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 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.
authors: Diversa Corporation, San Diego, CA 92121, USA.
authors: Mircea
authors: M
authors: Podar
authors: Carl B
authors: CB
authors: Abulencia
authors: Marion
authors: M
authors: Walcher
authors: Don
authors: D
authors: Hutchison
authors: Karsten
authors: K
authors: Zengler
authors: Joseph A
authors: JA
authors: Garcia
authors: Trevin
authors: T
authors: Holland
authors: David
authors: D
authors: Cotton
authors: Loren
authors: L
authors: Hauser
authors: Martin
authors: M
authors: Keller
mesh_terms: D001419:Bacteria / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D001431:Bacteriological Techniques; D001483:Base Sequence; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D005434:Flow Cytometry; D016680:Genome, Bacterial; D023281:Genomics; D017404:In Situ Hybridization, Fluorescence; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017421:Sequence Analysis; D012689:Sequence Homology, Nucleic Acid; D012988:Soil Microbiology
chemical_list: D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S