Targeted access to the genomes of low-abundance organisms in complex microbial communities

Mircea Podar, Carl B. Abulencia, Marion Walcher, Don Hutchison, Karsten Zengler, Joseph A. Garcia, Trevin Holland, David Cotton, Loren Hauser, Martin Keller

Research output: Contribution to journalArticlepeer-review

189 Scopus citations

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 frequencies, especially those representing yet-uncultured taxa, which include 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 isolated directly from the environment represents a powerful approach to access any specific members of a community and an alternative way to assess the community's metabolic potential.

Original languageEnglish
Pages (from-to)3205-3214
Number of pages10
JournalApplied and Environmental Microbiology
Volume73
Issue number10
DOIs
StatePublished - May 2007

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