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. 

Recent Publications (google scholar) 

Castelle CJ, Meheust R, Jaffe AL, Seitz KW, Gong X, Baker BJ, Banfield JF. (2021) Protein family content uncovers lineage relationships and bacterial pathway maintenance mechanisms in DPANN archaea. Frontiers in Micro. 12, 660052.

Langwig M, De Anda V, Dombrowski N, Seitz KW, Rambo I, Teske AP, Baker BJ. (2021) Large scale protein level comparison of Deltaproteobacteria reveals cohesive metabolic groups. ISME J. In press.

Baker BJ, Appler KE, Gong X. (2021) New microbial biodiversity in marine sediments. Ann Rev Mar Sci. 13, 161-175.

De Anda, 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 Comm. 12, 2404.

Murray AE, et al. (2020) Roadmap for naming uncultivated Archaea and Bacteria. Nature Microbiol. 5, 987-997.

Baker BJ, de Anda V, Seitz KW, Dombrowski N, Santoro A, Lloyd KA. (2020) Diversity, ecology, and evolution of Archaea. Nature Micro. 5, 887-900.

Rambo I, Dombrowski N, Constant, L, Erdner DL, Baker BJ. (2020) Metabolic reconstruction elucidates symbiotic relationships between bacteria and ciguatoxin-producing microalgae. Environ. Microbiol. 22, 1764-1783.

Mullis MM, Rambo IM, Baker BJ, Reese BK. (2019) Diversity, ecology, and prevalence of antimicrobials in nature. Front. Microbiol. 10, 2518.

Huang J-M, Baker BJ, Li J-T, Wang Y. (2019) New microbial lineages capable of carbon fixation and nutrient cycling in deep-sea sediments. Appl. Environ. Microbiol. 85, e00523-19.

Steen AD, Kevorkian RT, Bird JT, Dombrowski N, Baker BJ, Hagen SM, Mulligan KH, Schmidt JM, Webber AT, Alperin MJ. (2019) Kinetics and identities of extracellular peptidases in subsurface sediments of the White Oak River Estuary, NC. Appl. Environ. Microbiol. 85, e00102-19.

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 Comm. 10, 1822.

Spang A, Stairs C, Dombrowski N, Eme L, Lombard J, Caceres EF, Greening C, Baker BJ, Ettema TJG. (2019) Proposal of the reverse flow model for the origin of the eukaryotic cell based on comparative analysis of Asgard archaeal metabolism. Nature Micro. 4, 1138-1148.

Dombrowski N, Teske AP, Baker BJ. (2018) Expansive microbial metabolic versatility and biodiversity in dynamic Guaymas Basin hydrothermal sediments. Nature Comm. 9, 4999.

Thrash JC, Seitz KW, Baker BJ, Temperton B, Campbell LG, Rabalais NN, Henrissat B, Mason OU. (2018) Metagenomic assembly and prokaryotic MAGs from the northern Gulf of Mexico “Dead Zone”. Microbiol. Res. Announcements 7, e01033-18.

Narrowe AB, Spang A, Stairs C, Caceres EF, Baker BJ, Miller CS, Ettema TJG. (2018) Complex evolutionary history of translation elongation factor 2 and diphthamide biosynthesis in Archaea and parabasalids. Genome Biol Evol 10, 2380-2393.

Bacosa HP, Erdner DL, Rosenheim BE, Shetty P, Seitz KW, Baker BJ, Liu Z (2018) Hydrocarbon degradation and response of seafloor sediment bacterial community in the northern Gulf of Mexico to light Louisiana sweet crude oil. ISME J. 12,2532-2543.

Liu Y, Zhou Z, Pan J, Baker BJ, Gu J, Li M (2018) Comparative genomic inference reveals mixotrophic lifestyle of Thorarchaeota. ISME J. 12, 1021-1031.

Chen L, Mendez-Garcia C, Dombrowski N, Servin-Garciduenas LE, Eloe-Fadrosch EA, Fang Z-H, Zhi X-Y, Hua Z-S, Martinez-Romero E, Woyke T, Huang L-N, Sanchez J, Pelaez AI, Ferrer M, Baker BJ, Shu W-S (2018) Metabolic versatility of small deep-branching archaea. ISME J. 12, 756-775.

Thrash JC, Seitz KW, Baker BJ, Temperton B, Campbell LG, Rabalais NN, Henrissat B, Mason OU, (2017) Metabolic roles of uncultivated bacterioplankton lineages in the northern Gulf of Mexico "Dead Zone". MBio 8:e01017-17.

Bowers RM, et al., Baker BJ, Eren MA, Hedlund B, McMahon K, Fierer N, Eisen J, Knight R, Cochrane G, Finn R, Mizrachi I and Woyke T. (2017) Genome standards for single-cell genomes (MIxS-SCG) and genomes from metagenomes (MIxS-GFM) of bacteria and archaea. Nature Biotechnology 35, 725-731.

Dombrowski N, Seitz KW, Teske AP, Baker BJ (2017) New insights into microbial hydrocarbon cycling and metabolic interdependencies in hydrothermal sediments. Microbiome. 5:106.

Zaremba-Niedzwiedzka, K, Caceres EF, Saw JH, Bäckström D, Juzokaite L, Vancaester E, Seitz KW, Anantharaman, Stott MB, Nunoura T, Banfield JF, Schramm A, Baker BJ, Spang A, and Ettema TJG. (2017) Asgard archaea illuminates the origin of eukaryotic cellular complexity. Nature 541, 353-358.

Lazar CS, Baker BJ, Seitz KW, Hinrichs K-U, Teske AP (2017) Genomic reconstruction of multiple lineages of uncultured benthic archaea suggests distinct biogeochemical roles and ecological niches. ISME J. 11, 1119-1129.

Bird JT, Baker BJ, Probst AJ, Podar M, Lloyd K (2016) Culture independent genomic comparisons reveal environmental adaptations for Altiarchaeales. Frontiers in Microbiol. 7, 1221.

Wasmund K, Cooper M, Schreiber L, Lloyd KG, Baker BJ, Petersen DG, Schramm A, Stepanauskas R, Reinhardt R, Jørgensen BB, Loy A, Adrian L. (2016) Single Cell genome sequencing and targeted gene amplifications implicate members of the class Dehalococcoidia (phylum Chloroflexi) in sulfur cycling. MBio. 7, e00266-16.

Dombrowski N, Donaho J, Teske AP, Gutierrez T, Seitz KW, Baker BJ. (2016) Hydrocarbon degradation pathways in uncultured bacteria from the Deep Water Horizon Oil Spill. Nature Microbiol. 1, 16057.

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 Microbiol. 1, 16048.

Simons Early Career Microbial Ecology and Evolution, 2020

Sloan Foundation Fellowship in Ocean Sciences, 2016

University of Texas College of Natural Science visualizing Science Contest 2015 – 1st place

Rackham Pre-doctoral Graduate Fellowship – 2013 competition, University of Michigan
               Funding for summer and fall 2013 through summer 2014

Aquatic microbial ecology, UT Spring 2016-present

Scientific communications, UT Spring 2017-present

Genomics in ocean science, UT Fall 2017-present

Kathryn Appler, Ph.D. student (2019-present)

JD Carlton, Research technician and M.S. student (2020-present)

Sunny Sneed, lab technician (2020)

Maggie Langwig, M.S. student and Research Technician (2017-2021)

Kiley Seitz, Ph.D. student (2015-2019)

Ian Rambo, Ph.D. student (2016-2021)

Dr. Pedro Lopes Leao, Postdoctoral fellow (2021-present)

Dr. Mirna Vázquez Rosas Landa (2020-present)

Dr. Valerie de Anda, Postdoctoral fellow (2018-present)

Dr. Nina Dombrowski, Postdoctoral fellow (2015-2018)

Dr. Xianzhe Gong, Postdoctoral fellow and Visiting Scholar (2018-present)