a Soil DNA Library McGarvey, Kelly M.; Queitsch, Konstantin; Fields, Stanley Applied and Environmental Microbiology, Vol. 78, Issue 6 https://doi.org/10.1128/AEM.06759-11	journal	January 2012
The Light-Driven Proton Pump Proteorhodopsin Enhances Bacterial Survival during Tough Times DeLong, Edward F.; Béjà, Oded PLoS Biology, Vol. 8, Issue 4 https://doi.org/10.1371/journal.pbio.1000359	journal	April 2010
Functional screening of antibiotic resistance genes from human gut microbiota reveals a novel gene fusion Cheng, Gong; Hu, Yongfei; Yin, Yeshi FEMS Microbiology Letters, Vol. 336, Issue 1 https://doi.org/10.1111/j.1574-6968.2012.02647.x	journal	September 2012
Predictive microbial ecology Zhou, Jizhong Microbial Biotechnology, Vol. 2, Issue 2 https://doi.org/10.1111/j.1751-7915.2009.00090_21.x	journal	March 2009
Erratum: Using network analysis to explore co-occurrence patterns in soil microbial communities Barberán, Albert; Bates, Scott T.; Casamayor, Emilio O. The ISME Journal, Vol. 8, Issue 4 https://doi.org/10.1038/ismej.2013.236	journal	March 2014
Cross-biome metagenomic analyses of soil microbial communities and their functional attributes Fierer, N.; Leff, J. W.; Adams, B. J. Proceedings of the National Academy of Sciences, Vol. 109, Issue 52 https://doi.org/10.1073/pnas.1215210110	journal	December 2012
Molecular Diversity of Sulfate-Reducing Bacteria from Two Different Continental Margin Habitats Liu, X.; Bagwell, C. E.; Wu, L. Applied and Environmental Microbiology, Vol. 69, Issue 10 https://doi.org/10.1128/AEM.69.10.6073-6081.2003	journal	October 2003
Development and evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in Acid Mine Drainages and bioleaching systems Yin, Huaqun; Cao, Linhui; Qiu, Guanzhou Journal of Microbiological Methods, Vol. 70, Issue 1 https://doi.org/10.1016/j.mimet.2007.04.011	journal	July 2007
Assessment of the human faecal microbiota: II. Reproducibility and associations of 16S rRNA pyrosequences: FAECAL MICROBIOME REPRODUCIBILITY AND ASSOCIATIONS Flores, Roberto; Shi, Jianxin; Gail, Mitchell H. European Journal of Clinical Investigation, Vol. 42, Issue 8 https://doi.org/10.1111/j.1365-2362.2012.02659.x	journal	March 2012
Prevalence of Antibiotic Resistance in Drinking Water Treatment and Distribution Systems Xi, C.; Zhang, Y.; Marrs, C. F. Applied and Environmental Microbiology, Vol. 75, Issue 17 https://doi.org/10.1128/AEM.00382-09	journal	July 2009
Stable isotope probing — linking microbial identity to function Dumont, Marc G.; Murrell, J. Colin Nature Reviews Microbiology, Vol. 3, Issue 6 https://doi.org/10.1038/nrmicro1162	journal	May 2005
Analysis of Run-to-Run Variation of Bar-Coded Pyrosequencing for Evaluating Bacterial Community Shifts and Individual Taxa Dynamics Ge, Yuan; Schimel, Joshua P.; Holden, Patricia A. PLoS ONE, Vol. 9, Issue 6 https://doi.org/10.1371/journal.pone.0099414	journal	June 2014
Intracellular Diversity of the V4 and V9 Regions of the 18S rRNA in Marine Protists (Radiolarians) Assessed by High-Throughput Sequencing Decelle, Johan; Romac, Sarah; Sasaki, Eriko PLoS ONE, Vol. 9, Issue 8 https://doi.org/10.1371/journal.pone.0104297	journal	August 2014
Metagenome—a challenging source of enzyme discovery Lorenz, Patrick; Schleper, Christa Journal of Molecular Catalysis B: Enzymatic, Vol. 19-20 https://doi.org/10.1016/S1381-1177(02)00147-9	journal	December 2002
Unlocking the potential of metagenomics through replicated experimental design Knight, Rob; Jansson, Janet; Field, Dawn Nature Biotechnology, Vol. 30, Issue 6 https://doi.org/10.1038/nbt.2235	journal	June 2012
The Long-Term Stability of the Human Gut Microbiota Faith, Jeremiah J.; Guruge, Janaki L.; Charbonneau, Mark Science, Vol. 341, Issue 6141 https://doi.org/10.1126/science.1237439	journal	July 2013
Insights into the phylogeny and coding potential of microbial dark matter Rinke, Christian; Schwientek, Patrick; Sczyrba, Alexander Nature, Vol. 499, Issue 7459 https://doi.org/10.1038/nature12352	journal	July 2013
A microarray for assessing transcription from pelagic marine microbial taxa Shilova, Irina N.; Robidart, Julie C.; James Tripp, H. The ISME Journal, Vol. 8, Issue 7 https://doi.org/10.1038/ismej.2014.1	journal	January 2014
Niche specialization of terrestrial archaeal ammonia oxidizers Gubry-Rangin, C.; Hai, B.; Quince, C. Proceedings of the National Academy of Sciences, Vol. 108, Issue 52 https://doi.org/10.1073/pnas.1109000108	journal	December 2011
StressChip as a High-Throughput Tool for Assessing Microbial Community Responses to Environmental Stresses Zhou, Aifen; He, Zhili; Qin, Yujia Environmental Science & Technology, Vol. 47, Issue 17 https://doi.org/10.1021/es4018656	journal	August 2013
The Last Word: Books as a Statistical Metaphor for Microbial Communities Schloss, Patrick D.; Handelsman, Jo Annual Review of Microbiology, Vol. 61, Issue 1 https://doi.org/10.1146/annurev.micro.61.011507.151712	journal	October 2007
Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment Castelle, Cindy J.; Hug, Laura A.; Wrighton, Kelly C. Nature Communications, Vol. 4, Issue 1 https://doi.org/10.1038/ncomms3120	journal	August 2013
amoA-based consensus phylogeny of ammonia-oxidizing archaea and deep sequencing of amoA genes from soils of four different geographic regions: Archaeal amoA phylogeny and diversity in soils Pester, Michael; Rattei, Thomas; Flechl, Stefan Environmental Microbiology, Vol. 14, Issue 2 https://doi.org/10.1111/j.1462-2920.2011.02666.x	journal	December 2011
Microbial communities in wetlands of the Athabasca oil sands: genetic and metabolic characterization: Microbial communities in wetlands of the Athabasca oil sands Hadwin, Alison K. M.; Del Rio, Luis F.; Pinto, Linda J. FEMS Microbiology Ecology, Vol. 55, Issue 1 https://doi.org/10.1111/j.1574-6941.2005.00009.x	journal	January 2006
Biodiversity and ecosystem function in soil Fitter, A. H.; Gilligan, C. A.; Hollingworth, K. Functional Ecology, Vol. 19, Issue 3 https://doi.org/10.1111/j.0269-8463.2005.00969.x	journal	June 2005
Molecular phylogeny of Archaea from soil Bintrim, S. B.; Donohue, T. J.; Handelsman, J. Proceedings of the National Academy of Sciences, Vol. 94, Issue 1 https://doi.org/10.1073/pnas.94.1.277	journal	January 1997
Applying GeoChip Analysis to Disparate Microbial Communities: These high-throughput gene arrays, used to analyze microbial communities, link their structures to how they affect ecosystems Zhou, Jizhong; Deng, Ye; He, Zhili Microbe Magazine, Vol. 5, Issue 2 https://doi.org/10.1128/microbe.5.60.1	journal	February 2010
Biodiversity in a complex world: consolidation and progress in functional biodiversity research: Consolidation and progress in BDEF research Hillebrand, Helmut; Matthiessen, Birte Ecology Letters, Vol. 12, Issue 12 https://doi.org/10.1111/j.1461-0248.2009.01388.x	journal	October 2009
The identification of 100 ecological questions of high policy relevance in the UK: 100 ecological questions Sutherland, William J.; Armstrong-Brown, Susan; Armsworth, Paul R. Journal of Applied Ecology, Vol. 43, Issue 4 https://doi.org/10.1111/j.1365-2664.2006.01188.x	journal	May 2006
Microbial mediation of carbon-cycle feedbacks to climate warming Zhou, Jizhong; Xue, Kai; Xie, Jianping Nature Climate Change, Vol. 2, Issue 2 https://doi.org/10.1038/nclimate1331	journal	December 2011
Random Sampling Process Leads to Overestimation of β-Diversity of Microbial Communities Zhou, Jizhong; Jiang, Yi-Huei; Deng, Ye mBio, Vol. 4, Issue 3 https://doi.org/10.1128/mBio.00324-13	journal	June 2013
High-throughput sequencing shows inconsistent results with a microscope-based analysis of the soil prokaryotic community Ushio, Masayuki; Makoto, Kobayashi; Klaminder, Jonatan Soil Biology and Biochemistry, Vol. 76 https://doi.org/10.1016/j.soilbio.2014.05.010	journal	September 2014
Comparative Metagenomics of Microbial Communities Tringe, S. G. Science, Vol. 308, Issue 5721 https://doi.org/10.1126/science.1107851	journal	April 2005
Quantitative Monitoring of Gene Expression Patterns with a Complementary DNA Microarray Schena, M.; Shalon, D.; Davis, R. W. Science, Vol. 270, Issue 5235 https://doi.org/10.1126/science.270.5235.467	journal	October 1995
Metabolomics and systems biology: making sense of the soup Kell, D. Current Opinion in Microbiology, Vol. 7, Issue 3 https://doi.org/10.1016/j.mib.2004.04.012	journal	June 2004
Simultaneous Assessment of Soil Microbial Community Structure and Function through Analysis of the Meta-Transcriptome Urich, Tim; Lanzén, Anders; Qi, Ji PLoS ONE, Vol. 3, Issue 6 https://doi.org/10.1371/journal.pone.0002527	journal	June 2008
Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing Bokulich, Nicholas A.; Subramanian, Sathish; Faith, Jeremiah J. Nature Methods, Vol. 10, Issue 1 https://doi.org/10.1038/nmeth.2276	journal	December 2012
Validation of two ribosomal RNA removal methods for microbial metatranscriptomics He, Shaomei; Wurtzel, Omri; Singh, Kanwar Nature Methods, Vol. 7, Issue 10 https://doi.org/10.1038/nmeth.1507	journal	September 2010
Bioinformatics for the Human Microbiome Project Gevers, Dirk; Pop, Mihai; Schloss, Patrick D. PLoS Computational Biology, Vol. 8, Issue 11 https://doi.org/10.1371/journal.pcbi.1002779	journal	November 2012
GeoChip-based analysis of metabolic diversity of microbial communities at the Juan de Fuca Ridge hydrothermal vent Wang, F.; Zhou, H.; Meng, J. Proceedings of the National Academy of Sciences, Vol. 106, Issue 12 https://doi.org/10.1073/pnas.0810418106	journal	March 2009
A road map for the development of community systems (CoSy) biology Zengler, Karsten; Palsson, Bernhard O. Nature Reviews Microbiology, Vol. 10, Issue 5 https://doi.org/10.1038/nrmicro2763	journal	March 2012
Low sequencing efforts bias analyses of shared taxa in microbial communities Lemos, Leandro N.; Fulthorpe, Roberta R.; Roesch, Luiz F. W. Folia Microbiologica, Vol. 57, Issue 5 https://doi.org/10.1007/s12223-012-0155-0	journal	May 2012
Metagenomic and Metatranscriptomic Analysis of Microbial Community Structure and Gene Expression of Activated Sludge Yu, Ke; Zhang, Tong PLoS ONE, Vol. 7, Issue 5 https://doi.org/10.1371/journal.pone.0038183	journal	May 2012
Metagenomic insights into evolution of a heavy metal-contaminated groundwater microbial community Hemme, Christopher L.; Deng, Ye; Gentry, Terry J. The ISME Journal, Vol. 4, Issue 5 https://doi.org/10.1038/ismej.2009.154	journal	February 2010
Experimental factors affecting PCR-based estimates of microbial species richness and evenness Engelbrektson, Anna; Kunin, Victor; Wrighton, Kelly C. The ISME Journal, Vol. 4, Issue 5 https://doi.org/10.1038/ismej.2009.153	journal	January 2010
The PathoChip, a functional gene array for assessing pathogenic properties of diverse microbial communities Lee, Yong-Jin; van Nostrand, Joy D.; Tu, Qichao The ISME Journal, Vol. 7, Issue 10 https://doi.org/10.1038/ismej.2013.88	journal	June 2013
UPARSE: highly accurate OTU sequences from microbial amplicon reads Edgar, Robert C. Nature Methods, Vol. 10, Issue 10 https://doi.org/10.1038/nmeth.2604	journal	August 2013
Global distribution of microbial abundance and biomass in subseafloor sediment Kallmeyer, J.; Pockalny, R.; Adhikari, R. R. Proceedings of the National Academy of Sciences, Vol. 109, Issue 40 https://doi.org/10.1073/pnas.1203849109	journal	August 2012
Computational Improvements Reveal Great Bacterial Diversity and High Metal Toxicity in Soil Gans, J. Science, Vol. 309, Issue 5739 https://doi.org/10.1126/science.1112665	journal	August 2005
Genomic sequencing of uncultured microorganisms from single cells Lasken, Roger S. Nature Reviews Microbiology, Vol. 10, Issue 9 https://doi.org/10.1038/nrmicro2857	journal	August 2012
High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity Loman, Nicholas J.; Constantinidou, Chrystala; Chan, Jacqueline Z. M. Nature Reviews Microbiology, Vol. 10, Issue 9 https://doi.org/10.1038/nrmicro2850	journal	August 2012
The role of ecological theory in microbial ecology Prosser, James I.; Bohannan, Brendan J. M.; Curtis, Tom P. Nature Reviews Microbiology, Vol. 5, Issue 5 https://doi.org/10.1038/nrmicro1643	journal	May 2007
Environmental Genome Shotgun Sequencing of the Sargasso Sea Venter, J. C. Science, Vol. 304, Issue 5667 https://doi.org/10.1126/science.1093857	journal	April 2004
A metagenome-wide association study of gut microbiota in type 2 diabetes Qin, Junjie; Li, Yingrui; Cai, Zhiming Nature, Vol. 490, Issue 7418 https://doi.org/10.1038/nature11450	journal	September 2012
PCR Amplification-Independent Methods for Detection of Microbial Communities by the High-Density Microarray PhyloChip DeAngelis, Kristen M.; Wu, Cindy H.; Beller, Harry R. Applied and Environmental Microbiology, Vol. 77, Issue 18 https://doi.org/10.1128/AEM.05262-11	journal	July 2011
Palmitoylputrescine, an Antibiotic Isolated from the Heterologous Expression of DNA Extracted from Bromeliad Tank Water ^† Brady, Sean F.; Clardy, Jon Journal of Natural Products, Vol. 67, Issue 8 https://doi.org/10.1021/np0499766	journal	August 2004
Tetarimycin A, an MRSA-Active Antibiotic Identified through Induced Expression of Environmental DNA Gene Clusters Kallifidas, Dimitris; Kang, Hahk-Soo; Brady, Sean F. Journal of the American Chemical Society, Vol. 134, Issue 48 https://doi.org/10.1021/ja3093828	journal	November 2012
Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity Sorek, Rotem; Cossart, Pascale Nature Reviews Genetics, Vol. 11, Issue 1 https://doi.org/10.1038/nrg2695	journal	November 2009
Functional Characterization of the Antibiotic Resistance Reservoir in the Human Microflora Sommer, M. O. A.; Dantas, G.; Church, G. M. Science, Vol. 325, Issue 5944 https://doi.org/10.1126/science.1176950	journal	August 2009
Functional metagenomics for enzyme discovery: challenges to efficient screening Uchiyama, Taku; Miyazaki, Kentaro Current Opinion in Biotechnology, Vol. 20, Issue 6 https://doi.org/10.1016/j.copbio.2009.09.010	journal	December 2009
Scaling metagenome sequence assembly with probabilistic de Bruijn graphs Pell, J.; Hintze, A.; Canino-Koning, R. Proceedings of the National Academy of Sciences, Vol. 109, Issue 33 https://doi.org/10.1073/pnas.1121464109	journal	July 2012
Microbial community structure and its functional implications Fuhrman, Jed A. Nature, Vol. 459, Issue 7244 https://doi.org/10.1038/nature08058	journal	May 2009
Sizing up metatranscriptomics Moran, Mary Ann; Satinsky, Brandon; Gifford, Scott M. The ISME Journal, Vol. 7, Issue 2 https://doi.org/10.1038/ismej.2012.94	journal	August 2012
Metatranscriptomics reveals unique microbial small RNAs in the ocean’s water column Shi, Yanmei; Tyson, Gene W.; DeLong, Edward F. Nature, Vol. 459, Issue 7244 https://doi.org/10.1038/nature08055	journal	May 2009
Comparing microarrays and next-generation sequencing technologies for microbial ecology research Roh, Seong Woon; Abell, Guy C. J.; Kim, Kyoung-Ho Trends in Biotechnology, Vol. 28, Issue 6 https://doi.org/10.1016/j.tibtech.2010.03.001	journal	June 2010
Proteomics in multiplex Melton, Lisa Nature, Vol. 429, Issue 6987 https://doi.org/10.1038/429101a	journal	May 2004
Cloning the Soil Metagenome: a Strategy for Accessing the Genetic and Functional Diversity of Uncultured Microorganisms Rondon, M. R.; August, P. R.; Bettermann, A. D. Applied and Environmental Microbiology, Vol. 66, Issue 6 https://doi.org/10.1128/AEM.66.6.2541-2547.2000	journal	June 2000
Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw Mackelprang, Rachel; Waldrop, Mark P.; DeAngelis, Kristen M. Nature, Vol. 480, Issue 7377 https://doi.org/10.1038/nature10576	journal	November 2011
Generation of Multimillion-Sequence 16S rRNA Gene Libraries from Complex Microbial Communities by Assembling Paired-End Illumina Reads Bartram, Andrea K.; Lynch, Michael D. J.; Stearns, Jennifer C. Applied and Environmental Microbiology, Vol. 77, Issue 15 https://doi.org/10.1128/aem.05896-11	journal	July 2011
Microbial biogeography: putting microorganisms on the map Martiny, Jennifer B. Hughes; Bohannan, Brendan J. M.; Brown, James H. Nature Reviews Microbiology, Vol. 4, Issue 2 https://doi.org/10.1038/nrmicro1341	journal	February 2006
Phylogenetic Molecular Ecological Network of Soil Microbial Communities in Response to Elevated CO2 Zhou, Jizhong; Deng, Ye; Luo, Feng mBio, Vol. 2, Issue 4 https://doi.org/10.1128/mBio.00122-11	journal	July 2011
Functional ecology of an Antarctic Dry Valley Chan, Y.; Van Nostrand, J. D.; Zhou, J. Proceedings of the National Academy of Sciences, Vol. 110, Issue 22 https://doi.org/10.1073/pnas.1300643110	journal	May 2013
Application of phenotypic microarrays to environmental microbiology Borglin, Sharon; Joyner, Dominique; DeAngelis, Kristen M. Current Opinion in Biotechnology, Vol. 23, Issue 1 https://doi.org/10.1016/j.copbio.2011.12.006	journal	February 2012
Reproducibility of pyrosequencing data for biodiversity assessment in complex communities Zhan, Aibin; He, Song; Brown, Emily A. Methods in Ecology and Evolution, Vol. 5, Issue 9 https://doi.org/10.1111/2041-210X.12230	journal	July 2014
Reproducibility and quantitation of amplicon sequencing-based detection Zhou, Jizhong; Wu, Liyou; Deng, Ye The ISME Journal, Vol. 5, Issue 8 https://doi.org/10.1038/ismej.2011.11	journal	February 2011
GeoChip 3.0 as a high-throughput tool for analyzing microbial community composition, structure and functional activity He, Zhili; Deng, Ye; Van Nostrand, Joy D. The ISME Journal, Vol. 4, Issue 9 https://doi.org/10.1038/ismej.2010.46	journal	April 2010
The rational exploration of microbial diversity Quince, Christopher; Curtis, Thomas P.; Sloan, William T. The ISME Journal, Vol. 2, Issue 10 https://doi.org/10.1038/ismej.2008.69	journal	July 2008
Genomic approaches to studying the human microbiota Weinstock, George M. Nature, Vol. 489, Issue 7415 https://doi.org/10.1038/nature11553	journal	September 2012
Sequence assembly demystified Nagarajan, Niranjan; Pop, Mihai Nature Reviews Genetics, Vol. 14, Issue 3 https://doi.org/10.1038/nrg3367	journal	January 2013
Metagenomics approaches in systems microbiology Vieites, José M.; Guazzaroni, María-Eugenia; Beloqui, Ana FEMS Microbiology Reviews, Vol. 33, Issue 1 https://doi.org/10.1111/j.1574-6976.2008.00152.x	journal	January 2009
Experimental and analytical tools for studying the human microbiome Kuczynski, Justin; Lauber, Christian L.; Walters, William A. Nature Reviews Genetics, Vol. 13, Issue 1 https://doi.org/10.1038/nrg3129	journal	December 2011
Novel Natural Products from Soil DNA Libraries in a Streptomycete Host Wang, Gui-Yang-Sheng; Graziani, Edmund; Waters, Barbara Organic Letters, Vol. 2, Issue 16 https://doi.org/10.1021/ol005860z	journal	August 2000
Targeted metagenomics: a high-resolution metagenomics approach for specific gene clusters in complex microbial communities: Targeted metagenomics Suenaga, Hikaru Environmental Microbiology, Vol. 14, Issue 1 https://doi.org/10.1111/j.1462-2920.2011.02438.x	journal	March 2011
Stochasticity, succession, and environmental perturbations in a fluidic ecosystem Zhou, Jizhong; Deng, Ye; Zhang, Ping Proceedings of the National Academy of Sciences, Vol. 111, Issue 9 https://doi.org/10.1073/pnas.1324044111	journal	February 2014
Proteorhodopsin lateral gene transfer between marine planktonic Bacteria and Archaea Frigaard, Niels-Ulrik; Martinez, Asuncion; Mincer, Tracy J. Nature, Vol. 439, Issue 7078 https://doi.org/10.1038/nature04435	journal	February 2006
Use and misuse of PLFA measurements in soils Frostegård, Åsa; Tunlid, Anders; Bååth, Erland Soil Biology and Biochemistry, Vol. 43, Issue 8 https://doi.org/10.1016/j.soilbio.2010.11.021	journal	August 2011
Generation of Multimillion-Sequence 16S rRNA Gene Libraries from Complex Microbial Communities by Assembling Paired-End Illumina Reads Bartram, Andrea K.; Lynch, Michael D. J.; Stearns, Jennifer C. Applied and Environmental Microbiology, Vol. 77, Issue 11 https://doi.org/10.1128/AEM.02772-10	journal	April 2011
Untangling Genomes from Metagenomes: Revealing an Uncultured Class of Marine Euryarchaeota Iverson, V.; Morris, R. M.; Frazar, C. D. Science, Vol. 335, Issue 6068 https://doi.org/10.1126/science.1212665	journal	February 2012
PCR Biases Distort Bacterial and Archaeal Community Structure in Pyrosequencing Datasets Pinto, Ameet J.; Raskin, Lutgarde; Bertilsson, Stefan PLoS ONE, Vol. 7, Issue 8, Article No. e43093 https://doi.org/10.1371/journal.pone.0043093	journal	August 2012
Fundamental Questions in Biology Levin, Simon A. PLoS Biology, Vol. 4, Issue 9 https://doi.org/10.1371/journal.pbio.0040300	journal	September 2006
Functional metagenomics reveals diverse β-lactamases in a remote Alaskan soil Allen, Heather K.; Moe, Luke A.; Rodbumrer, Jitsupang The ISME Journal, Vol. 3, Issue 2 https://doi.org/10.1038/ismej.2008.86	journal	October 2008
Performance comparison of benchtop high-throughput sequencing platforms Loman, Nicholas J.; Misra, Raju V.; Dallman, Timothy J. Nature Biotechnology, Vol. 30, Issue 5 https://doi.org/10.1038/nbt.2198	journal	April 2012
Using stable isotope probing to obtain a targeted metatranscriptome of aerobic methanotrophs in lake sediment: SIP-metatranscriptomics of methanotrophs Dumont, Marc G.; Pommerenke, Bianca; Casper, Peter Environmental Microbiology Reports https://doi.org/10.1111/1758-2229.12078	journal	July 2013
GeoChip 4: a functional gene-array-based high-throughput environmental technology for microbial community analysis Tu, Qichao; Yu, Hao; He, Zhili Molecular Ecology Resources https://doi.org/10.1111/1755-0998.12239	journal	March 2014
Spatial scaling of functional gene diversity across various microbial taxa Zhou, J.; Kang, S.; Schadt, C. W. Proceedings of the National Academy of Sciences, Vol. 105, Issue 22 https://doi.org/10.1073/pnas.0709016105	journal	May 2008
Application of COMPOCHIP Microarray to Investigate the Bacterial Communities of Different Composts Franke-Whittle, Ingrid H.; Knapp, Brigitte A.; Fuchs, Jacques Microbial Ecology, Vol. 57, Issue 3 https://doi.org/10.1007/s00248-008-9435-2	journal	September 2008
Advances in monitoring environmental microbes Hazen, Terry C.; Rocha, Andrea M.; Techtmann, Stephen M. Current Opinion in Biotechnology, Vol. 24, Issue 3 https://doi.org/10.1016/j.copbio.2012.10.020	journal	June 2013
Microarray-Based Analysis of Subnanogram Quantities of Microbial Community DNAs by Using Whole-Community Genome Amplification Wu, L.; Liu, X.; Schadt, C. W. Applied and Environmental Microbiology, Vol. 72, Issue 7 https://doi.org/10.1128/AEM.02738-05	journal	July 2006
Functional Molecular Ecological Networks Zhou, Jizhong; Deng, Ye; Luo, Feng mBio, Vol. 1, Issue 4 https://doi.org/10.1128/mBio.00169-10	journal	October 2010
Comparative Analyses of the Bacterial Microbiota of the Human Nostril and Oropharynx Lemon, Katherine mBio https://doi.org/10.1128/mBio.00129-10	journal	January 2010
Fungal diversity driven by bark features affects phorophyte preference in epiphytic orchids from southern China Pecoraro, Lorenzo; Rasmussen, Hanne N.; Gomes, Sofia I. F. Scientific Reports, Vol. 11, Issue 1 https://doi.org/10.1038/s41598-021-90877-1	journal	May 2021
Comparative genomics of two newly isolated Dehalococcoides strains and an enrichment using a genus microarray Lee, Patrick K. H.; Cheng, Dan; Hu, Ping The ISME Journal, Vol. 5, Issue 6 https://doi.org/10.1038/ismej.2010.202	journal	January 2011
High-Throughput Analysis of Ammonia Oxidiser Community Composition via a Novel, amoA-Based Functional Gene Array Abell, Guy C. J.; Robert, Stan S.; Frampton, Dion M. F. PLoS ONE, Vol. 7, Issue 12 https://doi.org/10.1371/journal.pone.0051542	journal	December 2012
Succession and convergence of biofilm communities in fixed-film reactors treating aromatic hydrocarbons in groundwater. Massol-Deyá, A.; Weller, R.; Ríos-Hernández, L. Applied and environmental microbiology, Vol. 63, Issue 1 https://doi.org/10.1128/AEM.63.1.270-276.1997	journal	January 1997
Commercial DNA extraction kits impact observed microbial community composition in permafrost samples Vishnivetskaya, Tatiana A.; Layton, Alice C.; Lau, Maggie C. Y. FEMS Microbiology Ecology, Vol. 87, Issue 1 https://doi.org/10.1111/1574-6941.12219	journal	October 2013
GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes He, Zhili; Gentry, Terry J.; Schadt, Christopher W. The ISME Journal, Vol. 1, Issue 1 https://doi.org/10.1038/ismej.2007.2	journal	May 2007
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Community Proteomics of a Natural Microbial Biofilm Ram, Rachna J.; VerBerkmoes, Nathan C.; Thelen, Michael P. Science, Vol. 308, Issue 5730 https://doi.org/10.1126/science.1109070	journal	June 2005
Urban aerosols harbor diverse and dynamic bacterial populations Brodie, E. L.; DeSantis, T. Z.; Parker, J. P. M. Proceedings of the National Academy of Sciences, Vol. 104, Issue 1, p. 299-304 https://doi.org/10.1073/pnas.0608255104	journal	December 2006
Metagenome-wide analysis of antibiotic resistance genes in a large cohort of human gut microbiota Hu, Yongfei; Yang, Xi; Qin, Junjie Nature Communications, Vol. 4, Issue 1 https://doi.org/10.1038/ncomms3151	journal	July 2013
Microbial community gene expression in ocean surface waters Frias-Lopez, J.; Shi, Y.; Tyson, G. W. Proceedings of the National Academy of Sciences, Vol. 105, Issue 10 https://doi.org/10.1073/pnas.0708897105	journal	March 2008
Comparison of direct boiling method with commercial kits for extracting fecal microbiome DNA by Illumina sequencing of 16S rRNA tags Peng, Xin; Yu, Ke-Qiang; Deng, Guan-Hua Journal of Microbiological Methods, Vol. 95, Issue 3 https://doi.org/10.1016/j.mimet.2013.07.015	journal	December 2013
Sequencing technologies — the next generation Metzker, Michael L. Nature Reviews Genetics, Vol. 11, Issue 1 https://doi.org/10.1038/nrg2626	journal	December 2009
Design and Verification of a Pangenome Microarray Oligonucleotide Probe Set for Dehalococcoides spp. Hug, Laura A.; Salehi, Maryam; Nuin, Paulo Applied and Environmental Microbiology, Vol. 77, Issue 15 https://doi.org/10.1128/AEM.00063-11	journal	June 2011
Unexpected Diversity during Community Succession in the Apple Flower Microbiome Shade, Ashley; McManus, Patricia S.; Handelsman, Jo mBio, Vol. 4, Issue 2 https://doi.org/10.1128/mBio.00602-12	journal	February 2013
Carbohydrate Arrays for the Evaluation of Protein Binding and Enzymatic Modification Houseman, Benjamin T.; Mrksich, Milan Chemistry & Biology, Vol. 9, Issue 4 https://doi.org/10.1016/S1074-5521(02)00124-2	journal	April 2002
Uncultured soil bacteria are a reservoir of new antibiotic resistance genes Riesenfeld, Christian S.; Goodman, Robert M.; Handelsman, Jo Environmental Microbiology, Vol. 6, Issue 9 https://doi.org/10.1111/j.1462-2920.2004.00664.x	journal	September 2004
Identification and Characterization of Coenzyme B12-Dependent Glycerol Dehydratase- and Diol Dehydratase-Encoding Genes from Metagenomic DNA Libraries Derived from Enrichment Cultures Knietsch, A.; Bowien, S.; Whited, G. Applied and Environmental Microbiology, Vol. 69, Issue 6 https://doi.org/10.1128/AEM.69.6.3048-3060.2003	journal	June 2003
Fluostatins Produced by the Heterologous Expression of a TAR Reassembled Environmental DNA Derived Type II PKS Gene Cluster Feng, Zhiyang; Kim, Jeff H.; Brady, Sean F. Journal of the American Chemical Society, Vol. 132, Issue 34 https://doi.org/10.1021/ja104550p	journal	September 2010
Microbial Biogeography: From Taxonomy to Traits Green, J. L.; Bohannan, B. J. M.; Whitaker, R. J. Science, Vol. 320, Issue 5879 https://doi.org/10.1126/science.1153475	journal	May 2008
Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates Kunin, Victor; Engelbrektson, Anna; Ochman, Howard Environmental Microbiology, Vol. 12, Issue 1 https://doi.org/10.1111/j.1462-2920.2009.02051.x	journal	January 2010
Metaproteomics of a gutless marine worm and its symbiotic microbial community reveal unusual pathways for carbon and energy use Kleiner, M.; Wentrup, C.; Lott, C. Proceedings of the National Academy of Sciences, Vol. 109, Issue 19 https://doi.org/10.1073/pnas.1121198109	journal	April 2012
Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Liu, W. T.; Marsh, T. L.; Cheng, H. Applied and environmental microbiology, Vol. 63, Issue 11 https://doi.org/10.1128/AEM.63.11.4516-4522.1997	journal	January 1997
Generation and Analysis of a Mouse Intestinal Metatranscriptome through Illumina Based RNA-Sequencing Xiong, Xuejian; Frank, Daniel N.; Robertson, Charles E. PLoS ONE, Vol. 7, Issue 4 https://doi.org/10.1371/journal.pone.0036009	journal	April 2012
Recovery, Purification, and Cloning of High-Molecular-Weight DNA from Soil Microorganisms Liles, M. R.; Williamson, L. L.; Rodbumrer, J. Applied and Environmental Microbiology, Vol. 74, Issue 10 https://doi.org/10.1128/AEM.02630-07	journal	March 2008
Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage Haroon, Mohamed F.; Hu, Shihu; Shi, Ying Nature, Vol. 500, Issue 7464 https://doi.org/10.1038/nature12375	journal	July 2013
Using network analysis to explore co-occurrence patterns in soil microbial communities Barberán, Albert; Bates, Scott T.; Casamayor, Emilio O. The ISME Journal, Vol. 6, Issue 2 https://doi.org/10.1038/ismej.2011.119	journal	September 2011
Oligonucleotide Microarray for 16S rRNA Gene-Based Detection of All Recognized Lineages of Sulfate-Reducing Prokaryotes in the Environment Loy, A.; Lehner, A.; Lee, N. Applied and Environmental Microbiology, Vol. 68, Issue 10 https://doi.org/10.1128/AEM.68.10.5064-5081.2002	journal	October 2002
Community structure and metabolism through reconstruction of microbial genomes from the environment Tyson, Gene W.; Chapman, Jarrod; Hugenholtz, Philip Nature, Vol. 428, Issue 6978 https://doi.org/10.1038/nature02340	journal	February 2004
Oligonucleotide Microarray for the Study of Functional Gene Diversity in the Nitrogen Cycle in the Environment Taroncher-Oldenburg, G.; Griner, E. M.; Francis, C. A. Applied and Environmental Microbiology, Vol. 69, Issue 2 https://doi.org/10.1128/AEM.69.2.1159-1171.2003	journal	February 2003
Phylogenetic Microarray Analysis of a Microbial Community Performing Reductive Dechlorination at a TCE-Contaminated Site Lee, Patrick K. H.; Warnecke, F.; Brodie, Eoin L. Environmental Science & Technology, Vol. 46, Issue 2 https://doi.org/10.1021/es203005k	journal	December 2011
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms Caporaso, J. Gregory; Lauber, Christian L.; Walters, William A. The ISME Journal, Vol. 6, Issue 8 https://doi.org/10.1038/ismej.2012.8	journal	March 2012
Prokaryotic Diversity--Magnitude, Dynamics, and Controlling Factors Torsvik, V. Science, Vol. 296, Issue 5570 https://doi.org/10.1126/science.1071698	journal	May 2002
Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen Hess, M.; Sczyrba, A.; Egan, R. Science, Vol. 331, Issue 6016 https://doi.org/10.1126/science.1200387	journal	January 2011
Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies Schloss, Patrick D.; Gevers, Dirk; Westcott, Sarah L. PLoS ONE, Vol. 6, Issue 12 https://doi.org/10.1371/journal.pone.0027310	journal	December 2011
Deep-Sea Oil Plume Enriches Indigenous Oil-Degrading Bacteria Hazen, Terry C.; Dubinsky, Eric A.; DeSantis, Todd Z. Science, Vol. 330, Issue 6001 https://doi.org/10.1126/science.1195979	journal	August 2010
DNA recovery from soils of diverse composition. Zhou, J.; Bruns, M. A.; Tiedje, J. M. Applied and environmental microbiology, Vol. 62, Issue 2 https://doi.org/10.1128/aem.62.2.316-322.1996	journal	January 1996
Metagenomics: Application of Genomics to Uncultured Microorganisms Handelsman, Jo Microbiology and Molecular Biology Reviews, Vol. 69, Issue 1 https://doi.org/10.1128/mmbr.69.1.195.2005	journal	March 2005

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59 BASIC BIOLOGICAL SCIENCES

Title: High-throughput metagenomic technologies for complex microbial community analysis. Open and closed formats

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