Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth.
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.
Marcy
Yann
Y
Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
Ouverney
Cleber
C
Bik
Elisabeth M
EM
Lösekann
Tina
T
Ivanova
Natalia
N
Martin
Hector Garcia
HG
Szeto
Ernest
E
Platt
Darren
D
Hugenholtz
Philip
P
Relman
David A
DA
Quake
Stephen R
SR
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