Brett Baker
- Associate Professor
- co-director of the Center for Planetary Science and Habitability
- Marine Science
- Integrative Biology
- Interdisciplinary Life Sciences Graduate Programs
Contact Information
Biography
2021-present: Associate Professor, Integrative Biology and Marine Science, Univ. of Texas Austin
2015-2021: Assistant Professor, Marine Science, Univ. of Texas Austin, Marine Science Institute
2014-2015: Senior Research Fellow, Marine Science, Univ. of Texas Austin, Marine Science Institute
2010-2014: Ph.D., Dept. of Earth and Environmental Sciences, Univ. of Michigan, Ann Arbor, MI
2002-2010: Research Associate IV, Earth and Planetary Sciences, Univ. of California Berkeley
1997-2000: M.S. Student, Dept. Biological Sciences, Univ. of Wisconsin Milwaukee, WI
1997: B.S., Dept. of Biological Sciences, Univ. of Wisconsin-Milwaukee, WI
Research
Microorganisms (Bacteria, Archaea, and viruses) are key mediators in nearly all of the planet’s elemental cycles. However, our understanding of the ecological roles of many groups of microbes has been hampered by low-resolution analytical approaches to studying the staggering diversity present in nature. As a result the tree of life is full of branches, which remain undiscovered, and those, which have only been identified in single-gene sequencing surveys. This is a fundamental gap in our understanding of biology. Filling in the genomic gaps in the tree of life will provide a rich context to understand the evolution of life on the planet and will provide us with a genetic understanding of 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 since the beginning. I was involved in the first metaproteomic study of a microbial community and have been using these approaches to track fine-scale evolutionary processes. Using these techniques we have discovered deeply branching, novel groups of microbes.
The Baker laboratory has reconstructed the genomes of hundreds of widespread, uncultured sediment microbes to understand how ecological roles are partitioned in these microbial communities. Many of the genomes belong to phyla which have no previous genomic representation. Several of these branches belong to microbes that are closely related to eukaryotes. These genomes have provided rich insights into the origin of eukaryotes.
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)
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