ArticleApplied and environmental microbiology2003
Metagenomic profiling: microarray analysis of an environmental genomic library.
Article in Applied and environmental microbiology, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 138 citations in OpenAlex.
- Microbial community analysis using high-throughput sequencing technology: a beginner's guide for microbiologists.Journal of microbiology (Seoul, Korea) · 2020Article
- Experimental Microbial Alteration and Fe Mobilization From Basaltic Rocks of the ICDP HSDP2 Drill Core, Hilo, Hawaii.Frontiers in microbiology · 2018Article
- Use of functional gene arrays for elucidating in situ biodegradation.Frontiers in microbiology · 2012Article
- Shotgun isotope array for rapid, substrate-specific detection of microorganisms in a microbial community.Applied and environmental microbiology · 2011Article
- From wild strain to domesticated strain: the philosophy of microbial diversity in foods.Frontiers in microbiology · 2011Article
- Size Does Matter: Application-driven Approaches for Soil Metagenomics.Soil biology & biochemistry · 2010Article
- Shared probe design and existing microarray reanalysis using PICKY.BMC bioinformatics · 2010Article
- Microbiomic comparison of the intestine of the earthworm Eisenia fetida fed ergovaline.Current microbiology · 2010Article
- Identification and characterization of metagenomic fragments from tidal flat sediment.Journal of microbiology (Seoul, Korea) · 2009Article
- Interplay of metagenomics and in vitro compartmentalization.Microbial biotechnology · 2009Review
- Metagenomics: Future of microbial gene mining.Indian journal of microbiology · 2008Article
- From bacterial genomics to metagenomics: concept, tools and recent advances.Indian journal of microbiology · 2008Article
- Metagenome fragment classification using N-mer frequency profiles.Advances in bioinformatics · 2008Article
- Finding the needles in the metagenome haystack.Microbial ecology · 2007Article
- A solution for universal classification of species based on genomic DNA.International journal of plant genomics · 2007Article
- Microarray applications in microbial ecology research.Microbial ecology · 2006Review
- Suspension array analysis of 16S rRNA from Fe- and SO(4)2- reducing bacteria in uranium-contaminated sediments undergoing bioremediation.Applied and environmental microbiology · 2006Article
- Metagenomics: application of genomics to uncultured microorganisms.Microbiology and molecular biology reviews : MMBR · 2004Review
- Integration of microbial ecology and statistics: a test to compare gene libraries.Applied and environmental microbiology · 2004Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
Genomic libraries derived from environmental DNA (metagenomic libraries) are useful for characterizing uncultured microorganisms. However, conventional library-screening techniques permit characterization of relatively few environmental clones. Here we describe a novel approach for characterization of a metagenomic library by hybridizing the library with DNA from a set of groundwater isolates, reference strains, and communities. A cosmid library derived from a microcosm of groundwater microorganisms was used to construct a microarray (COSMO) containing approximately 1-kb PCR products amplified from the inserts of 672 cosmids plus a set of 16S ribosomal DNA controls. COSMO was hybridized with Cy5-labeled genomic DNA from each bacterial strain, and the results were compared with the results for a common Cy3-labeled reference DNA sample consisting of a composite of genomic DNA from multiple species. The accuracy of the results was confirmed by the preferential hybridization of each strain to its corresponding rDNA probe. Cosmid clones were identified that hybridized specifically to each of 10 microcosm isolates, and other clones produced positive results with multiple related species, which is indicative of conserved genes. Many clones did not hybridize to any microcosm isolate; however, some of these clones hybridized to community genomic DNA, suggesting that they were derived from microbes that we failed to isolate in pure culture. Based on identification of genes by end sequencing of 17 such clones, DNA could be assigned to functions that have potential ecological importance, including hydrogen oxidation, nitrate reduction, and transposition. Metagenomic profiling offers an effective approach for rapidly characterizing many clones and identifying the clones corresponding to unidentified species of microorganisms.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.