Targeting Microbial Needles in a Community Haystack

A workflow for capturing the genetic make-up of specific uncultivated microbes from complex environmental samples.

The Science

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.

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.


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.

Principal Investigator

Bernhard M. Fuchs
Max Planck Institute for Marine Microbiology

Co-Principal Investigator

Anissa Grieb
Max Planck Institute for Marine Microbiology

BER Program Manager

Ramana Madupu

U.S. Department of Energy, Biological and Environmental Research (SC-33)
Biological Systems Science Division
[email protected]


The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported under Contract No. DE-AC02-05CH11231. This study was funded by the Max Planck Society.


Grieb, A., R. M. Bowers, M. Oggerin, D. Goudeau, J. Lee, R. R. Malmstrom, T. Woyke, and B. M. Fuchs. 2020. “A Pipeline for Targeted Metagenomics of Environmental Bacteria,” Microbiome 8(1), 21. [DOI:10.1186/s40168-020-0790-7]