Research

Michael D. Lee, Ph.D.

Principal investigator in bioinformatics exploring microbial ecology

Email: MikeLee@bmsis.org
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AstrobioMike
AstrobioMike

Primary affiliations
National Biodefense Analysis and Countermeasures Center
Blue Marble Space Institute of Science
NASA Ames Research Center (2018-2024)
University of Southern California (2013-2018)

Current positions
NBACC Principal Investigator
BMSIS Research Scientist

Education

Research summary
I’m a microbial ecologist and bioinformatician who has been lucky enough to spend my science-life exploring microbial ecology and evolution in all kinds of different environments ranging from the bottoms of our oceans up to the International Space Station 👽

During my PhD at USC, I worked in various environments including: the deep biosphere, 3 km down at the bottom of the Pacific Ocean; the surface ocean focusing on the co-evolution between Trichodesmium and its perpetually associated microbial consortia; and more work with the surface ocean with interest in the global distribution and evolutionary aspects of Synechococcus. Following my PhD, I was at the NASA Ames Research Center from 2018-2024, initially as a post doc working on Space Biology, then as a contractor focusing on Astrobiology, and then I joined NASA GeneLab full-time for a few years.

My current role is as a principal investigator in bioinformatics at the National Biodefense Analysis and Countermeasures Center (NBACC) at Fort Detrick in Maryland.

Publication groupings:


Software

GToTree

Bioinformatics Tools (bit)



Publications

Space Biology

Gonzalez, E., Lee, M.D., Tierney, B.T., Lipieta, N., Mishra, M., Beckett, L., and Brereton, N.J. (2024). Spaceflight alters host-gut microbiota interactions. npj Biofilms and Microbiomes.
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Nguyen, H.N., Sharp, G.M., Stahl-Rommel, S., Justiniano, Y-A.V., Castro, C.L., Nelman-Gonzalez, M.N., et al. (2023). Microbial isolation and characterization from two flex lines from the urine processor assembly onboard the International Space Station. Biofilm.
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Lee, M.D., O’Rourke, A., Lorenzi, H., Bebout, B.M., Dupont, C.L., and Everroad, R.C. (2021). Reference-guided metagenomics reveals genome-level evidence of potential microbial transmission from the ISS environment to an astronaut’s microbiome. iScience.
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O’Rourke, A. and Lee, M.D., Nierman, W.C., Everroad, R.C., and Dupont, C.L. (2020). Genomic and phenotypic characterization of Burkholderia isolates from the potable water system of the International Space Station. PLoS ONE.
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Astrobiology

Zajkowski, T., Lee, M.D., Sharma, S., Vallota-Eastman, A., Kuska, M., Malczewska, M., and Rothschild, L.J. (2023). Conserved functions of prion candidates suggest a primeval role of protein self-templating. Proteins: Structure, Function, Bioinformatics.
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Zajkowski, T., Lee, M.D., Mondal, S.S., Carbajal, A., Dec, R., Brennock, P.D., Piast, R.W., Snyder, J.E., Bense, N.B., Dzwolak, W., Jarosz, D.F., and Rothschild, L.J. (2021). The hunt for ancient prions: Archaeal prion-like domains form amyloid-based epigenetic elements. Molecular Biology and Evolution.
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Seyler, L., Kujawinski, E.B., Azua-Bustos, A., Lee, M.D., Marlow, J., Perl, S.M., and Cleaves II, H.J (2020). Metabolomics As an Emerging Tool in the Search for Astrobiologically Relevant Biomarkers. Astrobiology.
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O’Rourke, A.O., Zoumplis, A., Wilburn, P., Lee, M.D., Lee, Z., Vecina, M., and Mercader, K. (2020). Following the Astrobiology roadmap: origins, habitability, and future exploration. Book chapter in Astrobiology: current, evolving, and emerging perspectives by Caister Academic Press.
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Momper, L.M., Jungbluth, S.P., Lee, M.D., and Amend, J.P. (2017). Energy and carbon metabolisms in a deep terrestrial subsurface fluid microbial community. ISMEJ.
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Lee, M.D., Walworth, N.G., Sylvan, J.B., Edwards, K.J., and Orcutt, B.N. (2015). Microbial communities on seafloor basalts at Dorado Outcrop reflect level of alteration and highlight global lithic clades. Frontiers in Microbiology.
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Marine Microbes

Kling, J.D., Lee, M.D., Walworth, N.G., Webb, E.A., Coelho, J.T., Wilburn, P., Anderson, S.I., Zhou, Q., Wang, C., Phan, M.D., Fu, F-X., Kremer, C.T., Litchman, E., Rynearson, T.A., and Hutchins, D.A. (2023). Dual thermal ecotypes coexist within a nearly genetically identical population of the unicellular marine cyanobacterium Synechococcus. PNAS.
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Webb, E.A., Held, N.A., Zhao, Y., Graham, E.D., Conover, A.E., Semones, J., Lee, M.D., Feng, Y., Fu, F-X., Saito, M.A., and Hutchins, D.A. (2023). Importance of mobile genetic element immunity in numerically abundant Trichodesmium clades. ISME Comunications.
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Walworth, N.G., Saito, M.A., Lee, M.D., McIlvin, M.R., Moran, D.M., Kellogg, R.M., Fu, F-X., Hutchins, D.A., and Webb, E.A. (2022). Why environmental biomarkers work: transcriptome–proteome correlations and modeling of multistressor experiments in the marine bacterium Trichodesmium. Journal of Proteome Research.
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Qu, P., Fu, F-X., Wang, X-W., Kling, J.D., Elghazzawy, M., Huh, M., Zhou, Q-Q., Want, C., Wing Kwan Mak, E., Lee, M.D., Yang, N., and Hutchins, D. (2022). Two co-dominant nitrogen-fixing cyanobacteria demonstrate distinct acclimation and adaptation responses to cope with ocean warming. Environmental Microbiology Reports.
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Maza-Márquez, P., Lee, M.D., Detweiler, A.M., and Bebout, B.M. (2022). Millimeter-scale vertical partitioning of nitrogen cycling in hypersaline mats reveals prominence of genes encoding multi-heme and prismane proteins. ISMEJ.
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McParland, E.L., Lee, M.D., Webb, E.A., Alexander, H., and Levine, N.M. (2021). DMSP synthesis genes distinguish two types of DMSP producer phenotypes. Environmental Microbiology.
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Maza-Márquez, P., Lee, M.D., and Bebout, B.M. (2021). The Abundance and Diversity of Fungi in a Hypersaline Microbial Mat from Guerrero Negro, Baja California, México. Journal of Fungi.
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Walworth, N.G., Lee, M.D., Dolzhenko, E., Fu, F-X., Smith, A.D., Webb, E.A., and Hutchins, D.A. (2020). Long-Term m5C Methylome Dynamics Parallel Phenotypic Adaptation in the Cyanobacterium Trichodesmium. Molecular Biology and Evolution.
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Lee, M.D., Ahlgren, N.A., Kling, J. D., Walworth, N.G., Rocap, G., Saito, M.A., Hutchins, D.A., and Webb, E.A. (2019). Marine Synechococcus isolates representing globally abundant genomic lineages demonstrate a unique evolutionary path of genome reduction without a decrease in GC content. Environmental Microbiology.
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Ahlgren, N.A., Belisle, B.S., and Lee, M.D. (2019). Genomic mosaicism underlies the adaptation of marine Synechococcus ecotypes to distinct oceanic iron niches. Environmental Microbiology.
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Kling, J.D., Lee, M.D., Fu, F-X., Phan, M.D., Wang, X., Qu, P., and Hutchins, D.A. (2019). Transient exposure to unusually high temperatures reshapes coastal phytoplankton communities. ISME.
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Lee, M.D., Kling, J.D., Araya, R., and Ceh, J. (2018). Jellyfish life stages shape associated microbial communities, while a core microbiome is maintained across all. Frontiers in Microbiology.
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Lee, M.D., Walworth, N.G., McParland, E.L., Fu, F.-X., Mincer, T.J., Levine, N.M., Hutchins, D.A., and Webb, E.A. (2017). The Trichodesmium consortium: conserved heterotrophic co-occurrence and genomic signatures of potential interactions. ISMEJ.
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Lee, M.D., Webb, E.A., Walworth, N.G., Fu, F.-X., Held, N.A., Saito, M.A., and Hutchins, D.A. (2017). Transcriptional activities of the microbial consortium living with the marine nitrogen-fixing cyanobacterium Trichodesmium reveal potential roles in community-level nitrogen cycling. Applied and Environmental Microbiology.
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Walworth, N.G. and Lee, M.D., Suffridge, C., Qu, P., Fu, F-X., Saito, M.A., Webb, E.A., Sañudo-Wilhelmy, S.A., and Hutchins, D.A (2017). Functional genomics and phylogenetic evidence suggest genus-wide cobalamin production by the globally distributed marine nitrogen fixer Trichodesmium. Frontiers in Microbiology.
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Walworth, N.G., Fu., F-X., Lee, M.D., Cai, X., Saito, M.A., Webb, E.A., and Hutchins, D.A (2017). Nutrient co-limited Trichodesmium as nitrogen source or sink in a future ocean. Applied and Environmental Microbiology.
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Hutchins, D.A., Fu, F.-X., Walworth, N.G., Lee, M.D., Saito, M.A., and Webb, E.A. (2017). Comment on “The complex effects of ocean acidification on the prominent N2-fixing cyanobacterium Trichodesmium”. Science.
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Walworth, N.G., Hutchins, D.A., Dolzhenko, E., Lee, M.D., Fu., F-X., Smith, A.D., and Webb, E.A. (2017). Biogeographic conservation of the cytosine epigenome in the globally important marine, nitrogen-fixing cyanobacterium Trichodesmium. Environmental Microbiology.
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Ramirez, G.A., Hoffman, C.L., Lee, M.D., Lesniewski, R.A., Barco, R., Garber, A., Toner, B.M., Wheat, C.G., Edwards, K.J., Orcutt, B.N. (2016). Assessing marine microbial induced corrosion monitored in Santa Catalina Island, California. Frontiers in Microbiology.
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Walworth, N.G., Lee, M.D., Fu, F.-X., Hutchins, D.A., and Webb, E.A. (2016). Molecular and physiological evidence of genetic assimilation to high CO2 in the marine nitrogen fixer Trichodesmium. PNAS.
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Walworth, N.G., Fu, F.-X., Webb, E.A., Saito, M.A., Moran, D., McIlvin, M.R., Lee, M.D., and Hutchins, D.A. (2016). Mechanisms of increased Trichodesmium fitness under iron and phosphorus co-limitation in the present and future ocean. Nature Communications.
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Software, platforms, workflows, and education

Teichman, S., Lee, M.D., and Willis, A.D. (2023). Analyzing microbial evolution through gene and genome phylogenies. Biostatistics.
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Lee, M.D. (2022). bit: a multipurpose collection of bioinformatics tools. F1000Research.
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Software | Documentation

Tully, B.J., Buongiorno, J., Cohen, A.B., Cram, J.A., Garber, A.I., Hu, S.K., et al. (2021). The Bioinformatics Virtual Coordination Network: An Open-Source and Interactive Learning Environment. Frontiers in Education.
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Overbey, E.G., Saravia-Butler, A.M., Zhang, Z., Rathi, K.S., Fogle, H., da Silveira, W.A., et al. (2021). NASA GeneLab RNA-seq consensus pipeline: Standardized processing of short-read RNA-seq data. iScience.
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Eren, A.M., Kiefl, E., Shaiber, A., Veseli, E., Miller, S.E., Schechter, M.S., et al. (2020). Community-led, integrated, reproducible multi-omics with anvi’o. Nature Microbiology.
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Lee, M.D. (2019). GToTree: a user-friendly workflow for phylogenomics. Bioinformatics.
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Software | Documentation

Lee, M.D. (2019). Applications and considerations of GToTree: a user-friendly workflow for phylogenomics. Evolutionary Bioinformatics.
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Lee, M.D. (2019). Happy Belly Bioinformatics: an open-source resource dedicated to helping biologists utilize bioinformatics. The Journal of Open-Source Education.
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CoVID-19

Jochum, M., Lee, M.D., Curry, K., Zaksas, V., Vitalis, E., Treangen, T., Aagaard, K., and Ternus, K. (2022). Analysis of bronchoalveolar lavage fluid metatranscriptomes among patients with COVID-19 disease. Scientific Reports.
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Sapoval, N., Mahmoud, M., Jochum, M., Liu, Y., Elworth, R.A.L., Wang, Q., Albin, D., Ogilvie, H., Lee, M.D., Villapol, S., Hernandez, K., Berry, I.M., Foox, J., Beheshti, A., Ternus, K., Aagaard, K., Posada, D., Mason, C., Sedlazeck, F.J., and Trangen, T.J. (2021). Hidden genomic diversity of SARS-CoV-2: implications for qRT- PCR diagnostics and transmission. Genome Research.
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Aquaponics

Day, J.A.,Diener, C., Otwell, A.E., Tams, K.E., Bebout, B.M., Detweiler, A.M., Lee, M.D., Scott, M.T., Ta, W., Ha, M., Carreon, S.A., Tong, K., Ali, A.A., Gibbons, S.M., and Baliga, N.S. (2021). Lettuce (Lactuca sativa) productivity influenced by microbial inocula under nitrogen-limited conditions in aquaponics. PLOS ONE.
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Genome Announcements

Becket, E. et al. (2020). Draft Genome Sequences of Bacillus glennii V44-8, Bacillus saganii V47-23a, Bacillus sp. Strain V59.32b, Bacillus sp. Strain MER_TA_151, and Paenibacillus sp. Strain MER_111, Isolated from Cleanrooms Where the Viking and Mars Exploration Rover Spacecraft Were Assembled. Microbiology Resource Announcements.
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Sharma, I. and Lee, M.D. (2019). Draft Genome Sequence of Cyclobacterium marinum Strain Atlantic-IS, Isolated from the Atlantic Slope off the Coast of Virginia, USA. Microbiology Resource Announcements.
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