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Probing individual environmental bacteria for viruses by using microfluidic digital PCR.

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.

Pubmed ID: 21719670


  • Tadmor AD
  • Ottesen EA
  • Leadbetter JR
  • Phillips R


Science (New York, N.Y.)

Publication Data

July 1, 2011

Associated Grants

  • Agency: NIH HHS, Id: DP1 OD000217
  • Agency: NIH HHS, Id: DP1 OD000217-05
  • Agency: NIGMS NIH HHS, Id: R01 GM085286
  • Agency: NIGMS NIH HHS, Id: R01 GM085286-01S
  • Agency: NIGMS NIH HHS, Id: R01 GM098465

Mesh Terms

  • Alleles
  • Amino Acid Sequence
  • Animals
  • Bacteriophages
  • Ecosystem
  • Endodeoxyribonucleases
  • Genes, Viral
  • Genes, rRNA
  • Genetic Variation
  • Intestines
  • Isoptera
  • Microbial Interactions
  • Microfluidic Analytical Techniques
  • Molecular Sequence Data
  • Phylogeny
  • Polymerase Chain Reaction
  • Prophages
  • Sequence Alignment
  • Treponema