Targeting Microbial Needles in a Community Haystack

The Science

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.

The Impact

  • 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.


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.


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