Katherine Louie

Dr. Louie joined the JGI in 2014 to develop the metabolomics program, and in 2019 became Platform Lead where she manages metabolomics production for community sequencing projects and heads R&D efforts to expand the metabolomics capabilities and product offerings for JGI users.  Using cutting-edge mass spectrometry-based techniques, the platform delivers rich metabolite profiles from diverse biological and environmental samples in support of user science.  Capabilities offered by the platform are a result of Dr. Louie’s establishment of a strong core foundation of robust mass spectrometry workflows for polar and nonpolar metabolite analysis, creation of large metabolite databases by running 1000s of metabolite standards, and development of high-throughput untargeted analysis pipelines.  Beyond profiling over 10k samples/year, Dr. Louie and her team work with other JGI scientists in development of new, advanced mass spectrometry research products such as stable isotope probing (SIP) to assess metabolite turnover, DNA-SIP for helping identify active micro-organisms within complex communities, and custom software for integrating metabolomics with genomic data (MAGI) for functional annotation and identifying unknown compounds (Pactolus).

Education

• B.S in Biomedical Engineering, Johns Hopkins University;
• Ph.D. in Bioengineering, Arizona State University

Selected Publications

• 1. Swift CL, Louie KB, Bowen BP, Olson HM, Purvine SO, Salamov A, et al. Anaerobic gut fungi are an untapped reservoir of natural products. Proc Natl Acad Sci U S A. 2021;118. doi:10.1073/pnas.2019855118
• 2. Murphy KM, Edwards J, Louie KB, Bowen BP, Sundaresan V, Northen TR, et al. Bioactive diterpenoids impact the composition of the root-associated microbiome in maize (Zea mays). Scientific Reports. 2021. doi:10.1038/s41598-020-79320-z
• 3. Louie KB, Kosina SM, Hu Y, Otani H, de Raad M, Kuftin AN, et al. Mass Spectrometry for Natural Product Discovery. 2020.  Reference Module in Chemistry, Molecular Sciences and Chemical Engineering.  DOI: 10.1016/b978-0-12-409547-2.14834-6
• 4. Roth MS, Gallaher SD, Westcott DJ, Iwai M, Louie KB, Mueller M, et al. Regulation of Oxygenic Photosynthesis during Trophic Transitions in the Green Alga Chromochloris zofingiensis. Plant Cell. 2019;31: 579–601.
• 5. Erbilgin O, Rübel O, Louie KB, Trinh M, Raad M de, Wildish T, et al. MAGI: A Method for Metabolite Annotation and Gene Integration. ACS Chem Biol. 2019;14: 704–714.
• 6. Zhalnina K, Louie KB, Hao Z, Mansoori N, da Rocha UN, Shi S, et al. Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly. Nat Microbiol. 2018;3: 470–480.
• 7. Louie KB, Bowen BP, McAlhany S, Huang Y, Price JC, Mao J-H, et al. Mass spectrometry imaging for in situ kinetic histochemistry. Sci Rep. 2013;3: 1656.