ArticleApplied and environmental microbiology2002
Analysis of bacterial community composition by oligonucleotide fingerprinting of rRNA genes.
Article in Applied and environmental microbiology, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 140 citations in OpenAlex.
- Trial
- Impact of Elevational Gradients and Chemical Parameters on Changes in Soil Bacterial Diversity Under Semiarid Mountain Region.Journal of microbiology (Seoul, Korea) · 2023Article
- Article
- Microbial community responses to organophosphate substrate additions in contaminated subsurface sediments.PloS one · 2014Article
- Improving oligonucleotide fingerprinting of rRNA genes by implementation of polony microarray technology.Journal of microbiological methods · 2012Article
- The role of coral-associated bacterial communities in Australian Subtropical White Syndrome of Turbinaria mesenterina.PloS one · 2012Article
- Improving probe set selection for microbial community analysis by leveraging taxonomic information of training sequences.BMC bioinformatics · 2011Article
- Neutral Zone Classifiers Using a Decision-Theoretic Approach With Application to DNA Array Analyses.Journal of agricultural, biological, and environmental statistics · 2010Article
- Dynamic of active microorganisms inhabiting a bioleaching industrial heap of low-grade copper sulfide ore monitored by real-time PCR and oligonucleotide prokaryotic acidophile microarray.Microbial biotechnology · 2009Article
- Bacterial diversity analysis of larvae and adult midgut microflora using culture-dependent and culture-independent methods in lab-reared and field-collected Anopheles stephensi-an Asian malarial vector.BMC microbiology · 2009Article
- Linking sequence to function in soil bacteria: sequence-directed isolation of novel bacteria contributing to soilborne plant disease suppression.Applied and environmental microbiology · 2009Article
- Bacteria and bacterial rRNA genes associated with the development of colitis in IL-10(-/-) mice.Inflammatory bowel diseases · 2008Article
- Manganese(II)-oxidizing Bacillus spores in Guaymas Basin hydrothermal sediments and plumes.Applied and environmental microbiology · 2006Article
- Abundant and diverse fungal microbiota in the murine intestine.Applied and environmental microbiology · 2006Article
- Phylum- and class-specific PCR primers for general microbial community analysis.Applied and environmental microbiology · 2005Article
- Bacterial community structure and diversity in a century-old manure-treated agroecosystem.Applied and environmental microbiology · 2004Article
- Isolation and biodiversity of hitherto undescribed soil bacteria related to Bacillus niacini.Microbial ecology · 2004Article
- Detection of genes involved in biodegradation and biotransformation in microbial communities by using 50-mer oligonucleotide microarrays.Applied and environmental microbiology · 2004Article
- Article
- Isolation, characterization, and U(VI)-reducing potential of a facultatively anaerobic, acid-resistant Bacterium from Low-pH, nitrate- and U(VI)-contaminated subsurface sediment and description of Salmonella subterranea sp. nov.Applied and environmental microbiology · 2004Article
Corrections and comments
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Authors and funding
11 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
One of the first steps in characterizing an ecosystem is to describe the organisms inhabiting it. For microbial studies, experimental limitations have hindered the ability to depict diverse communities. Here we describe oligonucleotide fingerprinting of rRNA genes (OFRG), a method that permits identification of arrayed rRNA genes (rDNA) through a series of hybridization experiments using small DNA probes. To demonstrate this strategy, we examined the bacteria inhabiting two different soils. Analysis of 1,536 rDNA clones revealed 766 clusters grouped into five major taxa: Bacillus, Actinobacteria, Proteobacteria, and two undefined assemblages. Soil-specific taxa were identified and then independently confirmed through cluster-specific PCR of the original soil DNA. Near-species-level resolution was obtained by this analysis as clones with average sequence identities of 97% were grouped in the same cluster. A comparison of these OFRG results with the results obtained in a denaturing gradient gel electrophoresis analysis of the same two soils demonstrated the significance of this methodological advance. OFRG provides a cost-effective means to extensively analyze microbial communities and should have applications in medicine, biotechnology, and ecosystem studies.
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Registered trials
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.