Michelle O'Malley

Biography

Michelle A. O’Malley is a Professor in the Department of Chemical Engineering at the University of California, Santa Barbara. She earned a B.S. in Chemical Engineering and Biomedical Engineering from Carnegie Mellon University in 2004 and a PhD in Chemical Engineering from the University of Delaware in 2009, where she worked with Prof. Anne Robinson to engineer overproduction of membrane proteins in yeast. O’Malley was a USDA-NIFA postdoctoral fellow in the Department of Biology at MIT, where she developed new strategies for cellulosic biofuel production. At UCSB, her research group engineers protein synthesis within anaerobes and consortia for sustainable chemical production, bioremediation, and natural product discovery. O’Malley’s research has been featured on NPR’s Science Friday, the BBC Newshour, the LA Times, and several other media outlets. She was named one of the 35 Top Innovators Under 35 in the world by MIT Technology Review in 2015, one of the 10 “Scientists to Watch” by Science News in 2019 and is the recipient of the Presidential Early Career Award for Scientists and Engineers (PECASE) – the highest honor bestowed on early career scientists by the US government. She is also the recipient of the Allan P. Colburn Award from the AIChE, the ASM Award for Early Career Applied and Biotechnological Research, the AIChE Division 15 Early Career Award, a DOE Early Career Award, an NSF CAREER award, the Camille Dreyfus Teacher-Scholar Award, the ACS BIOT Division Young Investigator Award, an ACS PMSE Division Young Investigator Award, an ACS WCC “Rising Star” Award, and a Hellman Faculty Fellowship. She was elected to the American Institute of Medical and Biological Engineers in 2020.

Research [video overview]

The O'Malley Lab develops new technologies to genetically engineer non-model microbes and anaerobic consortia for sustainable chemical production, remediation, and natural product discovery. Our approach combines classical microbiology with cutting-edge tools (genome sequencing, RNA-Seq) to engineer the processes that underlie protein and enzyme production. Current efforts include discovery of novel enzymes from anaerobic gut fungi, metabolic engineering for enhanced anaerobic cooperation, engineering of synthetic enzyme complexes for consolidated bioprocessing, and deciphering the structure-function relationship of membrane proteins.

Selected Publications

I. A. Podolsky, S. Seppälä, H. Xu, Y. S. Jin, M. A. O’Malley, “A SWEET surprise: anaerobic fungal sugar transporters and chimeras enhance sugar uptake in yeast,” Metabolic Engineering, 66: 137-147 (2021). https://doi.org/10.1016/j.ymben.2021.04.009

C. L. Swift, K. Louie, B. Bowen, H. M. Olsen, S. O. Purvine, A. Salamov, S. J. Mondo, K. V. Solomon, A. T. Wright, T. R. Northen, I. V. Grigoriev, N. P. Keller, M. A. O’Malley, “Anaerobic gut fungi are an untapped reservoir of natural products,” PNAS, 118 (18) e20198551118 (2021). https://doi.org/10.1073/pnas.2019855118

S. E. Wilken, J. M. Monk, P. A. Leggieri, C. A. Lawson, T. S. Lankiewicz, S. Seppälä, C. Daum, J. Jenkins, A. Lipzen, S. J. Mondo, K. W. Berry, I. V. Grigoriev, J. K. Henske, M. K. Theodorou, B. O. Palsson, L. R. Petzold, M. A. O’Malley, “Experimentally validated reconstruction and analysis of a genome-scale metabolic model of an anaerobic Neocallimastigomycota fungus,” mSystems, 6(1): e00002-21 (2021). http://dx.doi.org/10.1128/mSystems.00002-21

X. Peng, S. E. Wilken, T. S. Lankiewicz, S. P. Gilmore, J. L. Brown, J. K. Henske, C. L. Swift, A. Salamov, K. Barry, I. V. Grigoriev, M. K. Theodorou, D. L. Valentine, M. A. O’Malley, “Genomic and functional analyses of fungal and bacterial consortia that enable lignocellulose breakdown in goat gut microbiomes,” Nature Microbiology: 6(4): 499–511 (2021). (Invited submission) http://dx.doi.org/10.1038/s41564-020-00861-0

J. I. Yoo, S. Seppälä, M. A. O’Malley, “Engineered fluoride sensitivity enables biocontainment and selection of genetically-modified yeasts,” Nature Communications, 11: 5459 (2020). http://dx.doi.org/10.1038/s41467-020-19271-1

J. I. Yoo, P. S. Daugherty, M. A. O’Malley, “Bridging non-overlapping reads illuminates high-order epistasis between distal protein sites in a GPCR,” Nature Communications, 11, 690 (2020). http://dx.doi.org/10.1038/s41467-020-14495-7

C. L. Swift, J. L. Brown, S. Seppala, M. A. O’Malley, “Co-cultivation of the anaerobic fungus Anaeromyces robustus with Methanobacterium bryantii enhances transcription of carbohydrate active enzymes,” Journal of Industrial Microbiology, 46(9):1427-1433 (2019). (Invited article) http://dx.doi.org/10.1007/s10295-019-02188-0

S. P. Gilmoreǂ, T. Lankiewiczǂ, S. E. Wilken, J. L. Brown, J. A. Sexton, J. K. Henske, M. K. Theodorou, D. L. Valentine, M. A. O’Malley, “Top-down enrichment guides in formation of synthetic microbial consortia for biomass degradation,” ACS Synthetic Biology, 8: 2174-2185 (2019). ǂ equal author contributions http://dx.doi.org/10.1021/acssynbio.9b00271

J. I. Yoo, M. A. O’Malley, “Tuning vector stability and integration frequency elevates functional GPCR production and homogeneity in Saccharomyces cerevisiae.” ACS Synthetic Biology, 7(7): 1763-1772 (2018).

J. K. Henske, S. E. Wilken, K. V. Solomon, C. E. Smallwood, V. Shutthanandan, J. E. Evans, M. K. Theodorou, M. A. O’Malley, “Metabolic characterization of anaerobic fungi provides a path forward for bioprocessing of crude lignocellulose,” Biotechnology & Bioengineering, 115(4): 874-884 (2018).

C. H. Haitjemaǂ, S. P. Gilmoreǂ, J. K. Henske, K. V. Solomon, R. deGroot, A. Kuo, S. Mondo, A. Kuo, S. J. Mondo, A. A. Salamov, K. LaButti, Z. Zhao, J. Chiniquy, K. Barry, H. M. Brewer, S. O. Purvine, A. T. Wright, M. Hainaut, B. Boxma, T. van Alen, J. H. P. Hackstein, B. Henrissat, S. E. Baker, I. V. Grigoriev, M. A. O’Malley, “A parts list for fungal cellulosomes revealed by comparative genomics,” Nature Microbiology, 2(8): 17087 (2017). ǂ equal author contributions

S. J. Mondo, R. O. Dannebaum, R. Kuo, K. LaButti, S. Haridas, A. Kuo, A. Salamov, S. R. Ahrendt, A. Lipzen, W. Sullivan, W. Andreopolous, A. Clum, E. Lindquist, C. Daum, G. Ramamoorthy, A. Gryganskyi, D. Dulley, J. Magnuson, T. Y. James, M. A. O’Malley, J. E. Stajich, J. W. Spatafora, A. Visel, I. V. Grigoriev, “Widespread adenine N6-methylation of active genes in fungi”, Nature Genetics, 49: 964-968 (2017).

J. Niu, D. J. Lunn, A. Pusuluri, J. I. Yoo, M. A. O'Malley, S. Mitragotri, H. T. Soh, C. J. Hawker, "Engineering live cell surfaces with functional polymers via cytocompatible controlled radical polymerization," Nature Chemistry, 9: 537-545 (2017).

K. V. Solomon, C. H. Haitjema, J. K. Henske, S. P. Gilmore, D. Borges-Rivera, A. Lipzen, H. M. Brewer, S. O. Purvine, A. T. Wright, M. K. Theodorou, I. Grigoriev, A. Regev, D. A. Thompson, M. A. O’Malley, “Early-branching gut fungi possess a large, comprehensive array of biomass-degrading enzymes,” Science, 351: 1192-1195 (2016).

C. Haitjema, K. V. Solomon, J. K. Henske, M. K. Theodorou, M. A. O’Malley, “Anaerobic gut fungi: advances in isolation, culture, and cellulolytic enzyme discovery for biofuel production,” Biotechnology & Bioengineering, 111(8): 1471-1482 (2014).