title: Microfluidic digital PCR enables multigene analysis of individual environmental bacteria.
abstract: Gene inventory and metagenomic techniques have allowed rapid exploration of bacterial diversity and the potential physiologies present within microbial communities. However, it remains nontrivial to discover the identities of environmental bacteria carrying two or more genes of interest. We have used microfluidic digital polymerase chain reaction (PCR) to amplify and analyze multiple, different genes obtained from single bacterial cells harvested from nature. A gene encoding a key enzyme involved in the mutualistic symbiosis occurring between termites and their gut microbiota was used as an experimental hook to discover the previously unknown ribosomal RNA-based species identity of several symbionts. The ability to systematically identify bacteria carrying a particular gene and to link any two or more genes of interest to single species residing in complex ecosystems opens up new opportunities for research on the environment.
authors.affiliation: Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA.
authors.forename: Elizabeth A
authors.initials: EA
authors.lastname: Ottesen
authors.forename: Jong Wook
authors.initials: JW
authors.lastname: Hong
authors.forename: Stephen R
authors.initials: SR
authors.lastname: Quake
authors.forename: Jared R
authors.initials: JR
authors.lastname: Leadbetter
mesh_terms: D000818:Animals; D001419:Bacteria / Q000145:classification / Q000235:genetics*; D004275:DNA, Ribosomal / Q000235:genetics; D004064:Digestive System / Q000382:microbiology; D005456:Fluorescent Dyes; D005574:Formate-Tetrahydrofolate Ligase / Q000235:genetics*; D005798:Genes, Bacterial; D020459:Genes, rRNA; D020049:Isoptera / Q000382:microbiology*; D046210:Microfluidic Analytical Techniques; D044085:Microfluidics; D010802:Phylogeny; D016133:Polymerase Chain Reaction / Q000379:methods*; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D021521:Ribotyping; D013144:Spirochaetales / Q000145:classification / Q000235:genetics / Q000378:metabolism; D013559:Symbiosis; D014208:Treponema / Q000145:classification / Q000235:genetics* / Q000378:metabolism
chemical_list: D004275:DNA, Ribosomal; D005456:Fluorescent Dyes; D012336:RNA, Ribosomal, 16S; D005574:Formate-Tetrahydrofolate Ligase