U.S. Department of Energy Office of Biological and Environmental Research

BER Research Highlights

Sequencing FISH-Separated Microbes from Environmental Samples
Published: July 05, 2010
Posted: July 28, 2010

Most microbes found in environmental samples cannot be cultured in the laboratory making them very hard (or impossible) to study in detail and limiting their exploitation for DOE mission needs in energy, environmental remediation, and carbon cycling. One approach to overcoming this obstacle is to separate individual microbial cells from complex environmental samples using Fluorescence in situ Hybridization (FISH) and to study those with desired characteristics. The standard FISH protocol involved “fixing” cells with paraformaldehyde which complicated subsequent DNA sequencing. Researchers at DOE’s Joint Genome Institute have developed a new protocol that avoids the fixation step. Susan Yilmaz and her colleagues successfully used a variety of fluorescence probes to study freshly-collected, unfixed microbial samples from bioreactor sludge and the termite hind gut. These promising results constitute a significant technical advance for gaining access to otherwise hard to study microbes. The authors conclude: “This approach should facilitate subsequent genomic sequencing and analysis of targeted populations as DNA is not compromised by crosslinking during fixation”.

Reference: Yilmaz et al, The ISME Journal (27 May 2010)doi:10.1038/ismej.2010.73

Contact: Dan Drell, SC-23.2, (301) 903-4742
Topic Areas:

  • Research Area: Genomic Analysis and Systems Biology
  • Research Area: Microbes and Communities
  • Research Area: Sustainable Biofuels and Bioproducts
  • Research Area: DOE Joint Genome Institute (JGI)
  • Research Area: Research Technologies and Methodologies

Division: SC-23.2 Biological Systems Science Division, BER


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