Publications
The Microbiology Doctoral Training Program is a research-intensive academic program. Our students are integral members of research teams, leading to a constant stream of well-respected published work.
Please see below for a list of papers published January-October 2026 authored by MDTP students.
Larsen CIS, Abrahams RR, Majumder K. Molecular Mimics: How Viral Genomes Dupe Their Host by Usurping CTCF to Establish Infection. Viruses. 2026 Apr 10;18(4):456. doi: 10.3390/v18040456. PMID: 42043245; PMCID: PMC13120354.
Larsen CIS, Abrahams RR, Guertler R, Wilion EM, Erata E, Sykes ZH, Stoica L, Thirumoorthy G, Divya S, Rai R, Hofer EK, Hart E, Gamm DM, Fuller MS, Majumder K. CTCF regulates wild-type and recombinant AAV gene expression by shaping viral chromatin. bioRxiv [Preprint]. 2026 Jun 3:2026.06.03.729793. doi: 10.64898/2026.06.03.729793. PMID: 42282747; PMCID: PMC13252373.
Abrahams RR, Larsen CIS, Ha R, Majumder K. The interaction between virus-bound KLF4 and host-bound PARP1 directs the localization of wild-type adeno-associated virus type 2 (wtAAV2) to cellular sites of DNA damage. J Virol. 2026 May 19;100(5):e0030626. doi: 10.1128/jvi.00306-26. Epub 2026 Apr 29. PMID: 42053296; PMCID: PMC13185594.
Park H, Kingstad-Bakke B, Cleven T, Aguilar CC, Bussan H, Suresh M. Innate imprinting of transcriptional trajectories governs respiratory TRM fate and persistence. Cell Rep. 2026 Mar 24;45(4):117197. doi: 10.1016/j.celrep.2026.117197. Epub ahead of print. PMID: 41886452.
Li D, Wuerzberger-Davis SM, Chen Y, Phan FP, Yu M, Lisiero DN, Aguilar CC, Cleven T, Tejera MM, Khatri P, Medina N, Chen YC, Wang N, Tsourkas P, Ong I, Bednarski JJ, Dinh HQ, Hoffmann A, Sleckman BP, Suzuki A, Roopra A, Suresh M, Wang D, Miyamoto S. NF-κB/RelA signaling required for CD40-induced humoral immunity depends on specific NEMO lysine residues in mice. EMBO J. 2026 Sep;45(17):6229-6266. doi: 10.1038/s44318-026-00875-0. Epub 2026 Jul 30. PMID: 42533086; PMCID: PMC13534677.
Appel AE, Goetsch AG, van Wijngaarden EW, Novacek DJ, Burnham PM, Silberstein MN, Hershey DM. Diversification of biofilm architecture among freshwater Pararheinheimera isolates. Appl Environ Microbiol. 2026 Sep 23;92(9):e0040026. doi: 10.1128/aem.00400-26. Epub 2026 Aug 28. PMID: 42663477; PMCID: PMC13599514.
Barnes KL, Davis NM, Erazo BJ, Cataldo KM, Bertges EH, Knoll LJ. Isolation, validation, and long-term culture of mouse ear fibroblasts. Biol Open. 2026 May 15;15(5):bio062483. doi: 10.1242/bio.062483. Epub 2026 May 20. PMID: 42046527; PMCID: PMC13225709.
Vemuganti V, Kang JW, Zhang Q, McGregor ER, Hilser JR, Aquino-Martinez R, Harding S, Harpt JL, Beck KR, Bussan H, Kuehn JF, Deming Y, Studer R, Johnson SC, Asthana S, Zetterberg H, Blennow K, Engelman CD, Allayee H, Anderson RM, Ulland TK, Bäckhed F, Bendlin BB, Rey FE. Gut bacterial metabolite imidazole propionate potentiates Alzheimer’s disease pathology. Nat Commun. 2026 Jun 26;17(1):8017. doi: 10.1038/s41467-026-74744-z. PMID: 42362546; PMCID: PMC13454616.
Cataldo KM, Davis NM, Knoll LJ. Kinase inhibitors in organoid media influence Toxoplasma gondii growth and development. Microbiol Spectr. 2026 Apr 3;14(5):e0347225. doi: 10.1128/spectrum.03472-25. Epub ahead of print. PMID: 41930945; PMCID: PMC13141834.
Nickles GR, Stokes CK, Narh DL, Lynn KMT, Fuqua SR, Bryan C, Allen BM, Bivins CP, Woo Bok J, Brewer JS, Buthelezi ST, Clark JPRM, Coon KL, Corby LR, Coetzee MPA, Dewing C, Duong TA, Harris MA, Keller NP, Kopotsa K, Lane FA, Nichols HL, Nieuwoudt A, Nuñez MA, Medina Munoz ME, Park SC, Pham NQ, Ryan KT, Solís M, Vilgalys R, Wallace JM, Wang YW, Wingfield BD, Wingfield MJ, Worley TK, Zallek TA, Zamanian M, Hoeksema JD, Drott MT, Pringle A. Equipped for success: genomes and metabolomes of the European Amanita muscaria are conserved in its novel South African range. New Phytol. 2026 May;250(3):1863-1883. doi: 10.1111/nph.71064. Epub 2026 Mar 12. PMID: 41820030; PMCID: PMC13062730.
Souza JM, Silva LAF, Casali DM, Souza JCSM, Wolfe LA, Skarlupka JH, Zuniga-Chaves I, Steinberger AJ, Deblois CL, Scheftgen AJ, Lelis ALJ, Leiva T, Rodrigues MC, Barroso JPR, Lasmar PVF, Suen G, Millen DD. Rumen and cecum microbial dynamics following narasin inclusion in Nellore cattle diets. Front Microbiol. 2026 Feb 13;17:1645979. doi: 10.3389/fmicb.2026.1645979. PMID: 41767570; PMCID: PMC12946139.
Freeman MJ, Eral NJ, Debrine AM, Stevenson DM, Amador-Noguez D, Sauer J-D. Understanding the role of pyruvate dehydrogenase in Listeria monocytogenes virulence. Infect Immun. 2026 Jul 14;94(7):e0050525. doi: 10.1128/iai.00505-25. Epub 2026 May 29. PMID: 42214391; PMCID: PMC13367045.
Dobrila HA, Licha H, Hryckowian AJ. EndD mediates butyrate-dependent toxin release and sporulation in Clostridioides difficile. J Bacteriol. 2026 Oct 6:e0034126. doi: 10.1128/jb.00341-26. Epub ahead of print. PMID: 42836844. Dobrila HA, Licha H, Hryckowian AJ. EndD mediates butyrate-dependent toxin release in Clostridioides difficile. bioRxiv [Preprint]. 2026 Jun 23:2026.06.22.733756. doi: 10.64898/2026.06.22.733756. Update in: J Bacteriol. 2026 Oct 6:e0034126. doi: 10.1128/jb.00341-26. PMID: 42395417; PMCID: PMC13320862.
Daly RE, Feng CY, Hesser CR, Myasnikov I, Gaglia MM. N-terminal acetylation controls multiple functional aspects of the influenza A virus ribonuclease PA-X. J Virol. 2026 Feb 17;100(2):e0199925. doi: 10.1128/jvi.01999-25. Epub 2026 Jan 9. PMID: 41511082; PMCID: PMC12911887.
Spieles JA, Greengo SD, Holt AM, Barnes MC, Keller NP, Nett JE, Hull CM. Inhibitors of spore germination act against diverse human fungal pathogens. bioRxiv [Preprint]. 2026 Sep 16:2026.09.15.751812. doi: 10.64898/2026.09.15.751812. PMID: 42779664; PMCID: PMC13596307.
Keim P, Nottingham R, Guevara MA, Miller EF, Vogler AJ, Williamson CHD, Smith T, Posner RG, Pellett S, Lenski RE, Sahl JW. The historical domestication of a Clostridium botulinum strain used for the industrial production of botulinum neurotoxin. Proc Natl Acad Sci U S A. 2026 Oct 20;123(42):e2605155123. doi: 10.1073/pnas.2605155123. Epub 2026 Oct 15. PMID: 42879488; PMCID: PMC13684170.
Holt AM, Horton MV, Johnson CJ, Zarnowski R, Vang PC, Dean M, Kaas A, Andes BD, Jones R, Lowman D, Kruppa MD, Ma Z, Williams DL, Nett JE. Candida auris MNN1 contributes to human neutrophil evasion via mechanisms independent of β-glucan unmasking. mBio. 2026 Oct 14;17(10):e0170126. doi: 10.1128/mbio.01701-26. Epub 2026 Sep 24. PMID: 42782101; PMCID: PMC13712894.
Dong W, Yan C, Korwin-Mihavics B, Stack K, Hughes G, Schmidt A, Schwartz KJ, Caballero-Flores G, Alexander M. β-Hydroxybutyrate precursor 1,3-butanediol modulates enteric pathogen susceptibility and Th17 responses via commensal bacteria. mSystems. 2026 Aug 18;11(8):e0032426. doi: 10.1128/msystems.00324-26. Epub 2026 Jul 16. PMID: 42461015; PMCID: PMC13483238.
Dong W, Yan C, Korwin-Mihavics B, Stack K, Hughes G, Schmidt A, Schwartz K, Caballero-Flores G, Alexander M. β-hydroxybutyrate modulates enteric pathogen susceptibility through regulation of commensal bacteria and intestinal Th17 responses. bioRxiv [Preprint]. 2026 Mar 25:2026.03.20.713262. doi: 10.64898/2026.03.20.713262. Update in: mSystems. 2026 Aug 18;11(8):e0032426. doi: 10.1128/msystems.00324-26. PMID: 41929183; PMCID: PMC13041886.
Zhou K, Kosmopoulos JC, Colón ED, Badciong PJ, Anantharaman K. V- and VL-scores unveil viral signatures and origins of protein families. Nat Commun. 2026 Apr 28;17(1):5828. doi: 10.1038/s41467-026-72028-0. PMID: 42049755; PMCID: PMC13332234.
Kosmopoulos JC, Martin C, Wainaina JM, Bolduc B, Urvoy M, Sullivan MB, Anantharaman K. CheckAMG: Accurate Identification of Auxiliary Viral Genes with Genome-Language Models. bioRxiv [Preprint]. 2026 Sep 27:2026.09.23.753886. doi: 10.64898/2026.09.23.753886. PMID: 42818345; PMCID: PMC13622254.
Aitolo GL, Rambo IM, Weisend RE, Mullis MM, Tringe S, Kosmopoulos JC, Anantharaman K, Kiel Reese B, Baker BJ, De Anda V. Shifts in vegetation impact estuary microbiomes. mSystems. 2026 Oct 20;11(10):e0107126. doi: 10.1128/msystems.01071-26. Epub 2026 Sep 30. PMID: 42813975; PMCID: PMC13712854.
Kosmopoulos JC, Anantharaman K. Computational Microbial and Viral Ecology Analysis. Methods Mol Biol. 2026;3006:83-141. doi: 10.1007/978-1-0716-5080-6_6. PMID: 42156652.
Kosmopoulos JC, Pallier W, Malik AA, Anantharaman K. Ecosystem health shapes viral ecology in peatland soils. Nat Microbiol. 2026 Jan;11(1):142-154. doi: 10.1038/s41564-025-02199-x. Epub 2025 Dec 10. PMID: 41372637; PMCID: PMC12768967.
Zhou K, Kosmopoulos JC, Anantharaman K. vClassifier: a toolkit for high-resolution phylogenetic classification of prokaryotic viruses. Bioinform Adv. 2026 May 27;6(1):vbag149. doi: 10.1093/bioadv/vbag149. PMID: 42370331; PMCID: PMC13303284.
Evert S, Huss P, Kuppa Baskaran DK, Anantharaman K, Raman S. Mapping structural constraints and adaptive potential in a capsule-degrading phage tailspike protein. Sci Adv. 2026 Sep 11;12(37):eaed3641. doi: 10.1126/sciadv.aed3641. Epub 2026 Sep 11. PMID: 42726877; PMCID: PMC13564897.
Ling J, Joyce LR, Doran KS, Hryckowian AJ. A murine model of adult gastrointestinal colonization by Group B Streptococcus. Infect Immun. 2026 Mar 10;94(3):e0052725. doi: 10.1128/iai.00527-25. Epub 2026 Jan 30. PMID: 41616253; PMCID: PMC12974117.
Zheng L, Young MKM, Steinchen W, Guo Z, Jalomo-Khayrova E, Liu BX, Burchert F, Bedrunka P, Mais CN, Pané-Farré J, Girbig M, Linne U, Trinquier A, Li A, Hochberg G, Freitag J, Wang JD, Bange G. A protein adaptor mediating Ap4A-dependent control of protein acetylation. Nat Commun. 2026 Feb 23;17(1):3089. doi: 10.1038/s41467-026-70006-0. PMID: 41730913; PMCID: PMC13039410.
Manuel KA, Fraser TA, Shipley MA, Neumann DM. The HSV-1 LAT enhancer regulates locus-specific H3.1 enrichment during early lytic infection. bioRxiv [Preprint]. 2026 Oct 1:2026.09.30.755688. doi: 10.64898/2026.09.30.755688. PMID: 42856659; PMCID: PMC13648731.
Montoro RA, Chadwick B, Su C, Coon J, Overmyer K, Knoll LJ, Striker R. Proteotyping reactivant toxoplasmic encephalitis reveals virulence-associated dense granule protein GRA5 polymorphisms. J Infect Dis. 2026 Oct 14:jiag503. doi: 10.1093/infdis/jiag503. Epub ahead of print. PMID: 42874062.
Westerman TL, Scheuerell E, Nguyen VH, Johnson K, McClelland M, Elfenbein JR. YeiE regulates YeiH to implement sulfite stress resistance in Salmonella enterica serotype Typhimurium. J Bacteriol. 2026 Feb 19;208(2):e0043125. doi: 10.1128/jb.00431-25. Epub 2026 Jan 12. PMID: 41524521; PMCID: PMC12880088.
Nichols HL, Brettell LE, Saldaña MA, Hegde S, Heinz E, Vaccaro K, Hughes GL, Coon KL. Vertical transmission of mosquito microbiota and its effects on offspring development. Microbiome. 2026 Jul 30;14(1):240. doi: 10.1186/s40168-026-02477-8. PMID: 42934733; PMCID: PMC13711774.
Nickles GR, Stokes CK, Narh DL, Lynn KMT, Fuqua SR, Bryan C, Allen BM, Bivins CP, Woo Bok J, Brewer JS, Buthelezi ST, Clark JPRM, Coon KL, Corby LR, Coetzee MPA, Dewing C, Duong TA, Harris MA, Keller NP, Kopotsa K, Lane FA, Nichols HL, Nieuwoudt A, Nuñez MA, Medina Munoz ME, Park SC, Pham NQ, Ryan KT, Solís M, Vilgalys R, Wallace JM, Wang YW, Wingfield BD, Wingfield MJ, Worley TK, Zallek TA, Zamanian M, Hoeksema JD, Drott MT, Pringle A. Equipped for success: genomes and metabolomes of the European Amanita muscaria are conserved in its novel South African range. New Phytol. 2026 May;250(3):1863-1883. doi: 10.1111/nph.71064. Epub 2026 Mar 12. PMID: 41820030; PMCID: PMC13062730.
Nichols HL, Dhokiya V, Hoque AF, Heinz E, Hughes GL, Coon KL. Transplant of cryopreserved mosquito gut microbiota reveals strain-specific patterns of microbial acquisition and assembly. ISME Host Microbe. 2026 Sep 18;1(1):aazag010. doi: 10.1093/ismehm/aazag010. PMID: 42835783; PMCID: PMC13637714.
Ledwith MP, Nipper T, Davis KA, Uresin D, Zhang Z, Kleer M, Khaperskyy DA, McCormick C, Komarova AV, Mehle A. Influenza virus antagonizes self-sensing by RIG-I to enhance viral replication. Cell Rep. 2026 Oct 30;45(11):117763. doi: 10.1016/j.celrep.2026.117763. Epub ahead of print. PMID: 42961902.
Cumsille A, Putnam JHI, Chevrette MG. When context matters: community and environmental context to elicit natural products. Essays Biochem. 2026 Aug 19;70(2):229-237. doi: 10.1042/EBC20250020. PMID: 42233269; PMCID: PMC13500784.
Rosa BA, Han Z, Arun A, Tricoche N, Peguero R, Banas V, Shadrick M, Fath M, Suksomboon P, Bharti S, Bancks M, Rehborg EG, Zamanian M, Cho-Ngwa F, Lustigman S, Janetka JW, Mitreva M. Discovery of GPCR Antagonists with Potent In Vitro and In Vivo Macrofilaricidal Activity. J Med Chem. 2026 Aug 13;69(15):19130-19161. doi: 10.1021/acs.jmedchem.6c01435. PMID: 42470372.
Wang C, Bristol JA, Nelson SE, Chen T, Hendrickson C, Baiu DC, Riel M, Hayes M, Ranheim EA, Gumperz JE, Johannsen EC, Kenney SC. Epstein-Barr virus (EBV) infection causes human germinal center B cell-derived lymphomas in the absence of EBNA2 expression. Proc Natl Acad Sci U S A. 2026 Jun 2;123(22):e2525164123. doi: 10.1073/pnas.2525164123. Epub 2026 May 26. PMID: 42189985; PMCID: PMC13229203.
Simonton E, Cangelosi N, Zhou M, Hendricks PS, Woodruff AL, Anderson MZ. Paralogs of the Candida albicans TLO gene family form interconnected functional networks with incomplete redundancy. bioRxiv [Preprint]. 2026 Jul 20:2026.06.29.735307. doi: 10.64898/2026.06.29.735307. PMID: 42427580; PMCID: PMC13344963.
Setaro AC, Thomas C, Gaglia MM. Dual roles for influenza A protein PA-X: limiting inflammatory response and disrupting MHC I antigen presentation in human respiratory epithelium. bioRxiv [Preprint]. 2026 Jan 31:2026.01.30.702929. doi: 10.64898/2026.01.30.702929. PMID: 41659510; PMCID: PMC12874031.
Wilkes RA, Suthers PF, Borchert AJ, Callaghan MM, Thusoo E, Giannone RJ, Carper DL, Hendry JI, Benson AF, Gapuz MA, Merrill AN, Ramirez KJ, Salvachúa D, Hettich RL, Maranas CD, Amador-Noguez D, Beckham GT, Werner AZ. Engineered Pseudomonas putida reconfigures metabolic fluxes during muconate bioproduction from lignin-related aromatics. Metab Eng. 2026 Oct 26;99:102573. doi: 10.1016/j.ymben.2026.102573. Epub ahead of print. PMID: 42933594.
Sharma BD, Thusoo E, Stevenson DM, Amador-Noguez D, Lynd LR, Olson DG. Metabolic imbalance limits fermentation in microbes engineered for high-titer ethanol production. mSystems. 2026 Apr 21;11(4):e0007426. doi: 10.1128/msystems.00074-26. Epub 2026 Mar 25. PMID: 41879324; PMCID: PMC13098246.
Thusoo E, Jacobson T, Sharma BD, Colón IM, Lynd LR, Olson DG, Amador-Noguez D. Genetic and metabolic drivers of membrane remodeling in Clostridium thermocellum under alcohol stress. mSystems. 2026 Mar 24;11(3):e0134525. doi: 10.1128/msystems.01345-25. Epub 2026 Mar 5. PMID: 41784359; PMCID: PMC13011478.
Vander Griend JA, Ludvik DA, Nottage HC, Mehle A, Mandel MJ. RtmR is a membrane-embedded RRM family RNA-binding protein. mBio. 2026 Nov 4:e0196026. doi: 10.1128/mbio.01960-26. Epub ahead of print. PMID: 42980366.
Ye ZA, Shipley MA, Singh P, Neumann DM. In HSV-1, the LAT Enhancer Drives Pre-IE VP16 Transcription to Initiate Reactivation. bioRxiv [Preprint]. 2026 Jan 6:2026.01.06.697999. doi: 10.64898/2026.01.06.697999. PMID: 41542627; PMCID: PMC12803242.