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PMID: 15066821 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

GC fractionation enhances microbial community diversity assessment and detection of minority populations of bacteria by denaturing gradient gel electrophoresis.

Applied and environmental microbiology ·Vol. 70 ·No. 4 ·2004-04-00 ·Pages 2263-70

Holben WE, Feris KP, Kettunen A, Apajalahti JH

Abstract

Effectively and accurately assessing total microbial community diversity is one of the primary challenges in modern microbial ecology. This is particularly true with regard to the detection and characterization of unculturable populations and those present only in low abundance. We report a novel strategy, GC fractionation combined with denaturing gradient gel electrophoresis (GC-DGGE), which combines mechanistically different community analysis approaches to enhance assessment of microbial community diversity and detection of minority populations of microbes. This approach employs GC fractionation as an initial step to reduce the complexity of the community in each fraction. This reduced complexity facilitates subsequent detection of diversity in individual fractions. DGGE analysis of individual fractions revealed bands that were undetected or only poorly represented when total bacterial community DNA was analyzed. Also, directed cloning and sequencing of individual bands from DGGE lanes corresponding to individual G+C fractions allowed detection of numerous phylotypes that were not recovered using a traditional random cloning and sequencing approach.

MeSH Terms
Animals Bacteria/classification,genetics,isolation & purification Bacteriological Techniques Chickens Cloning, Molecular DNA, Bacterial/genetics,isolation & purification Ecology/methods Ecosystem Electrophoresis, Polyacrylamide Gel/methods Molecular Sequence Data Phylogeny
Chemicals
DNA, Bacterial
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Holben William E
Microbial Ecology Program, Division of Biological Sciences, The University of Montana, Missoula, Montana 59812, USA. bill.holben@mso.umt.edu
Feris Kevin P
Kettunen Anu
Apajalahti Juha H A
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Article Info
Journal
Applied and environmental microbiology
Abbr.
Appl Environ Microbiol
ISSN
0099-2240
DOI
10.1128/AEM.70.4.2263-2270.2004
Email
bill.holben@mso.umt.edu
Published
2004-04-00
Pages
2263-70
Language
English
Region
United States
NLM ID
7605801
PMCID
PMC383056
Subset
IM
Databases
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External Links
PubMed source DOI: 10.1128/AEM.70.4.2263-2270.2004 PMC Full Text View journal details
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