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BER Research Highlights

Targeting Microbial Needles in a Community Haystack
Published: February 15, 2020
Posted: August 06, 2021


Enabled by JGI’s Emerging Technologies Opportunity Program, researchers at the Max Planck Institute (MPI) for Marine Microbiology developed, tested, and deployed a pipeline to first target cells from communities of uncultivated microbes, and then efficiently retrieve and characterize their genomes.


Specific bacterial cells are tagged with multiple fluorescent signals, collected through fluorescence activated cell sorting (FACS) and then enriched. These enriched populations are then sequenced and analyzed.


  • Targeted pipeline tested on North Sea metagenomes as a proof of principle in selectively enriching low abundance microbial groups from complex natural communities.
  • Used a Vis6-specific probe to target bacteria linked to marine diatom blooms. Bacteria which accounted for <1% of the sequences from bulk metagenome reads were amplified to >50% of the target.
  • Approach could be applied toward gathering more complete view of a population’s genetic makeup and identifying viruses interacting with these populations.

Grieb, A. et al. “A pipeline for targeted metagenomics of environmental bacteria.” Microbiome 8(1), 21 (2020). [DOI:10.1186/s40168-020-0790-7]

Topic Areas:

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

Division: SC-33.2 Biological Systems Science Division, BER


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