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Method for analyzing microbial communities

Patent ·
OSTI ID:1012821

The present invention provides a method for quantitatively analyzing microbial genes, species, or strains in a sample that contains at least two species or strains of microorganisms. The method involves using an isothermal DNA polymerase to randomly and representatively amplify genomic DNA of the microorganisms in the sample, hybridizing the resultant polynucleotide amplification product to a polynucleotide microarray that can differentiate different genes, species, or strains of microorganisms of interest, and measuring hybridization signals on the microarray to quantify the genes, species, or strains of interest.

Research Organization:
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
Sponsoring Organization:
USDOE
DOE Contract Number:
AC05-00OR22725
Assignee:
UT-Battelle, LLC (Oak Ridge, TN)
Patent Number(s):
7,759,057
Application Number:
10/943,067
OSTI ID:
1012821
Country of Publication:
United States
Language:
English

References (17)

Detection of Genes Involved in Biodegradation and Biotransformation in Microbial Communities by Using 50-Mer Oligonucleotide Microarrays journal July 2004
Large-Scale Identification, Mapping, and Genotyping of Single-Nucleotide Polymorphisms in the Human Genome journal May 1998
Challenges in applying microarrays to environmental studies journal June 2002
Evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in environmental samples journal April 2004
Microarrays for bacterial detection and microbial community analysis journal June 2003
Oligonucleotide Microarray for the Study of Functional Gene Diversity in the Nitrogen Cycle in the Environment journal February 2003
DNA/DNA hybridization to microarrays reveals gene-specific differences between closely related microbial genomes journal August 2001
Exploring the Metabolic and Genetic Control of Gene Expression on a Genomic Scale journal October 1997
Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation journal March 2003
DNA Sequencing Using Rolling Circle Amplification and Precision Glass Syringes in a High-Throughput Liquid Handling System journal January 2003
Oligonucleotide Microarray for 16S rRNA Gene-Based Detection of All Recognized Lineages of Sulfate-Reducing Prokaryotes in the Environment journal October 2002
Development and Evaluation of Microarray-Based Whole-Genome Hybridization for Detection of Microorganisms within the Context of Environmental Applications journal December 2004
Comprehensive human genome amplification using multiple displacement amplification journal April 2002
Development and Evaluation of Functional Gene Arrays for Detection of Selected Genes in the Environment journal December 2001
Whole Genome Analysis of Genetic Alterations in Small DNA Samples Using Hyperbranched Strand Displacement Amplification and Array-CGH journal February 2003
Signal amplification by rolling circle amplification on DNA microarrays journal December 2001
Isothermal Strand-Displacement Amplification Applications for High-Throughput Genomics journal December 2002

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