title: Probing individual environmental bacteria for viruses by using microfluidic digital PCR.
abstract: Viruses may very well be the most abundant biological entities on the planet. Yet neither metagenomic studies nor classical phage isolation techniques have shed much light on the identity of the hosts of most viruses. We used a microfluidic digital polymerase chain reaction (PCR) approach to physically link single bacterial cells harvested from a natural environment with a viral marker gene. When we implemented this technique on the microbial community residing in the termite hindgut, we found genus-wide infection patterns displaying remarkable intragenus selectivity. Viral marker allelic diversity revealed restricted mixing of alleles between hosts, indicating limited lateral gene transfer of these alleles despite host proximity. Our approach does not require culturing hosts or viruses and provides a method for examining virus-bacterium interactions in many environments.
authors: Department of Biochemistry and Molecular Biophysics, California Institute of Technology, Pasadena, CA 91125, USA. arbel@caltech.edu
authors: Arbel D
authors: AD
authors: Tadmor
authors: Elizabeth A
authors: EA
authors: Ottesen
authors: Jared R
authors: JR
authors: Leadbetter
authors: Rob
authors: R
authors: Phillips
mesh_terms: D000483:Alleles; D000595:Amino Acid Sequence; D000818:Animals; D001435:Bacteriophages / Q000145:classification / Q000235:genetics / Q000502:physiology*; D017753:Ecosystem; D004706:Endodeoxyribonucleases / Q000235:genetics; D005814:Genes, Viral; D020459:Genes, rRNA; D014644:Genetic Variation; D007422:Intestines / Q000382:microbiology; D020049:Isoptera / Q000382:microbiology*; D056265:Microbial Interactions; D046210:Microfluidic Analytical Techniques; D008969:Molecular Sequence Data; D010802:Phylogeny; D016133:Polymerase Chain Reaction / Q000379:methods*; D039002:Prophages / Q000235:genetics; D016415:Sequence Alignment; D014208:Treponema / Q000145:classification / Q000235:genetics / Q000821:virology*
chemical_list: D004706:Endodeoxyribonucleases; C030894:terminase