Lab Publications

• Kelliher JM, Mirzayi C, Bordenstein SR, Oliver A, Kellogg CA, Hatcher EL, Berg M, Baldrian P, Aljumaah M, Miller CML, Mungall C, Novak V, Palucki A, Smith E, Tabassum N, Bonito G, Brister JR, Chain PSJ, Chen M, Degregori S, Dundore-Arias JP, Emerson JB, Fernandes VMC, Flores R, Gonzalez A, Hansen ZA, Jackson SA, Moustafa AM, Northen TR, Pariente N, Pett-Ridge J, Record S, Reji L, Reysenbach A-L, Rich VI, Richardson L, Roux S, Schriml LM, Shabman RS, Sierra MA, Sullivan MB, Sundaramurthy P, Thibault KM, Thompson LR, Tighe S, Vereen E, STREAMS Consortium*, and Eloe-Fadrosh EA * JL Klassen is a member of the STREAMS Consortium. 2025. STREAMS guidelines: standards for technical reporting in environmental and host-associated microbiome studies Nature Microbiology 10:3059-3068 PMID(41326814)
• Green EA, Klepacki I, and Klassen JL. 2025. Isolation and characterization of mollicute symbionts from a fungus-growing ant reveals high niche overlap leading to co-exclusion mBio 16(7):e00893-25 PMID(40492740)
• Bittleston L, Gilbert J, Klassen J, Mackelprang R, Mandel MJ, Newton RJ, Paudel A, Rodriguez-Verdugo A, Shade A, Wilhelm RC, and Zhang Y. 2025. Embracing the systems complexity of microbial ecology and evolution: call for papers mSystems :e00091-25 PMID(40099871)
• Kyle KE and Klassen JL. 2025. Untrimmed ITS2 metabarcode sequences cause artificially reduced abundances of specific fungal taxa Applied and Environmental Microbiology 91(1):e01537-24 PMID(39723817)
• Pavlopoulos GA, Baltoumas FA, Liu S, Selvitopi O, Camargo AP, Nayfach S, Azad A, Roux S, Call L, Ivanova NN, Chen IM, Paez-Espino D, Karatzas E, Novel Metagenome Protein Families Consortium, Iliopoulos I, Konstantinidis K, Tiedje JM, Pett-Ridge J, Baker D, Visel A, Ouzounis CA, Ovchinnikov S, Buluç A & Kyrpides NC *Klassen JL is a member of the Novel Metagenome Protein Families Consortium. 2023. Unraveling the functional dark matter through global metagenomics Nature 622:594-602 PMID(37821698)
• Klassen JL. 2023. Resistance waxes for mutualists protected by wasp secretions PNAS 120(36):e2311815120 PMID(37611065)
• 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 PMID(37319116)
• Truchon AN, Dalsing BL, Khokhani D, MacIntyre A, McDonald BR, Ailloud F, Klassen J, Gonzalez-Orta ET, Currie C, Prior P, Power TM, Allen C. 2023. Plant pathogenic Ralstonia phylotypes evolved divergent respiratory strategies and behaviors to thrive in xylem mBio :e03188-22 PMID(36744950)
• Milligan-McClellan KC, Dundore-Arias JP, Klassen JL, Shade A, Kinkel LL, Wolfe BE. 2022. Deciphering the Microbiome: Integrating Theory, New Technologies, and Inclusive Science mSystems :e00583-22 PMID(36073805)
• Green EA and Klassen JL. 2022. Trachymyrmex septentrionalis ant microbiome assembly is unique to individual colonies and castes. mSphere 7(4):e00989-21 PMID(35862804)
• 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 PMID(35732113)
• 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 PMID(34342533)
• 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). 2021. A genomic catalog of Earth’s microbiomes Nature Biotechnology 39:499-509 PMID(33169036)
• Green EA, Smedley SR, and Klassen JL. 2021. North American fireflies host low bacterial diversity Microb Ecol : PMID(33609143)
• Portelinha J, Duay SS, Yu SI, Heilemann K, Libardo MDJ, Juliano SA, Klassen JL*, and Angeles-Boza* AM. 2021. Antimicrobial Peptides and Copper(II) Ions: Novel Therapeutic Opportunities Chem. Rev. 121(4):2648-2712 PMID(33524257)
• Goldstein SL and Klassen JL. 2020. Pseudonocardia symbionts of fungus-growing ants and the evolution of defensive secondary metabolism Front. Microbiol. 11:621041 PMID(33424822)
• Green EA and Klassen JL. 2020. Draft Genome Sequence of Spiroplasma platyhelix ATCC 51748,isolated from a Dragonfly Microbiology Resource Announcements 9(47):e00422-20 PMID(33214290)
• Grubbs KJ, Surup F, Biedermann PHW, McDonald BR, Klassen J, Carlson CM, Clardy J, Currie CR. 2020. Cycloheximide-producing Streptomyces associated with Xyleborinus saxesenii and Xyleborus affinis fungus-farming ambrosia beetles Frontiers in Microbiology 11:562140 PMID(33101237)
• 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. 2020. Broadening participation in scientific conferences during the era of social distancing Trends in Microbiology 28(12):949-952 PMID(32978058)
• Trumbo S and Klassen J. 2020. Editorial overview: hidden players: microbes reshape the insect niche Current Opinion in Insect Science 39:vi-ix PMID(32546376)
• 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)
• Klassen JL. 2020. Ecology helps bound causal explanations in microbiology Biology & Philosophy 35:3
• Klassen JL, Lee SR, Poulsen M, Beemelmanns C, Kim KH. 2019. Efomycins K and L From a Termite-Associated Streptomyces sp. M56 and Their Putative Biosynthetic Origin Frontiers in Microbiology 10:1739 PMID(31447803)
• Klassen JL. 2019. Keeping it fresh eLife 8:e48268 PMID(31188127)
• McDonald BR, Chevrette MG, Klassen JL, Horn HA, Caldera EJ, Wendt-Pienkowski E, Cafaro MJ, Ruzzini AC, Van Arnam EB, Weinstock GM, Gerardo NM, Poulsen M, Suen G, Clardy J, Currie CR. 2019. Biogeography and microscale diversity shape the biosynthetic Potential of fungus-growing ant-associated Pseudonocardia bioRxiv :http://dx.doi.org/10.1101/545640
• Lee KM, Adams M, and Klassen JL. 2019. Evaluating DESS as a storage medium for microbial ecology studies PeerJ 7:e6414 PMID(30740279)
• 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. 2019. The antimicrobial potential of Streptomyces from insect microbiomes Nature Communications 10:516 PMID(30705269)
• Goldstein S, Beka L, Graf J, Klassen JL. 2019. Evaluation of strategies for the assembly of diverse bacterial genomes using MinION long read sequencing BMC Genomics 20:23 PMID(30626323)
• Klassen JL. 2018. Defining microbiome function Nature Microbiology 3:864-869 PMID(30046174)
• Kopac S, Beatty H, Gialoposos 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, and Klassen JL. 2018. High quality draft genomes of eight bacteria isolated from fungus gardens grown by Trachymyrmex septentrionalis ants Microbiology Resource Announcements 7:e00871-18 PMID(30533809)
• da Silva R, Wang M, Nothias L-F, van der Hooft JJJ, Caraballo-Rodríguez AM, Fox E, Balunas MJ, Klassen JL, Lopes NP, and Dorrestein PC. 2018. Propagating annotations of molecular networks using in silico fragmentation PLOS Computational Biology 14(4):e1006089 PMID(29668671)
• H Guo, R Benndorf, D Leichnitz, JL Klassen, J Vollmers, H Görls, M Steinacker, C Weigel, H-M Dahse, A-K Kaster, ZW de Beer, M Poulsen, and C Beemelmanns. 2017. Isolation, Biosynthesis and Chemical Modifications of Rubterolones A–F, Rare Tropolone Alkaloids from Actinomadura sp. 5-2 Chemistry - A European Journal 23(39):9338-9345 PMID(28463423)
• 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 19:1772-1775 PMID(28326787)
• Beemelmanns C, Ramadhar TR, Kim KH, Klassen JL, Cao S, Wyche TP, Hou Y, Poulsen M, Bugni TS, Currie CR, Clardy J. 2017. Macrotermycins A-D, glycosylated macrolactams from a termite-associated Amycloatopsis sp. M39 Organic Letters 19(5):1000-1003 PMID(28207275)
• SM Kopac, JL Klassen. 2016. Can they make it on their own? Hosts, microbes, and the holobiont niche Frontiers in Microbiology (7):1647 PMID(27818648)
• JA deMayo, KR Mass, JL Klassen, MJ Balunas. 2016. Draft Genome Sequence of Streptomyces sp. AVP053U2 Isolated from Styela clava, a Tunicate Collected in Long Island Sound Genome Announcements 4(5):e00874-16 PMID(27738023)
• Gromek SM, Sung, AA, Klassen JL, Balunas MJ. 2016. Draft genome sequence of Streptomyces sp. strain PTY087I2, isolated from Styela canopus, a Panamanian tunicate Genome Announcements 4(5):e00856-16 PMID(27634989)
• Theis KR, Dheilly NMM, Klassen JL, Brucker RM, Baines JF, Bosch TCG, Cryan JF, Gilbert SF, Goodnight CG, Lloyd EA, Sapp J, Vandenkoornhuyse P, Zilber-Rosenberg I, Rosenberg E, and Bordenstein SR. 2016. Getting the Hologenome Concept Right: an Eco-Evolutionary Framework for Hosts and Their Microbiomes mSystems 1(2):e00028-16 PMID(27822520)
• 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 Hydractini Genome Announcements 4(1):e00003-16. PMID(26893410)
• Klassen JL, Wolf T,Rischer M, Guo H, Shelest E, Clardy C, Beemelmanns C. 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 Metamor Genome Announcements 3(6):e01477-15 PMID(26679587)
• Klassen JL, Rischer M, Wolf T, Guo H, Shelest E, Clardy J, Beemelmanns C. 2015. Genome Sequences of Three Pseudoalteromonas Strains (P1-8, P1-11, and P1-30), Isolated from the Marine Hydroid Hydractinia echinata Genome Announcements 3(6):e01380-15 PMID(26659670)
• Murfin KE, Whooley AC, Jonathan L. Klassen JK Goodrich-Blair H. 2015. Comparison of Xenorhabdus bovienii bacterial strain genomes reveals diversity in symbiotic functions BMC Genomics 16:889 PMID(26525894)
• Medema et al. . 2015. Minimum Information about a Biosynthetic Gene cluster Nature Chemical Biology 11:625-631 PMID(26284661)
• Murfin KE, Lee M-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 PMID(26045536)
• Klassen JL. 2014. Microbial secondary metabolites and their impacts on insect symbioses Current Opinion in Insect Science 4:15-22 PMID(28043403)
• An D, Caffrey S, Soh J, Agrawal A, Brown D, Budwill K, Dong X, Dunfield P, Foght J, Gieg L, Hallam S, Hanson N, He Z, Jack T, Klassen J, Konwar K, Kuatsjah E, Li C, Larter S, Leopatra V, Nesbø C, Oldenburg T, Page A, Ramos-Padron E, Rochman F, Saidi-Mehrabad A, Sensen C, Sipahimalani P, Song Y, Wilson S, Wolbring G, Wong G, and Voordouw G. 2013. Metagenomics of Hydrocarbon Resource Environments Indicates Aerobic Taxa and Genes to be Unexpectedly Common Environmental Science and Technology 47(18):10708-10717 PMID(23889694)
• Klassen JL, Currie CR. 2013. ORFcor: identifying and accommodating ORF prediction inconsistencies for phylogenetic analysis. PLoS ONE 8(3):e58387 PMID(23484025)
• Siddique T, Penner T, Klassen J, Nesbø C, Foght JM. 2012. Microbial communities involved in methane production from hydrocarbons in oil sands tailings. Environmental Science and Technology 46(17):9802-10 PMID(22894132)
• Pitre MC, Mayne Correia P, Mankowski PJ, Klassen JL, Day MJ, Lovell NC and Currah R. 2013. Biofilm Growth in human skeletal material from Ancient Mesopotamia Journal of Archaeological Science 40(1):24-29
• Carr G, Poulsen M, Klassen JL, Hou Y, Wyche TP, Bugni TS, Currie CR, Clardy J. 2012. Microtermolides A and B from termite-associated Streptomyces sp. and structural revision of vinylamycin. Organic Letters 14(11):2822-5 PMID(22591554)
• Hou Y, Braun DR, Michel CR, Klassen JL, Adnani N, Wyche TP, Bugni TS. 2012. Microbial strain prioritization using metabolomics tools for the discovery of natural products. Analytical Chemistry 84(10):4277-83 PMID(22519562)
• Klassen JL, Currie CR. 2012. Gene fragmentation in bacterial draft genomes: extent, consequences and mitigation. BMC Genomics 13:14 PMID(22233127)
• Klassen JL, Adams SM, Bramhacharya S, Giles SS, Goodwin LA, Woyke T, Currie CR. 2011. Draft genome sequence of Streptomyces sp. strain Wigar10, isolated from a surface-sterilized garlic bulb. Journal of Bacteriology 193(24):6999-7000 PMID(22123757)
• 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. 2011. The Complete Genome Sequence of Streptomyces cf. griseus (XyelbKG-1), an Ambrosia Beetle-Associated Actinomycete. Journal of Bacteriology : PMID(21460079)
• Klassen JL, Foght JM. 2011. Characterization of Hymenobacter isolates from Victoria Upper Glacier, Antarctica reveals five new species and substantial non-vertical evolution with Extremophiles 15(1):45-57 PMID(21104190)
• Klassen JL. 2010. Phylogenetic and evolutionary patterns in microbial carotenoid biosynthesis are revealed by comparative genomics. PLoS ONE 5(6):e11257 PMID(20582313)
• Barker JD, Klassen JL, Sharp MJ, Fitzsimons FJ and Turner RJ. 2010. Detecting biogeochemical activity in basal ice using fluorescence spectroscopy Annals of Glaciology 51(56):47-55
• Klassen JL. 2009. Pathway Evolution by Horizontal Transfer and Positive Selection Is Accommodated by Relaxed Negative Selection upon Upstream Pathway Genes in Purple Bacterial Carotenoid Biosynthesis Journal of Bacteriology 191(24):7500-8 PMID(19820094)
• Klassen JL, McKay R, Foght JM. 2009. 2′-Methyl and 1′-xylosyl derivatives of 2′-hydroxyflexixanthin are major carotenoids of Hymenobacter species Tetrahedron Letters 50(22):2656-2660
• Aislabie J, Jordan S, Ayton J, Klassen JL, Barker GM and Turner S. 2009. Bacterial diversity associated with ornithogenic soil of the Ross Sea region, Antarctica Canadian Journal of Microbiology 55(1):21-36 PMID(19190698)
• Klassen JL, Foght JM. 2008. Differences in carotenoid composition among hymenobacter and related strains support a tree-like model of carotenoid evolution. Applied and Environmental Microbiology 74(7):2016-22 PMID(18263749)
• Boraston AB, Healey M, Klassen J, Ficko-Blean E, Lammerts van Bueren A, Law V. 2006. A Structural and Functional Analysis of a-Glucan Recognition by Family 25 and 26 Carbohydrate-binding Modules Reveals a Conserved Mode of Starch Recognition Journal of Biological Chemistry 281(1):587-98 PMID(16230347)
• Hill JE, Hemmingsen SM, Goldade BG, Dumonceaux TJ, Klassen J, Zijlstra RT, Goh SH, Van Kessel AG. 2005. Comparison of ileum microflora of pigs fed corn-, wheat-, or barley-based diets by chaperonin-60 sequencing and quantitative PCR. Applied and Environmental Microbiology 71(2):867-75 PMID(15691942)