CiteULike: vrich's microarray

Composition of microbial communities in hexachlorocyclohexane (HCH) contaminated soils from Spain revealed with a habitat-specific microarray

Josh Neufeld — 2005-12-11T23:53:47-00:00

Environmental Microbiology, Vol. 8, No. 1. (January 2006), pp. 126-140.

A nifH-based Oligonucleotide Microarray for Functional Diagnostics of Nitrogen-fixing Microorganisms

Zhang — 2007-07-02T21:31:42-00:00

Microbial Ecology, Vol. 53, No. 3. (April 2007), pp. 456-470.

Ammonia-oxidizing bacterial community composition in estuarine and oceanic environments assessed using a functional gene microarray

Ward — 2007-09-07T03:51:56-00:00

Environmental Microbiology, Vol. 9, No. 10. (October 2007), pp. 2522-2538.

Analysis of methanotrophic communities in landfill biofilters using diagnostic microarray

Gebert — 2008-04-09T15:21:03-00:00

Environmental Microbiology, Vol. 10, No. 5. (May 2008), pp. 1175-1188.

Novel Microarray Design Strategy To Study Complex Bacterial Communities

Antoine Huyghe — 2008-05-16T02:02:17-00:00

Appl. Environ. Microbiol., Vol. 74, No. 6. (15 March 2008), pp. 1876-1885.

Assessing bacterial flora composition appears to be of increasing importance to fields as diverse as physiology, development, medicine, epidemiology, the environment, and the food industry. We report here the development and validation of an original microarray strategy that allows analysis of the phylogenic composition of complex bacterial mixtures. The microarray contains [~]9,500 feature elements targeting 16S rRNA gene-specific regions. Probe design was performed by selecting oligonucleotide sequences specific to each node of the seven levels of the bacterial phylogenetic tree (domain, phylum, class, order, family, genus, and species). This approach, based on sequence information, allows analysis of the bacterial contents of complex bacterial mixtures to detect both known and unknown microorganisms. The presence of unknown organisms can be suspected and mapped on the phylogenetic tree, indicating where to refine analysis. Initial proof-of-concept experiments were performed on oral bacterial communities. Our results show that this hierarchical approach can reveal minor changes ([≤]1%) in gingival flora content when samples collected in individuals from similar geographical origins are compared. 10.1128/AEM.01722-07

Direct profiling of environmental microbial populations by thermal dissociation analysis of native rRNAs hybridized to oligonucleotide microarrays.

S El Fantroussi — 2008-05-12T16:39:52-00:00

Applied and environmental microbiology, Vol. 69, No. 4. (April 2003), pp. 2377-2382.

Oligonucleotide microarrays were used to profile directly extracted rRNA from environmental microbial populations without PCR amplification. In our initial inspection of two distinct estuarine study sites, the hybridization patterns were reproducible and varied between estuarine sediments of differing salinities. The determination of a thermal dissociation curve (i.e., melting profile) for each probe-target duplex provided information on hybridization specificity, which is essential for confirming adequate discrimination between target and nontarget sequences.

Microarray-Based Analysis of Subnanogram Quantities of Microbial Community DNAs by Using Whole-Community Genome Amplification

Liyou Wu — 2008-05-15T23:34:38-00:00

Appl. Environ. Microbiol., Vol. 72, No. 7. (1 July 2006), pp. 4931-4941.

Microarray technology provides the opportunity to identify thousands of microbial genes or populations simultaneously, but low microbial biomass often prevents application of this technology to many natural microbial communities. We developed a whole-community genome amplification-assisted microarray detection approach based on multiple displacement amplification. The representativeness of amplification was evaluated using several types of microarrays and quantitative indexes. Representative detection of individual genes or genomes was obtained with 1 to 100 ng DNA from individual or mixed genomes, in equal or unequal abundance, and with 1 to 500 ng community DNAs from groundwater. Lower concentrations of DNA (as low as 10 fg) could be detected, but the lower template concentrations affected the representativeness of amplification. Robust quantitative detection was also observed by significant linear relationships between signal intensities and initial DNA concentrations ranging from (i) 0.04 to 125 ng (r2 = 0.65 to 0.99) for DNA from pure cultures as detected by whole-genome open reading frame arrays, (ii) 0.1 to 1,000 ng (r2 = 0.91) for genomic DNA using community genome arrays, and (iii) 0.01 to 250 ng (r2 = 0.96 to 0.98) for community DNAs from ethanol-amended groundwater using 50-mer functional gene arrays. This method allowed us to investigate the oligotrophic microbial communities in groundwater contaminated with uranium and other metals. The results indicated that microorganisms containing genes involved in contaminant degradation and immobilization are present in these communities, that their spatial distribution is heterogeneous, and that microbial diversity is greatly reduced in the highly contaminated environment. 10.1128/AEM.02738-05

Microarray-Based Analysis of Microbial Community RNAs by Whole-Community RNA Amplification

Haichun Gao — 2008-05-15T23:32:04-00:00

Appl. Environ. Microbiol., Vol. 73, No. 2. (1 January 2007), pp. 563-571.

A new approach, termed whole-community RNA amplification (WCRA), was developed to provide sufficient amounts of mRNAs from environmental samples for microarray analysis. This method employs fusion primers (six to nine random nucleotides with an attached T7 promoter) for the first-strand synthesis. The shortest primer (T7N6S) gave the best results in terms of the yield and representativeness of amplification. About 1,200- to 1,800-fold amplification was obtained with amounts of the RNA templates ranging from 10 to 100 ng, and very representative detection was obtained with 50 to 100 ng total RNA. Evaluation with a Shewanella oneidensis Deltafur strain revealed that the amplification method which we developed could preserve the original abundance relationships of mRNAs. In addition, to determine whether representative detection of RNAs can be achieved with mixed community samples, amplification biases were evaluated with a mixture containing equal quantities of RNAs (100 ng each) from four bacterial species, and representative amplification was also obtained. Finally, the method which we developed was applied to the active microbial populations in a denitrifying fluidized bed reactor used for denitrification of contaminated groundwater and ethanol-stimulated groundwater samples for uranium reduction. The genes expressed were consistent with the expected functions of the bioreactor and groundwater system, suggesting that this approach is useful for analyzing the functional activities of microbial communities. This is one of the first demonstrations that microarray-based technology can be used to successfully detect the activities of microbial communities from real environmental samples in a high-throughput fashion. 10.1128/AEM.01771-06

Metagenome microarray for screening of fosmid clones containing specific genes

Soo Park — 2008-05-11T21:14:12-00:00

FEMS Microbiology Letters, Vol. 0, No. 0. (0), pp. ???-???.

Abstract A critical step in the process of metagenome analysis is to screen for clones that contain specific genes among a large number of clones. To form one of the sequence-based screening tools of a metagenome library, we designed a format of microarray [metagenome microarray (MGA)] that is arrayed with fosmid library clone DNA samples on a glass slide. We evaluated the MGA using random prime labeled fluorescent probes prepared from PCR products of the target gene and found that we could obtain specific hybridization signals only for the fosmid clone that contained the target gene. We found that the detection limit of the MGA was c. 10 ng muL-1 of fosmid clone DNA, and that the MGA-based hybridization was quantitative within a concentration range of 10-200 ng muL-1 of fosmid clone DNA. We used the MGA successfully to identify two fosmid clones that contained 16S rRNA genes from a fosmid library from the sediment of the East Sea, Korea. In conclusion, we have demonstrated that the MGA can be used for screening for fosmid clones containing specific genes in a metagenome library, and that this technology has potential application as a high-throughput metagenome screening tool.