Sean Jungbluth

Sean Jungbluth

Adjunct Professor of Biology
Environmental Genomics and Systems Biology


I'm broadly interested in exploring the microbial and viral diversity in our universe and especially on our planet through the lens of their genomic blueprints. More recently, I'm intrigued by the role of microorganisms in the environment and the potential for medical, biotechnological, and environmental applications. My interdisciplinary research on the vast unknown microbial diversity is at the intersection of microbial ecology, environmental genomics, biogeochemistry, computational biology, and data science. I leverage my expertise in these fields along with big data and high-performance computing to conduct basic research and, in part, develop open-access software for biologists.

My lab is co-managed by EOS Center faculty member and Adjunct Professor of Biology Dr. Michelle Jungbluth. Based on our mutual interests we are applying a molecular ecology toolkit, including metabarcoding eDNA methods, to aquatic food webs and the roles of plankton in the SF Bay and Delta, and beyond. To explore the ecology of these biological communities, we'll be infusing my knowledge and experience with latest techniques in molecular sequencing, bioinformatics, data science, data visualization, and software development to generate novel workflows for accessing all types of microbial genomes - bacteria, archaea, eukarya, viruses - existing in the natural environment.

I was raised in Wisconsin and earned my B.S. in Bacteriology and Biology at the University of Wisconsin at Madison. After a short post-bachelor experience working in biotechnology as a molecular biologist, I moved to Honolulu and pursued a Ph.D. in Biological Oceanography at the University of Hawaii at Manoa. I completed postdoctoral work at the University of Hawaii at Manoa, the University of Southern California, and the Lawrence Berkeley National Laboratory Joint Genome Institute. During my cumulative experience, I have logged nearly ½ of a year of at-sea research experience, including part-time spent at UNOLS Deep-Submergence Chief Scientist Training.

For a complete list of my publications, please visit Google Scholar.

Recent and Other Selected Publications

  • Chivian, D., Jungbluth, S. P., … & Arkin, A. P. (2023). Metagenome-assembled genome extraction and analysis from microbiomes using KBase. Nature Protocols, 18(1), 208–238.
  • Bowers, R. M., Nayfach, S., Schulz, F., Jungbluth, S. P., … & Woyke, T. (2022). Dissecting the dominant hot spring microbial populations based on community-wide sampling at single-cell genomic resolution. The ISME Journal, 16(5), 1337–1347.
  • Köstlbacher, S., Collingro, A., Halter, T., Schulz, F., Jungbluth, S. P., & Horn, M. (2021). Pangenomics reveals alternative environmental lifestyles among chlamydiae. Nature Communications, 12(1), 4021.
  • Marlow, J. J., Hoer, D., Jungbluth, S. P., … & Girguis, P. R. (2021). Carbonate-hosted microbial communities are prolific and pervasive methane oxidizers at geologically diverse marine methane seep sites. Proceedings of the National Academy of Sciences of the United States of America, 118(25).
  • Nayfach, S., … , Jungbluth, S. P., … & Eloe-Fadrosh, E. A. (2021). A genomic catalog of Earth’s microbiomes. Nature Biotechnology, 39(4), 499–509.
  • Schulz, F., Roux, S., Paez-Espino, D., Jungbluth, S., … & Woyke, T. (2020). Giant virus diversity and host interactions through global metagenomics. Nature, 578(7795), 432–436.
  • Marlow, J. J., Colocci, I., Jungbluth, S. P., Weber, N. M., Gartman, A., & Kallmeyer, J. (2020). Mapping metabolic activity at single cell resolution in intact volcanic fumarole sediment. FEMS Microbiology Letters, 367(1).
  • Jungbluth, S. P.*, Boyd, J. A.*, … & Tyson, G. W. (2019). Divergent methyl-coenzyme M reductase genes in a deep-subseafloor Archaeoglobi. The ISME Journal, 13(5), 1269–1279. (* co-first authors)
  • Carr, S. A., Jungbluth, S. P., … & Orcutt, B. N. (2019). Carboxydotrophy potential of uncultivated Hydrothermarchaeota from the subseafloor crustal biosphere. The ISME Journal, 13(6), 1457–1468.
  • Teehera, K. B., Jungbluth, S. P., … & Schorghofer, N. (2018). Cryogenic Minerals in Hawaiian Lava Tubes: A Geochemical and Microbiological Exploration. Geomicrobiology Journal, 35(3), 227–241.
  • McVeigh, D., Skarke, A., Dekas, A. E., Borrelli, C., Hong, W.-L., Marlow, J. J., Pasulka, A., Jungbluth, S. P., Barco, R. A., & Djurhuus, A. (2018). Characterization of benthic biogeochemistry and ecology at three methane seep sites on the Northern US Atlantic margin. Deep-Sea Research. Part II, Topical Studies in Oceanography, 150, 41–56.
  • Nigro, O. D., Jungbluth, S. P., Lin, H.-T., Hsieh, C.-C., Miranda, J. A., Schvarcz, C. R., Rappé, M. S., & Steward, G. F. (2017). Viruses in the Oceanic Basement. mBio, 8(2).
  • Marlow, J., Borrelli, C., Jungbluth, S. P., Hoffman, C., Marlow, J., Girguis, P. R., & AT-36 Team. (2017). Opinion: Telepresence is a potentially transformative tool for field science. Proceedings of the National Academy of Sciences of the United States of America, 114(19), 4841–4844.
  • Momper, L., Jungbluth, S. P., Lee, M. D., & Amend, J. P. (2017). Energy and carbon metabolisms in a deep terrestrial subsurface fluid microbial community. The ISME Journal, 11(10), 2319–2333.
  • Jungbluth, S. P., Amend, J. P., & Rappé, M. S. (2017). Metagenome sequencing and 98 microbial genomes from Juan de Fuca Ridge flank subsurface fluids. Scientific Data, 4, 170037.
  • Jungbluth, S. P., Glavina Del Rio, T., Tringe, S. G., Stepanauskas, R., & Rappé, M. S. (2017). Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems. PeerJ, 5, e3134.
  • Jungbluth, S. P., Bowers, R. M., Lin, H.-T., Cowen, J. P., & Rappé, M. S. (2016). Novel microbial assemblages inhabiting crustal fluids within mid-ocean ridge flank subsurface basalt. The ISME Journal, 10(8), 2033–2047.
  • Robador, A., Jungbluth, S. P., LaRowe, D. E., Bowers, R. M., Rappé, M. S., Amend, J. P., & Cowen, J. P. (2014). Activity and phylogenetic diversity of sulfate-reducing microorganisms in low-temperature subsurface fluids within the upper oceanic crust. Frontiers in Microbiology, 5, 748.
  • Jungbluth, S. P., Lin, H.-T., Cowen, J. P., Glazer, B. T., & Rappé, M. S. (2014). Phylogenetic diversity of microorganisms in subseafloor crustal fluids from Holes 1025C and 1026B along the Juan de Fuca Ridge flank. Frontiers in Microbiology, 5, 119.
  • Jungbluth, S. P., Grote, J., Lin, H.-T., Cowen, J. P., & Rappé, M. S. (2013). Microbial diversity within basement fluids of the sediment-buried Juan de Fuca Ridge flank. The ISME Journal, 7(1), 161–172.