Lisa Zeigler Allen, PhD

Assistant Professor

Dr. Lisa Zeigler Allen is an Assistant Professor in the Microbial and Environmental Genomics Department. Her research is directed towards understanding microbial and viral interactions through large-scale metagenomic, single cell/virion genomic and cultivation based approaches. She led the experimental design and implementation of the first single virion isolation and genomic characterization and is currently using these techniques to evaluate samples from the natural environment.  Through community level analyses of microbial and virioplankton consortia and culture-based virus/host dynamics, in particular eukaryotic phytoplankton host/virus, she is investigating the influence of viruses on host function, ecosystem performance, community-level diversity and the evolution of hosts.

Prior to becoming an Assistant Professor at JCVI, Lisa received her PhD in Oceanography from Scripps Institution of Oceanography where she studied marine natural products and microbial and viral ecology using genome-enabled approaches. She received her Bachelor of Science degree in Biological Sciences at Washington State University and conducted undergraduate research on plant genetics in the lab of Diter von Wettstein.


Influence of nutrient supply on plankton microbiome biodiversity and distribution in a coastal upwelling region.
Nature communications. 2022-05-04; 13.1: 2448.
PMID: 35508497
Draft Genome Sequence of Desulfurobacterium sp. Strain AV08, a Thermophilic Chemolithoautotroph Isolated from a Deep-Sea Hydrothermal Vent.
Microbiology resource announcements. 2021-08-26; 10.34: e0061521.
PMID: 34435861
Diploid genomic architecture of Nitzschia inconspicua, an elite biomass production diatom.
Scientific reports. 2021-08-02; 11.1: 15592.
PMID: 34341414
Isolation and genome analysis of single virions using 'single virus genomics'.
Journal of visualized experiments : JoVE. 2013-05-26; 75: e3899.
PMID: 23728084
Genome of the pathogen Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform.
Genome research. 2013-05-01; 23.5: 867-77.
PMID: 23564253
Influence of nutrients and currents on the genomic composition of microbes across an upwelling mosaic.
The ISME journal. 2012-07-01; 6.7: 1403-14.
PMID: 22278668
Metagenomic exploration of viruses throughout the Indian Ocean.
PloS one. 2012-01-01; 7.5: e42047.
PMID: 23082107
Identifying low pH active and lactate-utilizing taxa within oral microbiome communities from healthy children using stable isotope probing techniques.
PloS one. 2012-01-01; 7.5: e32219.
PMID: 22403637
Single virus genomics: a new tool for virus discovery.
PloS one. 2011-03-23; 6.3: e17722.
PMID: 21436882
Going deeper: metagenome of a hadopelagic microbial community.
PloS one. 2011-01-01; 6.12: e20388.
PMID: 21629664
Species-specific secondary metabolite production in marine actinomycetes of the genus Salinispora.
Applied and environmental microbiology. 2007-02-01; 73.4: 1146-52.
PMID: 17158611
Collaborator Release

Scientists announce comprehensive regional diagnostic of microbial ocean life using DNA testing

Large-scale ‘metabarcoding’ methods could revolutionize how society understands forces that drive seafood supply, planet’s ability to remove greenhouse gases


Ocean Sampling Day 2018