Jonathan Klassen

Associate Professor

Molecular and Cell Biology / Microbiology

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@klassenlab

Education: PhD: Microbiology and Biotechnology, University of Alberta; Postdoctoral Study: Bacteriology, University of Wisconsin-Madison.

Research Interests: My research studies microbial community ecology, especially using the fungus-growing ant symbiosis as a model system to understand how microbial interaction networks evolve across ecological gradients. I am particularly interested in how the differing ecologies and population structures of multiple symbiotic partners affect the stability and function of their overall symbioses, and couple genomics and chemical biology both to understand the molecular mechanisms underpinning such interactions and to exploit them for drug discovery.

Selected Publications:

Klassen JL. 2023. Resistance waxes for mutualists protected by wasp secretions PNAS 120(36):e2311815120 https://www.pnas.org/doi/10.1073/pnas.2311815120

Kyle KE*, Puckett SP*, Caraballo-Rodríguez AM, Rivera-Chávez J, Samples RM, Earp CE, Rajad HA, Pearce CJ, Ernst M, van der Hooft JJJ, Adams ME, Oberlies NH, Dorrestein PC, Klassen JL#, and Balunas MJ#. 2023. Trachymyrmex septentrionalis ants promote fungus garden hygiene using Trichoderma-derived metabolite cues PNAS 120(25):e2219373120 https://www.pnas.org/doi/10.1073/pnas.2219373120

Truchon, A. N., Dalsing, B. L., Khokhani, D., MacIntyre, A., McDonald, B. R., Ailloud, F., Klassen, J., Gonzalez-Orta, E. T., Currie, C., Prior, P., Power, T. M., Allen, C. 2023. Plant pathogenic Ralstonia phylotypes evolved divergent respiratory strategies and behaviors to thrive in xylem. mBio 14:e03188-22 https://doi.org/10.1128/mbio.03188-22

Green EA and Klassen JL. Trachymyrmex septentrionalis Ant Microbiome Assembly Is Unique to Individual Colonies and Castes. mSphere 7:00989-21 https://doi.org/10.1128/msphere.00989

Fremin BJ, Bhatt AS, Kyrpides NC, Global Phage Small Open Reading Frame (GP-SmORF) Consortium* (*JL Klassen is a member of the GP-SmORF Consortium). 2022. Thousands of small, novel genes predicted in global phage genomes Cell Reports 39:110984

Caraballo-Rodríguez AM, Pucket SP, Kyle KE, Petras D, da Silva RR, Nothias L-F, Ernst M, van der Hooft JJJ, Tripathi A, Wang M, Balunas MJ, Klassen JL, Dorrestein PC. 2021. Chemical Gradients of Plant Substrates in an Atta texana Fungus Garden mSystems 6(4):e00601-21

Green EA, Smedley SR, and Klassen JL. 2021. North American fireflies host low bacterial diversity Microb Ecol https://link.springer.com/article/10.1007%2Fs00248-021-01718-7

Jasmin Portelinha, Searle S. Duay, Seung I. Yu, Kara Heilemann, M. Daben J. Libardo, Samuel A. Juliano, Jonathan L. Klassen*, and Alfredo M. Angeles-Boza* Antimicrobial Peptides and Copper(II) Ions: Novel Therapeutic Opportunities Chem. Rev. 2021 https://pubs.acs.org/doi/full/10.1021/acs.chemrev.0c00921

Goldstein SL and Klassen JL. 2020. Pseudonocardia symbionts of fungus-growing ants and the evolution of defensive secondary metabolism Front. Microbiol. 11:621041 https://www.frontiersin.org/articles/10.3389/fmicb.2020.621041/full

Green EA and Klassen JL. 2020. Draft Genome Sequence of Spiroplasma platyhelix ATCC 51748,isolated from a Dragonfly. Microbiology Resource Announcments 9(47):e00422-20 https://mra.asm.org/content/9/47/e00422-20

Nayfach S, Roux S, Seshadri R, Udwary D, Varghese N, Schulz F, Wu D, Paez-Espino D, Chen I-M, Huntemann M, Palaniappan K, Ladau J, Mukherjee S, Reddy TBK, Nielsen T, Kirton E, Faria JP, Edirisinghe JN, Henry CS, Jungbluth SP, Chivian D, Dehal P, Wood-Charlson EM, Arkin AP, Tringe S, Visel A, IMG/M Data Consortium*, Woyke T, Mouncey NJ, Ivanova NN, Kyrpides NC, Eloe-Fadrosh EM (*JL Klassen is a member of the IGM/M Data Consortium). 2020. A Genomic Catalog of Earth’s Microbiomes. Nature Biotechnology https://www.nature.com/articles/s41587-020-0718-6

Michael R.Fulcher, Marian L.Bolton, Michael D.Millican, José PabloDundore-Arias, JoHandelsman, Jonathan L.Klassen, Kathryn C.Milligan-Myhre, Benjamin E.Wolfe, Linda L.Kinkel, Broadening Participation in Scientific Conferences during the Era of Social Distancing, Trends in Microbiology, September 2020, https://doi.org/10.1016/j.tim.2020.08.004

Grubbs KJ, Surup F, Biedermann PHW, McDonald BR, Klassen JL, Carlson CM, Clardy J and Currie CR (2020) Cycloheximide-Producing Streptomyces Associated With Xyleborinus saxesenii and Xyleborus affinis Fungus-Farming Ambrosia Beetles. Front. Microbiol. 11:562140. doi: 10.3389/fmicb.2020.562140

Trumbo, S., and Klassen, J. 2020. Editorial overview: Hidden players: microbes reshape the insect niche. Curr. Opin. Insect Sci. 39: vi-viii

Wang M, Jarmusch AK, Vargas F, Aksenov AA, Gauglitz JM, Weldon K, Petras D, da Silva R, Quinn R, Melnik AV, van der Hooft JJJ, Caraballo-Rodríguez AM, Nothias LF, Aceves CM, Panitchpakdi M, Brown E, Di Ottavio F, Sikora N, Elijah EO, Labarta-Bajo L, Gentry EC, Shalapour S, Kyle KE, Puckett SP, Watrous JD, Carpenter CS, Bouslimani A, Ernst M, Swafford AD, Zúñiga EI, Balunas MJ, Klassen JL, Loomba R, Knight R, Bandeira N and Dorrestein PC. 2020. Mass spectrometry searches using MASST Nature Biotechnology 38(1):23-26 PMID(31894142) https://www.ncbi.nlm.nih.gov/pubmed/31894142

Klassen, J.L. Ecology helps bound causal explanations in microbiology. Biol Philos (2020) 35: 3. doi.org/10.1007/s10539-019-9728-5 https://link.springer.com/article/10.1007/s10539-019-9728-5

JL Klassen, SR Lee, M Thomas-Poulsen, C Beemelmanns, KH Kim. (2019) Efomycins K and L from a Termite-associated Streptomyces sp. M56 and Their Putative Biosynthetic Origin. Frontiers in Microbiology 10:1739 https://www.frontiersin.org/articles/10.3389/fmicb.2019.01739/abstract

Klassen JL. 2019. Keeping it fresh eLife 8:e48268 https://elifesciences.org/articles/48268

Klassen JL (2018) Defining microbiome function Nature Microbiology volume 3, pages 864–869.

Sarah Kopac, Hannah Beatty, Philip Gialopsos, Marcel Huntemann, Alicia Clum, Alexander Spunde, Manoj Pillay, Krishnaveni Palaniappan, Neha Varghese, Natalia Mikhailova, Dimitrios Stamatis, T. B. K. Reddy, Chris Daum, Vivian Ng, Natalia Ivanova, Nikos Kyrpides, Tanja Woyke, Jonathan L. Klassen. 2018. High-Quality Draft Genome Sequences of Eight Bacteria Isolated from Fungus Gardens Grown by Trachymyrmex septentrionalis Ants. Microbiology Resource Announcements DOI: 10.1128/MRA.00871-18.

Ricardo R. da Silva, Mingxun Wang, Louis-Félix Nothias, Justin J. J. van der Hooft, Andrés Mauricio Caraballo-Rodríguez, Evan Fox, Marcy J. Balunas, Jonathan L. Klassen, Norberto Peporine Lopes, Pieter C. Dorrestein. (2018) Propagating annotations of molecular networks using in silico fragmentation. (2018) PLOS Computational Biology, doi.org/10.1371/journal.pcbi.1006089

H. Guo, R. Benndorf, D. Leichnitz, J. L. Klassen, J. Vollmers, H. Görls, M. Steinacker, C. Weigel, H.-M. Dahse, A.-K. Kaster, Z. W. de Beer, M. Poulsen, C. Beemelmanns. (2017) Isolation, Biosynthesis and Chemical Modifications of Rubterolones A–F: Rare Tropolone Alkaloids from Actinomadura sp. 5-2, Chem. Eur. J. DOI: 10.1002/chem.201701005.

Christine Beemelmanns, Timothy R. Ramadhar, Ki Hyun Kim, Jonathan L. Klassen, Shugeng Cao, Thomas P. Wyche, Yanpeng Hou, Michael Poulsen, Tim S. Bugni, Cameron R. Currie, and Jon Clardy (2017) Macrotermycins A–D, Glycosylated Macrolactams from a Termite-Associated Amycolatopsis sp. M39. Organic Letters, DOI: 10.1021/acs.orglett.6b03831.

Wyche TP, Ruzzini AC, Beemelmanns C, Kim KH, Klassen JL, Cao S, Poulsen M, Bugni TS, Currie CR, Clardy J (2017) Linear Peptides Are the Major Products of a Biosynthetic Pathway That Encodes for Cyclic Depsipeptides. Organic Letters, DOI:10.1021/acs.orglett.7b00545

Kopac SM and Klassen JL (2016) Can They Make It on Their Own? Hosts, Microbes, and the Holobiont Niche. Front. Microbiol. 7:1647. doi: 10.3389/fmicb.2016.01647.

Samantha M. Gromek, Anne A. Sung, Jonathan L. Klassen, Marcy J. Balunas (2016). Draft Genome Sequence of Streptomyces sp. Strain PTY087I2, Isolated from Styela canopus, a Panamanian Tunicate. Genome Announc. September/October 2016 vol. 4 no. 5 e00856-16. doi: 10.1128/genomeA.00856-16.

Theis KR, Dheilly NM, Klassen JL, Brucker RM, Baines JF, Bosch TCG, Cryan JF, Gilbert SF, Goodnight CJ, Lloyd EA, Sapp J, Vandenkoornhuyse P, Zilber-Rosenberg I, Rosenberg E, Bordenstein SR. 2016. Getting the hologenome concept right: an eco-evolutionary framework for hosts and their microbiomes. mSystems 1(2):e00028-16. doi:10.1128/mSystems.00028-16.

Rischer M, Klassen JL, Wolf T, Guo H, Shelest E, Clardy J, Beemelmanns C. 2016. Draft genome sequence of Shewanella sp. strain P1-14-1, a bacterial inducer of settlement and morphogenesis in larvae of the marine hydroid Hydractinia echinata. Genome Announc 4(1):e00003-16. doi:10.1128/genomeA.00003-16.

Jonathan L Klassen, Maja Rischer, Thomas Wolf, Huijuan Guo, Ekaterina Shelest, Jon Clardy, Christine Beemelmanns  Genome Sequences of Three Pseudoalteromonas Strains (P1-8, P1-11, and P1-30), Isolated from the Marine Hydroid Hydractinia echinata (2015) Genome Announcements 3(6): e01380-15

Jonathan L Klassen, Thomas Wolf, Maja Rischer, Huijuan Guo, Ekaterina Shelest, Jon Clardy, Christine Beemelmanns Draft genome sequences of six Pseudoalteromonas strains, P1-7a, P1-9, P1-13-1a, P1-16-1b, P1-25, and P1-26, which induce larval settlement and metamorphosis in Hydractinia echinata (2015) Genome Announcements 3(6): e01477-15

Murfin, K.E., Whooley, A.C., Klassen, J.L., Goodrich-Blair, H. Comparison of Xenorhabdus bovienii bacterial strain genomes reveals diversity in symbiotic functions. 2015. BMC Genomics doi:10.1186/s12864-015-2000-8.

Medema, M.H. et al. [150 authors, including Klassen, J.L.] 2015. Minimum Information about a Biosynthetic Gene cluster. Nature Chemical Biology. Nat Chem Biol 11:625-631

Murfin KE, Lee M, Klassen JL, McDonald BR, Larget B, Forst S, Stock SP, Currie CR, Goodrich-Blair H. 2015. Xenorhabdus bovienii strain diversity impacts coevolution and symbiotic maintenance with Steinernema spp. nematode hosts. mBio 6(3):e00076-15. doi:10.1128/mBio.00076-15.

Klassen, JL (2014) Microbial secondary metabolites and their impacts on insect symbioses. Current Opinion in Insect Science. DOI: 10.1016/j.cois.2014.08.004 [Epub ahead of print].
Klassen, J. L. and Currie, C. R. 2013. ORFcor: identifying and accommodating ORF prediction inconsistencies for phylogenetic analysis. PLoS One 8(3): e58387 (link)

Klassen, J. L. and Currie, C. R. 2012. Gene fragmentation in bacterial draft genomes: extent, consequences and mitigation. BMC Genomics 13: 14 (link) (“Highly Accessed”)

Siddique,T., Penner, T., Klassen, J., Nesbø, C. and Foght, J. M. 2012. Microbial communities involved in methane production by oil sands tailings. Environ. Sci. Technol.46 (17): 9802-9810 (link)

Pitre, M. C., Mayne Correia, P., Mankowski, P. J., Klassen, J. L., Day, M. J., Lovell, N. C. and Currah, R. 2012. Biofilm Growth in human skeletal material from Ancient Mesopotamia. J. Archaeol. Sci. 40 (1): 24-29 (link)

Carr, G., Poulsen, M., Klassen, J. L., Hou, Y., Wyche, T. P., Bugni, T. S., Currie, C. R. and Clardy, J. 2012. Microtermolides A and B from termite-associated Streptomyces sp. and structural revision of vinylamycin. Org. Lett. 14 (11): 2822-2825 (link)

Hou, Y., Braun, D. R., Michel, C. R., Klassen, J. L., Adnani, N., Wyche, T. P. and Bugni, T. S. 2012. UHPLC/HRMS-based secondary metabolomics as a broadly useful tool for rapid analysis of microbial natural products. Anal. Chem. 84 (10): 4277-4283 (link)

Klassen, J. L., Adams, S. M., Bramhacharya, S., Giles, S. S., Goodwin, L. A., Woyke, T. and Currie, C. R. 2011. Draft genome sequence of Streptomyces sp. Wigar10, isolated from a surface-sterilized garlic bulb. J. Bacteriol. 193 (24): 6999-7000

Grubbs, K. J., Biedermann, P. H. W., Suen, G., Adams, S., Moeller, J. A., Klassen, J. L., Goodwin, L. A., Woyke, T., Munk, A. C., Bruce, B., Detter, C., Tapia, R., Han, C. S. and Currie, C. R. 2011. The complete genome sequence of Streptomyces griseus strain XyelbKG-1, an ambrosia beetle—associated actinomycete. J. Bacteriol. 193(11): 2890-2891(link)

Klassen, J. L. and Foght, J. M. 2011. Characterization of Hymenobacter isolates from Victoria Upper Glacier, Antarctica reveals five new species and substantial non-vertical evolution within this genus. Extremophiles 11 (1): 45-57 (link)

Barker, J. D., Klassen, J. L., Sharp, M. J., Fitzsimons, F. J. and Turner, R. J. 2010. Detecting biogeochemical activity in basal ice using fluorescence spectroscopy. Ann. Glaciol. 51 (56): 47-55 (link)

Klassen, J. L. 2010. Phylogenetic and evolutionary patterns in microbial carotenoid biosynthesis are revealed by comparative genomics. PLoS One 5 (6): e11257 (link)

Klassen, J. L. 2009. Pathway evolution by horizontal transfer and positive selection is accommodated by relaxed negative selection upon upstream pathway genes in purple bacterial carotenoid biosynthesis. J. Bacteriol. 191 (24): 7500-7508 (link)

Klassen, J. L., McKay, R. and Foght, J. M. 2009. 2ʹ-Methyl and 1ʹ-xylosyl derivatives of 2ʹ-hydroxyflexixanthin are major carotenoids of Hymenobacter species. Tetrahedron Lett. 50 (22): 2656-2660 (link)

Aislabie, J., Jordan, S., Ayton, J., Klassen, J. L., Barker, G. M. and Turner, S. 2009. Bacterial diversity associated with ornithogenic soil of the Ross Sea region, Antarctica. Can. J. Microbiol. 55 (1): 21-36 (link)

Klassen, J. L. and Foght, J. M. 2008. Differences in carotenoid composition among Hymenobacter and related strains support a tree-like model of carotenoid evolution. Appl. Environ. Microbiol. 74 (7): 2016-2022 (link)