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UC Santa Barbara Dissertation Template UNIVERSITY OF CALIFORNIA Santa Barbara Deciphering the Functions of Natural Products from Anaerobic Fungi for Applications in Biotechnology A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Chemical Engineering by Candice Lee Swift Committee in charge: Professor Michelle A. O’Malley, Chair Professor Siddharth Dey Professor Song-I-Han Professor David Low December 2020 The dissertation of Candice Lee Swift is approved. ____________________________________________ Siddharth Dey ____________________________________________ Song-I Han ____________________________________________ David Low ____________________________________________ Michelle A. O’Malley, Committee Chair December 2020 ACKNOWLEDGEMENTS I would like to thank my advisor, Michelle O’Malley, for the opportunity to work in her lab and achieve the work described in this dissertation. I would also like to thank all O’Malley lab members, both past and present. I am extremely grateful for the training I received from others in the lab and for the foundation that previous lab members laid in isolating anaerobic fungi and sequencing their genomes and transcriptomes. I also want to thank Nikola Malinov, the diligent undergraduate researcher whose help in lab was invaluable to me and who contributed to the experiments in Chapter five. I would also like to thank our collaborators at the Joint Genome Institute, the Environmental Molecular Sciences Laboratory, and both the Keller lab at the University of Wisconsin-Madison as well as the Solomon lab at Purdue for their experimental contributions and insight. Dr. Jennifer Smith at the Biological Nanostructures Laboratory at UCSB was particularly helpful to me during the library preparation steps of Chapter five. I am grateful to professors Jennifer Reed, Nicholas Abbott, and Betty Chewning for writing letters of recommendation for me when I applied to graduate school after working for five years in industry. Finally, I want to thank my family and friends for their encouragement and support, as well as my husband and son. iii VITA OF CANDICE LEE SWIFT December 2020 EDUCATION 2015-2020 Doctor of Philosophy in Chemical Engineering University of California – Santa Barbara 2006-2010 Bachelor of Science in Chemical Engineering University of Wisconsin – Madison PUBLICATIONS 1. C.L. Swift, J.L. Brown, S. Seppälä, 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 and Biotechnology. 46, 1427-1433, 2019. 2. T.A. Rush, V. Puech-Pagès, A. Bascaules, P. Jargeat, F. Maillet, A. Haouy, A. QuyManh Maës, C.C. Carriel, D. Khokhani, M. Keller-Pearson, J. Tannous, K.R. Cope, K. Garcia, J. Maeda, C. Johnson, B. Kleven, Q.J. Choudhury, J. Labbé, C.L. Swift, M.A. O’Malley, J.W. Bok, S. Cottaz, S. Fort , V. Poinsot, M.R. Sussman, C. Lefort, J. Nett, N.P. Keller, G. Bécard, J Ané, “Lipo-chitooligosaccharides as regulatory signals of fungal growth and development,” Nature Communications, 11(1), 2020. 3. I.A. Podolsky, S. Seppala, T.S. Lankiewicz, J.L. Brown, C.L. Swift, M.A. O’Malley, “Harnessing Nature’s Anaerobes for Biotechnology and Bioprocessing,” Annual Review of Chemical and Biomolecular Engineering 13(27), 6.1-6.24, 2019. 4. S.E. Wilken, C.L. Swift, I.A. Podolsky, T.S. Lankiewicz, S. Seppala, M.A. O’Malley, “Linking ‘omics’ to function unlocks the biotech potential of non-model fungi,” Current Opinion in Systems Biology 14, 9-17, 2019. 5. X. Peng, C.L. Swift, M.K. Theodorou, M.A. O’Malley, in 53–67 (Humana Press, New York, NY, 2018). doi:10.1007/978-1-4939-7804-5_5 6. R.J. Carlton, J.K. Gupta, C.L. Swift, N.L. Abbott, “Influence of Simple Electrolytes on the Orientational Ordering of Thermotropic Liquid Crystals at Aqueous Interfaces,” Langmuir 28(1), 31-36, 2012. PLANNED PUBLICATIONS 1. X. Peng, X., S.E. Wilken, T.S. Lankiewicz, S.P. Gilmore1, J.L. Brown, J.K. Henske, C.L. Swift, A. Salamov, K.Barry, I.V. Grigoriev, M.K. Theodorou5, D.L. Valentine6, M.A. O’Malley, “Sculpting gut microbial communities alters fermentation products and methane release,” Nature Microbiology, In press 2020. iv 2. C.L. Swift, K.B. Louie, B.P. Bowen, H.M. Olson, 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,” In progress. 3. C.L. Swift, N.G. Malinov, S.J. Mondo, A. Salamov, I.V. Grigoriev, M.A. O’Malley, “Anaerobic fungal genomes encode stress response genes similar to early eukaryotic parasites,” In progress. 4. C.L Swift, K.B. Louie, B.P. Bowen, C.A. Hooker, K.V. Solomon, T.R. Northen, I.V. Grigoriev, M.A. O’Malley, “Co-cultivation of anaerobic fungi with rumen bacteria establishes an antagonistic relationship,” In progress. 5. C.L. Swift, L.V. Butkovich, K.L. Dickson, C.E.Lawson, X. Peng, K. Barry, M.A. O’Malley, “Fungal and bacterial secondary metabolites shape consortia membership in an enriched goat fecal microbiome,” In progress. PRESENTATIONS Swift CL, O’Malley MA. “Discovery of natural products from anaerobic gut fungi,” oral and poster presentations at the 30th Fungal Genetics Conference; 2019 Mar 14; Pacific Grove, California. Swift CL, Louie KB, Bowen BP, Bingol K, Heyman HM, Northen TR, O’Malley MA. “Enabling natural products discovery from anaerobic fungi via integrated ‘omics’ approaches,” oral presentation at the 255th ACS National Meeting, Division of Biochemical Technology (BIOT); 2018 Mar 22; New Orleans, Louisiana. Swift CL, O’Malley MA. “Deciphering the role of fungal secondary metabolites in anaerobic microbial communities,” oral presentation at Joint Genome Institute 2017 Microbial and Plant Systems Modulated by Secondary Metabolites Meeting; 2017 July; Walnut Creek, California. Swift CL, O’Malley MA, Louie KB, Northen TR. “Identifying and characterizing the secondary metabolites of anaerobic fungi,” poster presentation at 253rd ACS National meeting, Division of Biochemical Technology (BIOT); 2017 Apr; San Francisco, California. SELECTED AWARDS Graduate Division Dissertation Fellowship (2020) Connie Frank Fellowship (2019) MIT CHEME Rising Stars (2019) National Science Foundation Graduate Research Fellowships Program (2016-2019) Genetics Society of America member Best poster at Clorox-Amgen Graduate Student Symposium (October 2018) Runner-up for best poster at the 50th anniversary of the UCSB Chemical Engineering department Undergraduate scholarships (2006-2010): American Chemical Society Scholar, Chancellor’s Scholar, Leaders in Engineering Excellence and Diversity v PROFESSIONAL EMPLOYMENT 2014-2015 Veolia Water Solutions & Technologies 2013-2014 Valero Energy Corporation 2010-2012 Honeywell UOP vi ABSTRACT Deciphering the Functions of Natural Products from Anaerobic Fungi for Applications in Biotechnology by Candice Lee Swift Natural products, or secondary metabolites, are small molecules produced primarily by bacteria, fungi, and plants. Their chemical diversity has conferred many usefuiiul bioactivities, such as antibacterial, antifungal, cholesterol-lowering, and immunosuppressant. In addition to their value as medicinal drugs, these molecules also serve important ecological roles in their native environments, by mediating interactions between microorganisms. Natural products are crucial to future microbiome engineering efforts for their natural ability to modulate microbial communities. The digestive tracts of large herbivores, including the rumen, harbor complex microbial communities, consisting of fungi, bacteria, protozoa, and methanogenic archaea. This vast reservoir of chemical diversity is almost completely untapped with regards to the discovery of natural products. These microbiomes are of interest both for their potential to yield new drug candidates and as a microbial platform for chemical production from renewable feedstocks. In this work, we explore the biosynthetic potential of anaerobic fungi native to the digestive tracts of herbivores to synthesize natural products. The genomes, transcriptomes, vii proteomes, and metabolomes of anaerobic fungi reveal that these underexplored fungi synthesize novel natural products, some of which are used to compete with rumen bacteria. Groundbreaking dual transcriptomics of rumen fungi co-cultured with rumen bacteria provides evidence that the relationship between these two organisms is antagonistic and that the presence of bacteria stimulates the expression of biosynthetic genes encoding enzymes that synthesize potential antibiotics. By sequencing the active genes of microbiomes inoculated from a source microbiome (goat fecal pellet), we demonstrated that the bacterial and fungal biosynthetic genes of natural products were active in sequential cultures passaged in vitro. We found that fungal biosynthetic genes were upregulated at later generations of batch passaging. This finding revealed that the expression of fungal biosynthetic genes is dynamic and suggested that natural products may function in the stability of the microbial community. Overall this dissertation points to the potential of natural products sourced from the rumen as drug candidates, as well as their importance in future microbiome engineering efforts. viii TABLE OF CONTENTS 1 Introduction ........................................................................................................ 1 1.1 Motivation...............................................................................................
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