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Title: Targeted Access to the Genomes of Low Abundance Organisms in Complex Microbial Communities

Abstract

Current metagenomic approaches to the study of complex microbial consortia provide a glimpse into the community metabolism, and occasionally allow genomic assemblies for the most abundant organisms. However, little information is gained for the members of the community present at low frequency, especially those representing yet uncultured taxa-which includes the bulk of the diversity present in most environments. Here we used phylogenetically directed cell separation by fluorescence in situ hybridization and flow cytometry, followed by amplification and sequencing of a fraction of the genomic DNA of several bacterial cells that belong to the TM7 phylum. Partial genomic assembly allowed, for the first time, a look into the evolution and potential metabolism of a soil representative from this group of organisms for which there are no species in stable laboratory cultures. Genomic reconstruction from targeted cells of uncultured organisms directly isolated from the environment represents a powerful approach to access any specific members of a community and an alternative way to assess the community metabolic potential.

Authors:
 [1];  [2];  [2];  [2];  [2];  [2];  [2];  [2];  [1];  [1]
  1. ORNL
  2. Diversa Corporation
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Laboratory Directed Research and Development (LDRD) Program
OSTI Identifier:
1185308
DOE Contract Number:  
DE-AC05-00OR22725
Resource Type:
Journal Article
Resource Relation:
Journal Name: Applied and Environmental Microbiology; Journal Volume: 73; Journal Issue: 10
Country of Publication:
United States
Language:
English
Subject:
Environmental microbial single cell genomics

Citation Formats

Podar, Mircea, Abulencia, Carl, Walcher, Marion, Hutchinson, Don, Zengler, Karsten, Garcia, Joseph, Holland, Trevin, Cotton, Dave, Hauser, Loren John, and Keller, Martin. Targeted Access to the Genomes of Low Abundance Organisms in Complex Microbial Communities. United States: N. p., 2007. Web. doi:10.1128/AEM.02985-06.
Podar, Mircea, Abulencia, Carl, Walcher, Marion, Hutchinson, Don, Zengler, Karsten, Garcia, Joseph, Holland, Trevin, Cotton, Dave, Hauser, Loren John, & Keller, Martin. Targeted Access to the Genomes of Low Abundance Organisms in Complex Microbial Communities. United States. doi:10.1128/AEM.02985-06.
Podar, Mircea, Abulencia, Carl, Walcher, Marion, Hutchinson, Don, Zengler, Karsten, Garcia, Joseph, Holland, Trevin, Cotton, Dave, Hauser, Loren John, and Keller, Martin. Mon . "Targeted Access to the Genomes of Low Abundance Organisms in Complex Microbial Communities". United States. doi:10.1128/AEM.02985-06.
@article{osti_1185308,
title = {Targeted Access to the Genomes of Low Abundance Organisms in Complex Microbial Communities},
author = {Podar, Mircea and Abulencia, Carl and Walcher, Marion and Hutchinson, Don and Zengler, Karsten and Garcia, Joseph and Holland, Trevin and Cotton, Dave and Hauser, Loren John and Keller, Martin},
abstractNote = {Current metagenomic approaches to the study of complex microbial consortia provide a glimpse into the community metabolism, and occasionally allow genomic assemblies for the most abundant organisms. However, little information is gained for the members of the community present at low frequency, especially those representing yet uncultured taxa-which includes the bulk of the diversity present in most environments. Here we used phylogenetically directed cell separation by fluorescence in situ hybridization and flow cytometry, followed by amplification and sequencing of a fraction of the genomic DNA of several bacterial cells that belong to the TM7 phylum. Partial genomic assembly allowed, for the first time, a look into the evolution and potential metabolism of a soil representative from this group of organisms for which there are no species in stable laboratory cultures. Genomic reconstruction from targeted cells of uncultured organisms directly isolated from the environment represents a powerful approach to access any specific members of a community and an alternative way to assess the community metabolic potential.},
doi = {10.1128/AEM.02985-06},
journal = {Applied and Environmental Microbiology},
number = 10,
volume = 73,
place = {United States},
year = {Mon Jan 01 00:00:00 EST 2007},
month = {Mon Jan 01 00:00:00 EST 2007}
}