title: Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth.
abstract: We have developed a microfluidic device that allows the isolation and genome amplification of individual microbial cells, thereby enabling organism-level genomic analysis of complex microbial ecosystems without the need for culture. This device was used to perform a directed survey of the human subgingival crevice and to isolate bacteria having rod-like morphology. Several isolated microbes had a 16S rRNA sequence that placed them in candidate phylum TM7, which has no cultivated or sequenced members. Genome amplification from individual TM7 cells allowed us to sequence and assemble >1,000 genes, providing insight into the physiology of members of this phylum. This approach enables single-cell genetic analysis of any uncultivated minority member of a microbial community.
authors.affiliation: Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
authors.forename: Yann
authors.initials: Y
authors.lastname: Marcy
authors.forename: Cleber
authors.initials: C
authors.lastname: Ouverney
authors.forename: Elisabeth M
authors.initials: EM
authors.lastname: Bik
authors.forename: Tina
authors.initials: T
authors.lastname: Lösekann
authors.forename: Natalia
authors.initials: N
authors.lastname: Ivanova
authors.forename: Hector Garcia
authors.initials: HG
authors.lastname: Martin
authors.forename: Ernest
authors.initials: E
authors.lastname: Szeto
authors.forename: Darren
authors.initials: D
authors.lastname: Platt
authors.forename: Philip
authors.initials: P
authors.lastname: Hugenholtz
authors.forename: David A
authors.initials: DA
authors.lastname: Relman
authors.forename: Stephen R
authors.initials: SR
authors.lastname: Quake
mesh_terms: D000328:Adult; D001419:Bacteria / Q000166:cytology / Q000235:genetics* / Q000302:isolation & purification*; D002874:Chromosome Mapping; D005798:Genes, Bacterial; D006801:Humans; D008297:Male; D044085:Microfluidics; D009055:Mouth / Q000382:microbiology*; D010802:Phylogeny; D012689:Sequence Homology, Nucleic Acid