PNNL

Dr. Joshua Elmore is a staff scientist in the Earth and Biological Sciences Directorate at Pacific Northwest National Laboratory (PNNL). His research leverages microbial genetics, integrative omics, and systems biology approaches for the development of genetic tools for non-model organisms, identification of novel metabolic pathways, and engineering of microbes for societally beneficial functions. Through his research, he aims to clarify how bacteria sense and respond to complex environments (e.g., plant rhizospheres and mixed waste streams) and use this information to guide engineering efforts that enhance existing functions (e.g., plant growth promotion), add new-to-nature functions, and prevent uncontrolled spread in the environment. Dr. Elmore is a task lead on PNNL’s Persistence Control of Engineered Functions in Complex Soil Microbiomes science focus area, which is supported by the Department of Energy’s Genomic Science program. He is also a principal investigator for a project in PNNL’s Predictive Phenomics Initiative, focused on understanding how bacterial protein posttranslational modifications can be controlled to manipulate biomanufacturing phenotypes.

He was the chair for the Environmental Topic Area at the 2024 Society for Industrial Microbiology and Biotechnology Annual Meeting. In 2025, he was selected to serve on the Environmental Topic Area committee for another 3-year term, and he will be the chair for the 2027 annual meeting.

• Bacterial physiology, with a primary focus on the discovery of previously unknown metabolic pathways and cellular functions
• Development of design principles for engineering microbes with nonnative and new-to-nature functions
• Bacterial solutions for the production of next-generation biofuels and biochemicals as well as other critical materials
• Microbe-microbe and interkingdom metabolic exchange and other interactions
• Effective methods for the biocontainment of engineered microbes

• Microbial physiology and molecular genetics in non-model organisms
   
• Synthetic biology and genetic tool development
   
• Transcriptional and posttranslational regulation
   
• RNA biology
   
• Metabolic engineering
   
• High-throughput functional genomics and transcriptomics 
   

• Postdoctoral Research Associate, Oak Ridge National Laboratory 01/2016 to 12/2018

Metabolic Engineering and Microbial Physiology

• Doctorate of Philosophy, University of Georgia 12/2015

Biochemistry and Molecular Biology

• Bachelor of Arts, North Carolina State University 6/2008

Chemistry, Genetics, and Computer Science

Society for Industrial and Microbial Biotechnology

SIMB Mentorship Program

Chair, Environmental Topic Area, Society for Industrial Microbiology and Biotechnology Annual Meeting, 2024

Committee member, Environmental Topic Area, Society for Industrial Microbiology and Biotechnology Annual Meeting, 2025–2027

Editorial board member, Microbial Technology, 2022–present

Editorial board member, Frontiers in Synthetic Biology, 2023–present

BESTie Award: Above and Beyond – Persistence Control SFA renewal, Earth and Biological Sciences Directorate, PNNL, 2023

Johnson, C.W., St. John, P.C., Beckham, G.T., Elmore, J.R., Guss, A.M., Salvachua, D., Bentley, G.J. Engineered microorganisms for the production of intermediates and final products. U.S.P.T.O. Patent Number: 11,518,975

Huenemann J., Elmore J.R., Guss A.M.. Engineered microbes for the conversion of organic compounds to medium chain length alcohols, and methods of use. U.S.P.T.O. Patent Number: 11,326,151

Elmore, J.R., Huenemann, J.D., Salvachua, D., Beckham, G.T., and Guss, A.M. (2019). Production of itaconic acid and related molecules from aromatic compounds, U.S.P.T.O. Patent Number: 10,738,333

Terns, R.M., Terns, M.P., Elmore, J.R., Methods for cleaving DNA and RNA molecules. U.S.P.T.O. Patent Number: 11,193,127

Google Scholar Link

Select Primary and Corresponding Author Publications

* primary authors

#  corresponding authors

2025

Van Fossen, E. M.#; Stephenson, M.; Frank, A.; Akella, S.; Wooldridge, R.; Wilson, A.; You, Y.; Nakayasu, E.; Egbert, R.; Elmore, J. R.# Efficient genetic code expansion tools enable in vivo study of lysine acetylation in non-model bacteria. bioRxiv 2025, 2025.04.14.648644, DOI: https://doi.org/10.1101/2025.04.14.648644. 

Elmore, J. R.#; Shrestha, R.; Wilson, A.; Van Fossen, E.; Frank, A.; Francis, R.; Baldino, H.; Stephenson, M.; Gupta, B.; Rivera, J.; Egbert, R#. Reinforced CRISPR interference enables reliable multiplex gene repression in phylogenetically distant bacteria. bioRxiv 2025, 2025.04.14.648646, DOI: https://doi.org/10.1101/2025.04.14.648646.

2024

Elmore, J. R.#; Breysse (van Fossen), E. M. Developing a pipeline to expand the genetic code of diverse bacteria for microbial engineering; Pacific Northwest National Laboratory (PNNL), Richland, WA (United States): United States, 2024; p Medium: ED; Size: 15 p., DOI: 

2023

Wilson, A.; Fossen, E. V.; Shrestha, R.; Trotter, V.; Poirier, B.; Frank, A.; Nelson, W.; Kim, Y.-M.; Deutschbauer, A.; Egbert, R.; Elmore, J. R.# A novel phenylpropanoid methyl esterase enables catabolism of aromatic compounds that inhibit biological nitrification. bioRxiv 2023, 2023.06.02.543320, DOI: https://doi.org/10.1101/2023.06.02.543320. 

Oda, Y.*; Elmore, J. R.*; Nelson, W. C.; Wilson, A.; Farris, Y.; Shrestha, R.; Garcia, C. F.; Pettinga, D.; Ogden, A. J.; Baldino, H.; Alexander, W. G.; Deutschbauer, A. M.; Hurtado, C. V.; McDermott, J. E.; Guss, A. M.; Coleman-Derr, D.; McClure, R.; Harwood, C. S.; Egbert, R. G. Sorgoleone degradation by sorghum-associated bacteria; an opportunity for enforcing plant growth promotion. bioRxiv 2023, 2023.05.26.542311, DOI: https://doi.org/10.1101/2023.05.26.542311. 

Elmore, J. R.*; Dexter, G. N.; Baldino, H.; Huenemann, J. D.; Francis, R.; Peabody, G. L. t.; Martinez-Baird, J.; Riley, L. A.; Simmons, T.; Coleman-Derr, D.; Guss, A. M.; Egbert, R. G. High-throughput genetic engineering of nonmodel and undomesticated bacteria via iterative site-specific genome integration. Science Advances 2023, 9, eade1285, DOI: https://doi.org/10.1126/sciadv.ade1285.

2022

Elmore, J. R.#; Peabody, G.; Jha, R. K.; Dexter, G. N.; Dale, T.; Guss, A.# Dynamic control systems that mimic natural regulation of catabolic pathways enable rapid production of lignocellulose-derived bioproducts. bioRxiv 2022, 2022.01.12.475730, DOI: https://doi.org/10.1101/2022.01.12.475730. 

Alfaro, T.*; Elmore, J. R.*; Stromberg, Z. R.*; Hutchison, J. R.; Hess, B. M. Engineering Citrobacter freundii using CRISPR/Cas9 system. Journal of Microbiology Methods 2022, 200, 106533, DOI: https://doi.org/10.1016/j.mimet.2022.106533. 

Elmore, J. R.*; Dexter, G. N.; Salvachua, D.; Martinez-Baird, J.; Hatmaker, E. A.; Huenemann, J. D.; Klingeman, D. M.; Peabody, G. L. t.; Peterson, D. J.; Singer, C.; Beckham, G. T.; Guss, A. M. Production of itaconic acid from alkali pretreated lignin by dynamic two stage bioconversion. Nature Communications 2021, 12, 2261, DOI: https://doi.org/10.1038/s41467-021-22556-8. 

Elmore, J. R.*; Dexter, G. N.; Salvachua, D.; O'Brien, M.; Klingeman, D. M.; Gorday, K.; Michener, J. K.; Peterson, D. J.; Beckham, G. T.; Guss, A. M. Engineered Pseudomonas putida simultaneously catabolizes five major components of corn stover lignocellulose: Glucose, xylose, arabinose, p-coumaric acid, and acetic acid. Metabolic Engineering 2020, 62, 62-71, DOI: https://doi.org/10.1016/j.ymben.2020.08.001. 

Peabody, G. L.*; Elmore, J. R.*; Martinez-Baird, J.; Guss, A. M. Engineered Pseudomonas putida KT2440 co-utilizes galactose and glucose. Biotechnology for Biofuels 2019, 12, DOI: https://doi.org/10.1186/s13068-019-1627-0. 

Elmore, J. R.*; Furches, A.; Wolff, G. N.; Gorday, K.; Guss, A. M. Development of a high efficiency integration system and promoter library for rapid modification of Pseudomonas putida KT2440. Metabolic Engineering Communications 2017, 5, 1-8, DOI: https://doi.org/10.1016/j.meteno.2017.04.001. 

Elmore, J. R.*; Sheppard, N. F.; Ramia, N.; Deighan, T.; Li, H.; Terns, R. M.; Terns, M. P. Bipartite recognition of target RNAs activates DNA cleavage by the Type III-B CRISPR-Cas system. Genes and Development 2016, 30, 447-59, DOI: https://doi.org/10.1101/gad.272153.115.

Elmore, J.*; Deighan, T.; Westpheling, J.; Terns, R. M.; Terns, M. P. DNA targeting by the type I-G and type I-A CRISPR-Cas systems of Pyrococcus furiosus. Nucleic Acids Research 2015, 43, 10353-63, DOI: https://doi.org/10.1093/nar/gkv1140.

Elmore, J. R.*; Yokooji, Y.*; Sato, T.; Olson, S.; Glover, C. V., 3rd; Graveley, B. R.; Atomi, H.; Terns, R. M.; Terns, M. P. Programmable plasmid interference by the CRISPR-Cas system in Thermococcus kodakarensis. RNA Biology 2013, 10, 828-40, DOI: https://doi.org/10.4161/rna.24084.

Other Publications

McDermott, J. E.; Nelson, W. C.; Zimmerman, A. E.; Anthony, W.; Coleman-Derr, D.; Elmore, J.; Nitka, T.; McClure, R. S.; Handakumbura, P. P.; Guss, A.; Wheeler, T. J.; Egbert, R. G. Describing the Persistence Landscape for Introducing Microbes into Complex Communities. arXiv, 2025 p:2503.22133.

Van Fossen, E. M.; Kroll, J. O.; Anderson, L. N.; McNaughton, A. D.; Herrera, D.; Oda, Y.; Wilson, A. J.; Nelson, W. C.; Kumar, N.; Frank, A. R.; Elmore, J. R.; Handakumbura, P.; Lin, V. S.; Egbert, R. G. Profiling sorghum-microbe interactions with a specialized photoaffinity probe identifies key sorgoleone binders in Acinetobacter pittii. Applied and Environmental Microbiology 2024, 90, e0102624, DOI: .

Fonseca-García, C.; Wilson, A.; Elmore, J.; Pettinga, D.; McClure, R.; Atim, J.; Pedraza, J.; Hutmacher, R.; Egbert, R.; Coleman-Derr, D. Defined synthetic microbial communities colonize and benefit field-grown sorghum. The ISME journal 2024, DOI: .

Werner, A. Z.; Clare, R.; Mand, T. D.; Pardo, I.; Ramirez, K. J.; Haugen, S. J.; Bratti, F.; Dexter, G. N.; Elmore, J. R.; Huenemann, J. D.; Peabody, G. L. t.; Johnson, C. W.; Rorrer, N. A.; Salvachua, D.; Guss, A. M.; Beckham, G. T. Tandem chemical deconstruction and biological upcycling of poly(ethylene terephthalate) to beta-ketoadipic acid by Pseudomonas putida KT2440. Metabolic Engineering 2021, 67, 250-261, DOI: .

Salvachua, D.; Rydzak, T.; Auwae, R.; De Capite, A.; Black, B. A.; Bouvier, J. T.; Cleveland, N. S.; Elmore, J. R.; Furches, A.; Huenemann, J. D.; Katahira, R.; Michener, W. E.; Peterson, D. J.; Rohrer, H.; Vardon, D. R.; Beckham, G. T.; Guss, A. M. Metabolic engineering of Pseudomonas putida for increased polyhydroxyalkanoate production from lignin (vol 13, pg 290, 2019). Microbial Biotechnology 2020, 13, 813-813, DOI: .

Chaves, J. E.; Wilton, R.; Gao, Y.; Munoz, N. M.; Burnet, M. C.; Schmitz, Z.; Rowan, J.; Burdick, L. H.; Elmore, J.; Guss, A.; Close, D.; Magnuson, J. K.; Burnum-Johnson, K. E.; Michener, J. K. Evaluation of chromosomal insertion loci in the Pseudomonas putida KT2440 genome for predictable biosystems design. Metabolic Engineering Communications 2020, 11, e00139, DOI: https://doi.org/10.1016/j.mec.2020.e00139.

Bentley, G. J.; Narayanan, N.; Jha, R. K.; Salvachua, D.; Elmore, J. R.; Peabody, G. L.; Black, B. A.; Ramirez, K.; De Capite, A.; Michener, W. E.; Werner, A. Z.; Klingeman, D. M.; Schindel, H. S.; Nelson, R.; Foust, L.; Guss, A. M.; Dale, T.; Johnson, C. W.; Beckham, G. T. Engineering glucose metabolism for enhanced muconic acid production in Pseudomonas putida KT2440. Metabolic Engineering 2020, 59, 64-75, DOI: .

Johnson, C. W.; Salvachua, D.; Rorrer, N. A.; Black, B. A.; Vardon, D. R.; St John, P. C.; Cleveland, N. S.; Dominick, G.; Elmore, J. R.; Grundl, N.; Khanna, P.; Martinez, C. R.; Michener, W. E.; Peterson, D. J.; Ramirez, K. J.; Singh, P.; VanderWall, T. A.; Wilson, A. N.; Yi, X. N.; Biddy, M. J.; Bomble, Y. J.; Guss, A. M.; Beckham, G. T. Innovative Chemicals and Materials from Bacterial Aromatic Catabolic Pathways. Joule 2019, 3, 1523–1537, DOI: .

Ramia, N. F.; Spilman, M.; Tang, L.; Shao, Y.; Elmore, J.; Hale, C.; Cocozaki, A.; Bhattacharya, N.; Terns, R. M.; Terns, M. P.; Li, H.; Stagg, S. M. Essential structural and functional roles of the Cmr4 subunit in RNA cleavage by the Cmr CRISPR-Cas complex. Cell Reports 2014, 9, 1610–1617, DOI: .

Terns, B.; Hale, C.; Carte, J.; Elmore, J.; Majumdar, S.; Glover, C. V. C.; Graveley, B.; Terns, M. The CRISPR-Cas system: small RNA-guided invader silencing in prokaryotes. Faseb Journal 2012, 26, WOS:000310711306050.

Hale, C. R.; Majumdar, S.; Elmore, J.; Pfister, N.; Compton, M.; Olson, S.; Resch, A. M.; Glover, C. V., 3rd; Graveley, B. R.; Terns, R. M.; Terns, M. P. Essential features and rational design of CRISPR RNAs that function with the Cas RAMP module complex to cleave RNAs. Molecular Cell 2012, 45, 292-302, DOI: https://doi.org/10.1016/j.molcel.2011.10.023.