title: Cultivating the uncultured.
abstract: The recent application of molecular phylogeny to environmental samples has resulted in the discovery of an abundance of unique and previously unrecognized microorganisms. The vast majority of this microbial diversity has proved refractory to cultivation. Here, we describe a universal method that provides access to this immense reservoir of untapped microbial diversity. This technique combines encapsulation of cells in gel microdroplets for massively parallel microbial cultivation under low nutrient flux conditions, followed by flow cytometry to detect microdroplets containing microcolonies. The ability to grow and study previously uncultured organisms in pure culture will enhance our understanding of microbial physiology and metabolic adaptation and will provide new sources of microbial metabolites. We show that this technology can be applied to samples from several different environments, including seawater and soil.
authors.affiliation: Diversa Corporation, San Diego, CA 92121, USA.
authors.forename: Karsten
authors.initials: K
authors.lastname: Zengler
authors.forename: Gerardo
authors.initials: G
authors.lastname: Toledo
authors.forename: Michael
authors.initials: M
authors.lastname: Rappe
authors.forename: James
authors.initials: J
authors.lastname: Elkins
authors.forename: Eric J
authors.initials: EJ
authors.lastname: Mathur
authors.forename: Jay M
authors.initials: JM
authors.lastname: Short
authors.forename: Martin
authors.initials: M
authors.lastname: Keller
mesh_terms: D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D001431:Bacteriological Techniques; D004339:Drug Compounding; D005434:Flow Cytometry; D005618:Fresh Water / Q000382:microbiology; D005782:Gels; D005869:Ghana; D007630:Kenya; D010316:Particle Size; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D012335:RNA, Ribosomal / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012623:Seawater / Q000382:microbiology; D012988:Soil Microbiology; D013045:Species Specificity; D014871:Water Microbiology
chemical_list: D005782:Gels; D012335:RNA, Ribosomal; D012336:RNA, Ribosomal, 16S