Publications: Jonathan Klassen
2023
- Resistance waxes for mutualists protected by wasp secretions.
Klassen JL
Proceedings of the National Academy of Sciences of the United States of America (2023) 120(36):e2311815120 PMC8983117 10.1073/pnas.2311815120 - ants promote fungus garden hygiene using -derived metabolite cues.
Kyle KE, Puckett SP, Caraballo-Rodríguez AM, Rivera-Chávez J, Samples RM, Earp CE, Raja HA, Pearce CJ, Ernst M, van der Hooft JJJ, Adams ME, Oberlies NH, Dorrestein PC, Klassen JL, Balunas MJ
Proceedings of the National Academy of Sciences of the United States of America (2023) 120(25):e2219373120 PMC10288546 10.7910/DVN/MAYHMQ 2022
- Trachymyrmex septentrionalis Ant Microbiome Assembly Is Unique to Individual Colonies and Castes.
Green EA, Klassen JL
mSphere (2022) 7(4):e0098921 PMC3998144 10.1093/bioinformatics/btu033 2021
- Chemical Gradients of Plant Substrates in an Fungus Garden.
Caraballo-Rodríguez AM, Puckett SP, Kyle KE, Petras D, da Silva R, Nothias LF, Ernst M, van der Hooft JJJ, Tripathi A, Wang M, Balunas MJ, Klassen JL, Dorrestein PC
mSystems (2021) 6(4):e0060121 PMC8409729 10.1128/mSystems.00601-21 - North American Fireflies Host Low Bacterial Diversity.
Green EA, Smedley SR, Klassen JL
Microbial ecology (2021) 82(3):793-804 10.7717/peerj.1190 - Symbionts of Fungus-Growing Ants and the Evolution of Defensive Secondary Metabolism.
Goldstein SL, Klassen JL
Frontiers in microbiology (2021) 11:621041 PMC7793712 10.3389/fmicb.2020.621041 2020
- Draft Genome Sequence of Spiroplasma platyhelix ATCC 51748, Isolated from a Dragonfly.
Green EA, Klassen JL
Microbiology resource announcements (2020) 9(47): PMC7679083 10.1128/MRA.00422-20 - Cycloheximide-Producing Associated With and Fungus-Farming Ambrosia Beetles.
Grubbs KJ, Surup F, Biedermann PHW, McDonald BR, Klassen JL, Carlson CM, Clardy J, Currie CR
Frontiers in microbiology (2020) 11:562140 PMC7546818 10.3389/fmicb.2020.562140 - Broadening Participation in Scientific Conferences during the Era of Social Distancing.
Fulcher MR, Bolton ML, Millican MD, Michalska-Smith MJ, Dundore-Arias JP, Handelsman J, Klassen JL, Milligan-Myhre KC, Shade A, Wolfe BE, Kinkel LL
Trends in microbiology (2020) 28(12):949-952 PMC7507981 10.1016/j.tim.2020.08.004 - Mass spectrometry searches using MASST.
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, Dorrestein PC
Nature biotechnology (2020) 38(1):23-26 PMC7236533 10.1007/s11306-007-0082-2 2019
- Efomycins K and L From a Termite-Associated sp. M56 and Their Putative Biosynthetic Origin.
Klassen JL, Lee SR, Poulsen M, Beemelmanns C, Kim KH
Frontiers in microbiology (2019) 10:1739 PMC6691879 10.3389/fmicb.2019.01739 - Keeping it fresh.
Klassen JL
eLife (2019) 8: PMC6561751 10.7554/eLife.48268 - Evaluation of DESS as a storage medium for microbial community analysis.
Lee KM, Adams M, Klassen JL
PeerJ (2019) 7:e6414 PMC6368006 10.7717/peerj.6414 - The antimicrobial potential of Streptomyces from insect microbiomes.
Chevrette MG, Carlson CM, Ortega HE, Thomas C, Ananiev GE, Barns KJ, Book AJ, Cagnazzo J, Carlos C, Flanigan W, Grubbs KJ, Horn HA, Hoffmann FM, Klassen JL, Knack JJ, Lewin GR, McDonald BR, Muller L, Melo WGP, Pinto-Tomás AA, Schmitz A, Wendt-Pienkowski E, Wildman S, Zhao M, Zhang F, Bugni TS, Andes DR, Pupo MT, Currie CR
Nature communications (2019) 10(1):516 PMC6355912 10.1038/s41467-019-08438-0 - Evaluation of strategies for the assembly of diverse bacterial genomes using MinION long-read sequencing.
Goldstein S, Beka L, Graf J, Klassen JL
BMC genomics (2019) 20(1):23 PMC6325685 10.1186/s12864-018-5381-7 2018
- High-Quality Draft Genome Sequences of Eight Bacteria Isolated from Fungus Gardens Grown by Trachymyrmex septentrionalis Ants.
Kopac S, Beatty H, Gialopsos P, Huntemann M, Clum A, Spunde A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy TBK, Daum C, Ng V, Ivanova N, Kyrpides N, Woyke T, Klassen JL
Microbiol Resour Announc (2018) 7(2): (PMC6211366) 10.1128/MRA.00871-18 - Defining microbiome function.
Klassen JL
Nat Microbiol (2018) 3(8):864-869 10.1038/s41564-018-0189-4 - Propagating annotations of molecular networks using in silico fragmentation.
da Silva RR, Wang M, Nothias LF, van der Hooft JJJ, Caraballo-Rodríguez AM, Fox E, Balunas MJ, Klassen JL, Lopes NP, Dorrestein PC
PLoS Comput. Biol. (2018) 14(4):e1006089 (PMC5927460) 10.1371/journal.pcbi.1006089 2017
- Isolation, Biosynthesis and Chemical Modifications of Rubterolones A-F: Rare Tropolone Alkaloids from Actinomadura sp. 5-2.
Guo H, Benndorf R, Leichnitz D, Klassen JL, Vollmers J, Görls H, Steinacker M, Weigel C, Dahse HM, Kaster AK, de Beer ZW, Poulsen M, Beemelmanns C
Chemistry (2017) 23(39):9338-9345 - Linear Peptides Are the Major Products of a Biosynthetic Pathway That Encodes for Cyclic Depsipeptides.
Wyche TP, Ruzzini AC, Beemelmanns C, Kim KH, Klassen JL, Cao S, Poulsen M, Bugni TS, Currie CR, Clardy J
Org. Lett. (2017) 19(7):1772-1775 (PMC6013059) - Macrotermycins A-D, Glycosylated Macrolactams from a Termite-Associated Amycolatopsis sp. M39.
Beemelmanns C, Ramadhar TR, Kim KH, Klassen JL, Cao S, Wyche TP, Hou Y, Poulsen M, Bugni TS, Currie CR, Clardy J
Org. Lett. (2017) 19(5):1000-1003 (PMC6006516) 2016
- Getting the Hologenome Concept Right: an Eco-Evolutionary Framework for Hosts and Their Microbiomes.
Theis KR, Dheilly NM, Klassen JL, Brucker RM, Baines JF, Bosch TC, Cryan JF, Gilbert SF, Goodnight CJ, Lloyd EA, Sapp J, Vandenkoornhuyse P, Zilber-Rosenberg I, Rosenberg E, Bordenstein SR
mSystems (2016) 1(2): (PMC5069740) - Can They Make It on Their Own? Hosts, Microbes, and the Holobiont Niche.
Kopac SM, Klassen JL
Front Microbiol (2016) 7:1647 (PMC5073103) - Draft Genome Sequence of Streptomyces sp. AVP053U2 Isolated from Styela clava, a Tunicate Collected in Long Island Sound.
deMayo JA, Maas KR, Klassen JL, Balunas MJ
Genome Announc (2016) 4(5): (PMC5064096) - Draft Genome Sequence of Streptomyces sp. Strain PTY087I2, Isolated from Styela canopus, a Panamanian Tunicate.
Gromek SM, Sung AA, Klassen JL, Balunas MJ
Genome Announc (2016) 4(5): (PMC5026429) - 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.
Rischer M, Klassen JL, Wolf T, Guo H, Shelest E, Clardy J, Beemelmanns C
Genome Announc (2016) 4(1): (PMC4759057) 2015
- 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.
Klassen JL, Wolf T, Rischer M, Guo H, Shelest E, Clardy J, Beemelmanns C
Genome Announc (2015) 3(6): (PMC4683232) - Genome Sequences of Three Pseudoalteromonas Strains (P1-8, P1-11, and P1-30), Isolated from the Marine Hydroid Hydractinia echinata.
Klassen JL, Rischer M, Wolf T, Guo H, Shelest E, Clardy J, Beemelmanns C
Genome Announc (2015) 3(6): (PMC4675935) - Comparison of Xenorhabdus bovienii bacterial strain genomes reveals diversity in symbiotic functions.
Murfin KE, Whooley AC, Klassen JL, Goodrich-Blair H
BMC Genomics (2015) 16:889 (PMC4630870) - Minimum Information about a Biosynthetic Gene cluster.
Medema MH, Kottmann R, Yilmaz P, Cummings M, Biggins JB, Blin K, de Bruijn I, Chooi YH, Claesen J, Coates RC, Cruz-Morales P, Duddela S, Düsterhus S, Edwards DJ, Fewer DP, Garg N, Geiger C, Gomez-Escribano JP, Greule A, Hadjithomas M, Haines AS, Helfrich EJ, Hillwig ML, Ishida K, Jones AC, Jones CS, Jungmann K, Kegler C, Kim HU, Kötter P, Krug D, Masschelein J, Melnik AV, Mantovani SM, Monroe EA, Moore M, Moss N, Nützmann HW, Pan G, Pati A, Petras D, Reen FJ, Rosconi F, Rui Z, Tian Z, Tobias NJ, Tsunematsu Y, Wiemann P, Wyckoff E, Yan X, Yim G, Yu F, Xie Y, Aigle B, Apel AK, Balibar CJ, Balskus EP, Barona-Gómez F, Bechthold A, Bode HB, Borriss R, Brady SF, Brakhage AA, Caffrey P, Cheng YQ, Clardy J, Cox RJ, De Mot R, Donadio S, Donia MS, van der Donk WA, Dorrestein PC, Doyle S, Driessen AJ, Ehling-Schulz M, Entian KD, Fischbach MA, Gerwick L, Gerwick WH, Gross H, Gust B, Hertweck C, Höfte M, Jensen SE, Ju J, Katz L, Kaysser L, Klassen JL, Keller NP, Kormanec J, Kuipers OP, Kuzuyama T, Kyrpides NC, Kwon HJ, Lautru S, Lavigne R, Lee CY, Linquan B, Liu X, Liu W, Luzhetskyy A, Mahmud T, Mast Y, Méndez C, Metsä-Ketelä M, Micklefield J, Mitchell DA, Moore BS, Moreira LM, Müller R, Neilan BA, Nett M, Nielsen J, O'Gara F, Oikawa H, Osbourn A, Osburne MS, Ostash B, Payne SM, Pernodet JL, Petricek M, Piel J, Ploux O, Raaijmakers JM, Salas JA, Schmitt EK, Scott B, Seipke RF, Shen B, Sherman DH, Sivonen K, Smanski MJ, Sosio M, Stegmann E, Süssmuth RD, Tahlan K, Thomas CM, Tang Y, Truman AW, Viaud M, Walton JD, Walsh CT, Weber T, van Wezel GP, Wilkinson B, Willey JM, Wohlleben W, Wright GD, Ziemert N, Zhang C, Zotchev SB, Breitling R, Takano E, Glöckner FO
Nat. Chem. Biol. (2015) 11(9):625-31 (PMC5714517) - Xenorhabdus bovienii Strain Diversity Impacts Coevolution and Symbiotic Maintenance with Steinernema spp. Nematode Hosts.
Murfin KE, Lee MM, Klassen JL, McDonald BR, Larget B, Forst S, Stock SP, Currie CR, Goodrich-Blair H
MBio (2015) 6(3):e00076 (PMC4462624) 2014
- Microbial secondary metabolites and their impacts on insect symbioses.
Klassen JL
Curr Opin Insect Sci (2014) 4:15-22 2013
- ORFcor: identifying and accommodating ORF prediction inconsistencies for phylogenetic analysis.
Klassen JL, Currie CR
PLoS ONE (2013) 8(3):e58387 (PMC3590147) 2012
- Microtermolides A and B from termite-associated Streptomyces sp. and structural revision of vinylamycin.
Carr G, Poulsen M, Klassen JL, Hou Y, Wyche TP, Bugni TS, Currie CR, Clardy J
Org. Lett. (2012) 14(11):2822-5 (PMC3365539) - Microbial strain prioritization using metabolomics tools for the discovery of natural products.
Hou Y, Braun DR, Michel CR, Klassen JL, Adnani N, Wyche TP, Bugni TS
Anal. Chem. (2012) 84(10):4277-83 (PMC3352271) - Gene fragmentation in bacterial draft genomes: extent, consequences and mitigation.
Klassen JL, Currie CR
BMC Genomics (2012) 13:14 (PMC3322347) 2011
- Draft genome sequence of Streptomyces sp. strain Wigar10, isolated from a surface-sterilized garlic bulb.
Klassen JL, Adams SM, Bramhacharya S, Giles SS, Goodwin LA, Woyke T, Currie CR
J. Bacteriol. (2011) 193(24):6999-7000 (PMC3232846) - Genome sequence of Streptomyces griseus strain XylebKG-1, an ambrosia beetle-associated actinomycete.
Grubbs KJ, Biedermann PH, Suen G, Adams SM, Moeller JA, Klassen JL, Goodwin LA, Woyke T, Munk AC, Bruce D, Detter C, Tapia R, Han CS, Currie CR
J. Bacteriol. (2011) 193(11):2890-1 (PMC3133108) 2010
- Characterization of Hymenobacter isolates from Victoria Upper Glacier, Antarctica reveals five new species and substantial non-vertical evolution within this genus.
Klassen JL, Foght JM
Extremophiles (2010) 15(1):45-57 - Phylogenetic and evolutionary patterns in microbial carotenoid biosynthesis are revealed by comparative genomics.
Klassen JL
PLoS ONE (2010) 5(6):e11257 (PMC2889829) 2009
- Pathway evolution by horizontal transfer and positive selection is accommodated by relaxed negative selection upon upstream pathway genes in purple bacterial carotenoid biosynthesis.
Klassen JL
J. Bacteriol. (2009) 191(24):7500-8 (PMC2786601) - Bacterial diversity associated with ornithogenic soil of the Ross Sea region, Antarctica.
Aislabie J, Jordan S, Ayton J, Klassen JL, Barker GM, Turner S
Can. J. Microbiol. (2009) 55(1):21-36 2008
- Differences in carotenoid composition among hymenobacter and related strains support a tree-like model of carotenoid evolution.
Klassen JL, Foght JM
Appl. Environ. Microbiol. (2008) 74(7):2016-22 (PMC2292609)