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Photo of Michelle O'Malley

Michelle O'Malley

ICB Systems and Synthetic Biology Co-Leader
Professor
Chemical Engineering
UC Santa Barbara
Phone:
+1 805-893-4769
Email:
momalley@engineering.ucsb.edu
Website:
Website
Twitter Link:
@omalleylab

Research Focus Areas

Research Interests

My research 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.

News

Displaying 1 - 20 of 48

ICB Supported Publications

Increased aluminum exposure induces widespread changes in silicon, carbon, and nitrogen metabolism in Entomoneis vertebralis

Ramya Ragunathan, Hugh M. Purdy, Susanna Seppala, Hosu Gwak, Sara Calhoun, Benjamin S. Twining, Igor V. Grigoriev, Bradley F. Chmelka, Mark A. Brzezinski & Michelle A. O’Malley
BMC Genomics,
https://doi.org/10.1186/s12864-025-12106-7

A large-scale screening campaign of putative carbohydrate-active enzymes reveals a novel xylanase from anaerobic gut fungi

S. Jin, I. R. Farrand, Y. Chen, J. W. Gin, B. Zhang, E. Kirschke, C. J. Petzold, P. D. Adams, M. A. O’Malley
mBio,
10.1128/mbio.01007-25

Genomic and transcriptomic characterization of carbohydrate-active enzymes in novel isolate, Neocallimastix cameroonii var. constans

E. M. Blair, T. A. Navaratna, C. B. Ahern, R. Ragunathan, J. L. Brown, S. J. Mondo, A. Lipzen, R. A. Hanafy, J. Gonzalez, X. Peng, I. V. Grigoriev, M. A. O’Malley
G3 - Genes|Genomes|Genetics,
10.1093/g3journal/jkaf137

An argument for using anaerobes as microbial cell factories to advance synthetic biology and biomanufacturing

Thomas S. Lankiewicz, Nathalie H. Elisabeth, David L. Valentine, Michelle A. O'Malley
AIChE Journal,
10.1002/aic.18797

Separation of life stages within anaerobic fungi (Neocallimastigomycota) highlights differences in global transcription and metabolism

L. V. Butkovich, P. A. Leggieri, S. P. Lillington, T. A. Navaratna, C. L. Swift, N. G. Malinov, T. R. Zalunardo, O. B. Vining, A. Lipzen, M. Wang, J. Yan, V. Ng, I. V. Grigoriev, M. A. O’Malley
Fungal Genetics and Biology,
10.1016/j.fgb.2024.103958

New approaches to secondary metabolite discovery from anaerobic gut microbes

Butkovich, L.V., Vining, O.B. & O’Malley, M.A
Applied Microbiology and Biotechnology,
10.1007/s00253-024-13393-y

Toward a Circular Bioeconomy: Designing Microbes and Polymers for Biodegradation

V. Mubayi, C. B. Ahern, M. Calusinska, M. A. O'Malley
ACS Synthetic Biology,
10.1021/acssynbio.4c00077

Targeted hypermutation of putative antigen sensors in multicellular bacteria

H. Doré, A. R. Eisenberg, E. N. Junkins, G. E. Leventhal, Anakha Ganesh, O. X. Cordero, B. G. Paul, D. Valentine, M. A. O’Malley, E. G. Wilbanks
PNAS,
10.1073/pnas.2316469121

Targeted rRNA depletion enables efficient mRNA sequencing in diverse bacterial species and complex co-cultures

K. A. Heom, C. Wangsanuwat, L. V. Butkovich, S. C. Tam, A. R. Rowe, M. A. O'Malley, S. S. Dey
mSystems,
10.1128/msystems.00281-23

Structure and Enzymatic Characterization of CelD Cellulase from the Anaerobic Fungus Piromyces finnis

Alexey Dementiev, Stephen P. Lillington, Shiyan Jin, Youngchang Kim, Robert Jedrzejczak, Karolina Michalska, Andrzej Joachimiak and Michelle A. O’Malley
Applied Microbiology and Biotechnology,
10.1007/s00253-023-12684-0

High-quality RNA extraction and the regulation of genes encoding cellulosomes are correlated with growth stage in anaerobic fungi

J. L. Brown, T. Gierke, L. Butkovich, C. L. Swift, V. Singan, C. Dawum, K. Berry, I. V. Grigoriev, M. A. O'Malley
Frontiers in Fungal Biology,
10.3389/ffunb.2023.1171100

Expression and characterization of spore coat CotH kinases from the cellulosomes of anaerobic fungi (Neocallimastigomycetes)

Stephen P. Lillington, Matthew Hamilton, Jan-Fang Cheng, Yasuo Yoshikuni, Michelle A. O'Malley
Protein Expression and Purification,
10.1016/j.pep.2023.106323

Lignin deconstruction by anaerobic fungi

Thomas S. Lankiewicz, Hemant Choudhary, Yu Gao, Bashar Amer, Stephen P. Lillington, Patrick A. Leggieri, Jennifer L. Brown, Candice L. Swift, Anna Lipzen, Hyunsoo Na, Mojgan Amirebrahimi, Michael K. Theodorou, Edward E. K. Baidoo, Kerrie Barry, Igor V. Grigoriev, Vitaliy I. Timokhin, John Gladden, Seema Singh, Jenny C. Mortimer, John Ralph, Blake A. Simmons, Steven W. Singer & Michelle A. O’Malley
Nature Microbiology,
10.1038/s41564-023-01336-8

Lipid membrane mimetics and oligomerization tune functional properties of proteorhodopsin

C.-T. Han, K.D.Q. Nguyen, M.W. Berkow, S. Hussain, A. Kiani, M. Kinnebrew, M.N. Idso, N. Baxter, E. Chang, E. Aye, E. Winslow, M. Rahman, S. Seppala, M. O’Malley, B.F. Chmelka, B. Mertz, S. Han
Biophysical Journal,
10.1016/j.bpj.2022.11.012

Co‑cultivation of anaerobic fungi with Clostridium acetobutylicum bolsters butyrate and butanol production from cellulose and lignocellulose

Jennifer L Brown, Matthew A Perisin, Candice L Swift, Marcus Benyamin, Sanchao Liu, Vasanth Singan, Yu Zhang, Emily Savage, Christa Pennacchio, Igor V Grigoriev, Michelle A O'Malley
Journal of Industrial Microbiology and Biotechnology,
10.1093/jimb/kuac024

Enzyme Discovery in Anaerobic Fungi (Neocallimastigomycetes) Enables Lignocellulosic Biorefinery Innovation

Thomas S. Lankiewicz, Stephen P. Lillington, Michelle A. O’Malley
Microbiology and Molecular Biology Reviews,
10.1128/mmbr.00041-22

Co‑cultivation of the anaerobic fungus Caecomyces churrovis with Methanobacterium bryantii enhances transcription of carbohydrate binding modules, dockerins, and pyruvate formate lyases on specific substrates

Jennifer L. Brown, Candice L. Swift, Stephen J. Mondo, Susanna Seppala, Asaf Salamov, Vasanth Singan,
Bernard Henrissat, Elodie Drula, John K. Henske, Samantha Lee, Kurt LaButti, Guifen He, Mi Yan,
Kerrie Barry, Igor V. Grigoriev, and Michelle A. O’Malley
Biotechnology for Biofuels,
10.1186/s13068-021-02083-w

Identification of novel membrane proteins for improved lignocellulose conversion

Igor A. Podolsky, Elizabeth E. Schauer, Susanna Seppälä, Michelle A. O’Malley
Current Opinion in Biotechnology,
10.1016/j.copbio.2021.08.010

Cellulosome Localization Patterns Vary across Life Stages of Anaerobic Fungi

Lillington SP, Chrisler W, Haitjema CH, Gilmore SP, Smallwood CR, Shutthanandan V, Evans JE, O’Malley MA.
mBio,
10.1128/mBio.00832-21

Genomic and functional analyses of fungal and bacterial consortia that enable lignocellulose breakdown in goat gut microbiomes

Xuefeng Peng, St. Elmo Wilken, Thomas S. Lankiewicz, Sean P. Gilmore, Jennifer L. Brown, John K. Henske, Candice L. Swift, Asaf Salamov, Kerrie Barry, Igor V. Grigoriev, Michael K. Theodorou, David L. Valentine & Michelle A. O’Malley
Nature Microbiology ,
10.1038/s41564-020-00861-0
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