Brett Baker
- Associate Professor
- Co-director, Center for Planetary Science and Habitability
- Marine Science
- Integrative Biology
- Interdisciplinary Life Sciences Graduate Programs
Contact Information
Biography
Brett Baker is an associate professor of integrative biology and marine science at The University of Texas at Austin. He joined UT Austin’s Marine Science Institute as a senior research fellow in 2014, became an assistant professor in 2015, and was promoted to associate professor in 2021. Baker earned a Ph.D. in Earth and Environmental Sciences from the University of Michigan in 2014, following eight years as a research associate in Earth and Planetary Sciences at the University of California, Berkeley. He received both his B.S. and M.S. in biological sciences from the University of Wisconsin-Milwaukee.
Research
Brett Baker studies microorganisms, including bacteria, archaea and viruses, which are key mediators of nearly all the planet’s elemental cycles. His research addresses a fundamental gap in biology: many branches of the tree of life remain undiscovered or have only been identified through single-gene sequencing surveys. By filling genomic gaps in the tree of life, Baker seeks to better understand the evolution of life on Earth and how microbial communities drive biogeochemical cycles.
Recent advances in DNA sequencing technologies and computational analyses have made it possible to reconstruct the genomes and transcriptomes of uncultured natural populations. The Baker Lab has been involved in the development and implementation of environmental omics approaches since their inception, including some of the earliest metaproteomic studies of microbial communities. Using these techniques, his team has tracked fine-scale evolutionary processes and discovered deeply branching, previously unknown groups of microbes.
The Baker Lab has reconstructed the genomes of hundreds of widespread, uncultured sediment microbes to understand how ecological roles are partitioned within microbial communities. Many of these genomes belong to phyla with no previous genomic representation, including several lineages closely related to eukaryotes. These discoveries have provided important insights into the origins and evolution of complex life.
Research Areas
- Molecular Biology or Genetics
- Biodiversity, Ecology or Sustainability
- Oceans and Freshwater
Fields of Interest
- Microbial Processes
- Nutrient Cycling
- Biodiversity
- Marine Population Dynamics
- Marine Ecosystem Dynamics
- Marine Chemistry
- Cell & Molecular Biology
- Microbiology
- Bioinformatics & Computational Biology
- Biomolecular Structure & Function
- Comparative Biology and Phylogenetics
- Microbial Ecology, Microbiomes and Disease
- Computational Biology
- Genomics, Genetics and Development
Education
- Ph.D., Earth and Environmental Sciences, University of Michigan, 2014
- MS, Department of Biological Sciences, University of Wisconsin-Milwaukee, 2000
- B.S., Biological Sciences, University of Wisconsin-Milwaukee, 1997
Publications
- Key Publications (google scholar)
- Appler KE, Lingford JP, Gong X, Panagiotou K, Leao P, Langwig M, Greening C, Ettema TJG, Anda V, Baker BJ. (2026) Oxygen metabolism in descendants of the archaeal-eukaryotic ancestor. Nature https://doi.org/10.1038/s41586-026-10
- Koestlbacher S, van Hooff JJE, Panagiotou K, Tamarit D, Anda V, Appler KE, Baker BJ, Ettema TJG. (2026) Prediction of eukaryotic cellular complexity in Asgard archaea using structural modelling. Nature Microbiology https://doi.org/10.1038/s41564-026-02273-y
- Acosta DJ, Daryl R. Barth, Bondy J, Appler KE, Anda V, Ngo PHT, Alper HS, Baker BJ, Edward M. Marcotte, Ellington AD (2025) Plastic degradation by enzymes from uncultured deep sea microorganisms. ISME J. 19, wraf068. https://doi.org/10.1093/ismejo/wraf068
Rohwer RR, Kirkpatrick M, Sarcia SL, Kellom M, McMahon KD, Baker BJ. (2025) Two decades of bacterial ecology and evolution in a freshwater lake. Nature Microbiology 10, 246-257. https://doi.org/10.1038/s41564-024-01888-3
Zhou Z, Tran PQ, Martin C, Rohwer RR, Baker BJ, McMahon KD, Anantharaman K. (2025) Unravelling viral ecology and evolution over 20 years in a freshwater lake. Nature Microbiology 10, 231-245. https://doi.org/10.1038/s41564-024-01876-7
Eme L, Tamarit, D, Caceres EF, Stairs CW, Anda VD, Schon ME, Seitz KW, Dombrowski N, Lewis WH, Homa F, Saw JH, Lombard J, Nunoura T, Li W-J, Hua Z-S, Chen L-X, Banfield JF, St John E, Reysenbach A-L, Stott MB, Schramm A, Kjeldsen KU, Teske AP, Baker BJ, Ettema TJG. (2023) Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes. Nature. 618, 992-999.
Baker BJ, Hyde E, Leao P. Nature should be the model for microbial sciences (2024) J. Bacteriology 0:e00228-2410.1128/jb.00228-24
Valentin-Alvarado LE, Appler KE, Anda VD, Schoelmerich MC, West-Roberts J, Kivenson V, Crists-Christoph A, Ly L, Sachdeva R, Savage DF, Baker BJ, Banfield JF. (2024) Asgard archaea modulate potential methanogenesis substrates in wetland soil. Nature Communications 15, 6384. 10.1038/s41467-024-49872-z
Leão P, Little ME, Appler KE, Sahaya D, Aguilar-Pine E, Currie K, Finkelstein I, Anda VD, Baker BJ. (2024) Extensive defense systems in Asgard archaea and their role in the origin of eukaryotic immunity. Nature Communications 15, 6386. https://doi.org/10.1038/s41467-024-50195-2
Gong X, Rodrigquez A, Xu L, Langwig M, Su L, Sun L, Sun M, Huerta-Cepas, Anda VD, Baker BJ. (2022) New globally distributed bacteria phyla with the FCB superphylum. Nature Communications 13, 7516. 10.1016/j.cbpa.2023.111368
Rambo I, Anda VD, Langwig M, Baker BJ. (2022) Genomes of six viruses that infect Asgard archaea from deep-sea sediments. Nature Microbiology 7, 953-961. 10.1038/s41564-022-01150-8
Langwig M, De Anda V, Dombrowski N, Seitz KW, Rambo I, Teske AP, Baker BJ. (2022) Large scale protein level comparison of Deltaproteobacteria reveals cohesive metabolic groups. ISME J. 16, 307-320. 10.1038/s41396-021-01057-y
Baker BJ, Appler KE, Gong X. (2021) New microbial biodiversity in marine sediments. Annual Reviews in Marine Science 13, 161-175. 10.1146/annurev-marine-032020-014552
Anda VD, Chen L-X, Dombrowski N, Hua Z-S, Jiang H-C, Banfield JF, Li W-J, Baker, BJ. (2021) Brockarchaeota, a new archaeal phylum with unique and versatile pathways for carbon cycling. Nature Communications 12, 2404. 10.1038/s41467-021-22736-6
Baker BJ, Anda VD, Seitz KW, Dombrowski N, Santoro A, Lloyd KA. (2020) Diversity, ecology, and evolution of Archaea. Nature Microbiology 5, 887-900. 10.1038/s41564-020-0741-x
Seitz KW, Dombrowski N, Eme L, Spang A, Lombard J, Seiber J, Teske AP, Ettema TJG, Baker BJ. (2019) Asgard archaea capable of anaerobic hydrocarbon cycling. Nature Communications 10, 1822. 10.1038/s41467-019-09364-x
Dombrowski N, Teske AP, Baker BJ. (2018) Expansive microbial metabolic versatility and biodiversity in dynamic Guaymas Basin hydrothermal sediments. Nature Communications 9, 4999. 10.1038/s41467-018-07418-0
Hug L, Baker BJ, Anantharaman K, Brown CT, Probst AJ, Castelle C, Butterfield CN, Hernsdorf AW, Amano Y, Suzuki Y, Dudek N, Relman DA, Thomas BC, Banfield JF (2016) A new view of the tree of life. Nature Microbiology 1, 16048. 10.1038/nmicrobiol.2016.48
Seitz KW, Lazar CS, Hinrichs K-U, Teske A, Baker BJ. (2016) Genomic reconstruction of a novel, deeply-branched sediment archaeal phylum with pathways for acetogenesis and sulfur reduction. ISME J. 10, 1696-1705. 10.1038/ismej.2015.233
Baker BJ, Comolli LR, Dick GJ, Hauser L., Land M, Hyatt, D, VerBerkmoes N, Hettich B, Banfield JF. (2010) Enigmatic, ultra-small uncultivated Archaea. Proc. Natl. Acad. Sci. 107, 8806-8811. 10.1073/pnas.0914470107
Baker BJ, Tyson, GW, Webb RI, Flanagan J, Hugenholtz P, Banfield JF (2006) Lineages of acidophilic Archaea revealed by community genomic analysis. Science 314, 1933-1935. 10.1126/science.1132690
Awards
- Elected to the American Academy of Microbiology - 2024
- Sloan Foundation Fellowship in Ocean Sciences, 2016
- Simons Early Career Microbial Ecology and Evolution, 2020
- University of Texas College of Natural Science visualizing Science Contest 2015 – 1st place