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 2025 authored by MDTP students.
| Abrahams RR, Majumder K. Small Genomes, Big Disruptions: Parvoviruses and the DNA Damage Response. Viruses. 2025 Mar 29;17(4):494. doi: 10.3390/v17040494. PMID: 40284937; PMCID: PMC12031541. |
| Silva MR, Paraíso F, Al-Oboudi J, Abegg M, Aires A, Barros KO, Brito PH, Jarzyna M, Sylvester K, Langdon QK, Opulente DA, Carriconde F, Fell JW, Hofmann TA, Lachance MA, Legras JL, Libkind D, Pontes A, Gonçalves P, Rosa CA, Groenewald M, Hittinger CT, Sampaio JP. A taxogenomic view of the genus Torulaspora: an expansion from ten to twenty-two species. Persoonia. 2025 Jun;54:265-283. doi: 10.3114/persoonia.2025.54.08. Epub 2025 May 23. PMID: 40746710; PMCID: PMC12308288. |
| Barros KO, Al-Oboudi J, Freitas LFD, Sousa FMP, Batista TM, Santos ARO, Morais PB, Sampaio JP, Lachance MA, Hittinger CT, Rosa CA. Taxogenomic analysis of Pichia senei sp. nov. and new insights into hybridization events in the Pichia cactophila species complex. FEMS Yeast Res. 2025 Jan 30;25:foaf037. doi: 10.1093/femsyr/foaf037. PMID: 40796109; PMCID: PMC12359136. |
| Arellano AA, Prack JL, Coon KL. Host-mediated niche construction of bacterial communities in an aquatic microecosystem. ISME J. 2025 Oct 17:wraf233. doi: 10.1093/ismejo/wraf233. Epub ahead of print. PMID: 41105100. |
| Otoo B, Calise DG, Park SC, Bok JW, Keller NP, Rawa MSA. ZfpA-Dependent Quorum Sensing Shifts in Morphology and Secondary Metabolism in Aspergillus flavus. Environ Microbiol. 2025 Apr;27(4):e70100. doi: 10.1111/1462-2920.70100. PMID: 40262766; PMCID: PMC12014256. |
| Yñigez-Gutierrez AE, Conley E, Thomas MG, Pfleger BF. Uncovering the substrate of olefin synthase loading domains in cyanobacteria Picosynechococcus sp. strain PCC 7002. RSC Chem Biol. 2025 Jan 14;6(2):307-316. doi: 10.1039/d4cb00234b. PMID: 39817101; PMCID: PMC11730487. |
| Banta AB, Hall AN, Myers KS, Ward RD, Davis BC, Cuellar RA, Place M, Freeh CC, Bacon EE, Peters JM. Targeted, Genome-scale Overexpression in Proteobacteria. bioRxiv [Preprint]. 2025 Aug 2:2024.03.01.582922. doi: 10.1101/2024.03.01.582922. PMID: 38496613; PMCID: PMC10942329. |
| Banta AB, Cuellar RA, Nadig N, Davis BC, Peters JM. The promise of CRISPR-associated transposons for bacterial functional genomics. Curr Opin Microbiol. 2025 Feb;83:102563. doi: 10.1016/j.mib.2024.102563. Epub 2024 Dec 3. PMID: 39631148; PMCID: PMC11830528. |
| Sommer AJ, Deblois CL, Tu ADJ, Suen G, Coon KL. Opportunistic pathogens are prevalent across the culturable exogenous and endogenous microbiota of stable flies captured at a dairy facility. Vet Res. 2025 Feb 11;56(1):40. doi: 10.1186/s13567-025-01458-3. PMID: 39934928; PMCID: PMC11817017. |
| Dieppa-Colón E, Martin C, Kosmopoulos JC, Anantharaman K. Prophage-DB: a comprehensive database to explore diversity, distribution, and ecology of prophages. Environ Microbiome. 2025 Jan 13;20(1):5. doi: 10.1186/s40793-024-00659-1. PMID: 39806487; PMCID: PMC11730488. |
| Dobrila HA, Hryckowian AJ. The emerging view on the roles of butyrate in Clostridioides difficile pathogenesis. Infect Immun. 2025 Oct 14;93(10):e0004725. doi: 10.1128/iai.00047-25. Epub 2025 Sep 24. PMID: 40991236; PMCID: PMC12519787. |
| Emery HL, Kerby RL, Rey FE. The Central Role of Gut Microbes in Host Purine Homeostasis. Annu Rev Microbiol. 2025 Sep 3. doi: 10.1146/annurev-micro-041522-100126. Epub ahead of print. PMID: 40902203. |
| Daly RE, Feng CY, Hesser C, Myasnikov I, Gaglia MM. N-terminal acetylation controls multiple functional aspects of the influenza A virus ribonuclease PA-X. bioRxiv [Preprint]. 2025 Jul 15:2023.12.01.569683. doi: 10.1101/2023.12.01.569683. PMID: 38076881; PMCID: PMC10705558. |
| Fer E, Yao T, McGrath KM, Goldman AD, Kaçar B. The origins and evolution of translation factors. Trends Genet. 2025 Jul;41(7):590-600. doi: 10.1016/j.tig.2025.02.004. Epub 2025 Mar 24. PMID: 40133153; PMCID: PMC12237606. |
| Gregory AL, Bussan HE, Topf MA, Hryckowian AJ. Impacts of perR on oxygen sensitivity, gene expression, and murine infection in Clostridioides difficile 630∆erm. J Bacteriol. 2025 Feb 20;207(2):e0046824. doi: 10.1128/jb.00468-24. Epub 2025 Jan 23. PMID: 39846733; PMCID: PMC11841134. |
| Hellenbrand CN, Stevenson DM, Gromek KA, Amador-Noguez D, Hershey DM. A deoxynucleoside triphosphate triphosphohydrolase promotes cell cycle progression in Caulobacter crescentus. J Bacteriol. 2025 Jun 24;207(6):e0014525. doi: 10.1128/jb.00145-25. Epub 2025 Jun 2. PMID: 40454833; PMCID: PMC12186491. |
| Tran M, Hernandez Viera AJ, Tran PQ, Nilsen ED, Tran L, Mo CY. Bacteriophage infection drives loss of β-lactam resistance in methicillin-resistant Staphylococcus aureus. Elife. 2025 Jul 10;13:RP102743. doi: 10.7554/eLife.102743. PMID: 40637714; PMCID: PMC12245174. |
| Kissi-Twum AA, Pionek K, Loeb DD. The HBV variant CpF97L supports the secretion of pgRNA-containing virions at a level much greater than WT HBV. J Virol. 2025 May 20;99(5):e0010025. doi: 10.1128/jvi.00100-25. Epub 2025 Apr 15. PMID: 40231820; PMCID: PMC12090816. |
| Kosmopoulos JC, Anantharaman K. Viral Dark Matter: Illuminating Protein Function, Ecology, and Biotechnological Promises. ArXiv [Preprint]. 2025 Jun 13:arXiv:2506.11942v1. PMID: 40980756; PMCID: PMC12447712. |
| Ling J, Joyce LR, Doran KS, Hryckowian AJ. A murine model of adult gastrointestinal colonization by Group B Streptococcus. bioRxiv [Preprint]. 2025 Sep 26:2025.09.25.678695. doi: 10.1101/2025.09.25.678695. PMID: 41040350; PMCID: PMC12485754. |
| Richman A, Kogut S, Edwards T, Boyd J, Rodriguez P, Mariani M, Shipley MA, Manuel KA, Ye ZA, Bloom DC, Frietze S, Neumann DM. Multiple long-range cis interactions generate CTCF insulator-dependent viral chromatin domains in quiescent HSV-1 genomes. mBio. 2025 Oct 8;16(10):e0163825. doi: 10.1128/mbio.01638-25. Epub 2025 Aug 28. PMID: 40874617; PMCID: PMC12506143. |
| Anantharaman K, Martin C. Genetic keys to microbial gut colonization. Cell Host Microbe. 2025 May 14;33(5):605-607. doi: 10.1016/j.chom.2025.04.016. PMID: 40373743. |
| Langwig MV, Koester F, Martin C, Zhou Z, Joye SB, Reysenbach AL, Anantharaman K. Endemism shapes viral ecology and evolution in globally distributed hydrothermal vent ecosystems. Nat Commun. 2025 May 1;16(1):4076. doi: 10.1038/s41467-025-59154-x. PMID: 40307239; PMCID: PMC12043954. |
| Salamzade R, Tran PQ, Martin C, Manson AL, Gilmore MS, Earl AM, Anantharaman K, Kalan LR. zol and fai: large-scale targeted detection and evolutionary investigation of gene clusters. Nucleic Acids Res. 2025 Jan 24;53(3):gkaf045. doi: 10.1093/nar/gkaf045. PMID: 39907107; PMCID: PMC11795205. |
| Zhou Z, Tran PQ, Martin C, Rohwer RR, Baker BJ, McMahon KD, Anantharaman K. Unravelling viral ecology and evolution over 20 years in a freshwater lake. Nat Microbiol. 2025 Jan;10(1):231-245. doi: 10.1038/s41564-024-01876-7. Epub 2025 Jan 3. PMID: 39753667. |
| Martin C, Emerson JB, Roux S, Anantharaman K. A call for caution in the biological interpretation of viral auxiliary metabolic genes. Nat Microbiol. 2025 Sep;10(9):2122-2129. doi: 10.1038/s41564-025-02095-4. Epub 2025 Aug 27. PMID: 40866482. |
| Martin C, Gitter A, Anantharaman K. Protein Set Transformer: A protein-based genome language model to power high diversity viromics. bioRxiv [Preprint]. 2025 Jun 4:2024.07.26.605391. doi: 10.1101/2024.07.26.605391. PMID: 39131363; PMCID: PMC11312453. |
| Chitboonthavisuk C, Martin C, Huss P, Peters JM, Anantharaman K, Raman S. Systematic genome-wide mapping of host determinants of bacteriophage infectivity. Cell Syst. 2025 Oct 15:101427. doi: 10.1016/j.cels.2025.101427. Epub ahead of print. PMID: 41101316. |
| Montoro RA, Moran M, Overmyer KA, Periaccante A, Coon JJ, Lanjewar S, Knoll LJ, Striker R. Fatal toxoplasmic encephalitis triggered by anti-TNF therapy. Heliyon. 2025 Jan 21;11(3):e41965. doi: 10.1016/j.heliyon.2025.e41965. PMID: 39959486; PMCID: PMC11830312. |
| Sullivan OM, Nesbitt DJ, Schaack GA, Feltman EM, Nipper T, Kongsomros S, Reed SG, Nelson SL, King CR, Shishkova E, Coon JJ, Mehle A. IFIT3 RNA-binding activity promotes influenza A virus infection and translation efficiency. J Virol. 2025 Jul 22;99(7):e0028625. doi: 10.1128/jvi.00286-25. Epub 2025 Jun 11. PMID: 40497724; PMCID: PMC12282055. |
| 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. bioRxiv [Preprint]. 2025 Jul 27:2025.07.27.662810. doi: 10.1101/2025.07.27.662810. PMID: 40777443; PMCID: PMC12330677. |
| Nichols HL, Coon KL. Leveraging microbial ecology for mosquito-borne disease control. Trends Parasitol. 2025 Aug;41(8):670-684. doi: 10.1016/j.pt.2025.06.010. Epub 2025 Jul 17. PMID: 40681451; PMCID: PMC12320179. |
| Medina Muñoz M, Nichols HL, Coon KL. Microbiota isolate collections: A key to global vector-borne disease control. PLoS Biol. 2025 Mar 18;23(3):e3003078. doi: 10.1371/journal.pbio.3003078. PMID: 40100886; PMCID: PMC12135935. |
| Ledwith MP, Nipper T, Davis KA, Uresin D, Komarova AV, Mehle A. Influenza virus antagonizes self sensing by RIG-I to enhance viral replication. bioRxiv [Preprint]. 2025 Mar 12:2025.03.12.642847. doi: 10.1101/2025.03.12.642847. PMID: 40161615; PMCID: PMC11952396. |
| Zhang Z, Aziati ID, Nipper T, Boon ACM, Mehle A. ANP32 proteins from ticks and vertebrates are key host factors for replication of Bourbon virus across species. J Virol. 2025 Jun 17;99(6):e0052225. doi: 10.1128/jvi.00522-25. Epub 2025 May 14. PMID: 40366164; PMCID: PMC12172476. |
| Sullivan OM, Nesbitt DJ, Schaack GA, Feltman E, Nipper T, Kongsomros S, Reed SG, Nelson SL, King CR, Shishkova E, Coon JJ, Mehle A. IFIT3 RNA-binding activity promotes influenza A virus infection and translation efficiency. bioRxiv [Preprint]. 2025 Apr 12:2025.02.17.638785. doi: 10.1101/2025.02.17.638785. Update in: J Virol. 2025 Jul 22;99(7):e0028625. doi: 10.1128/jvi.00286-25. PMID: 40027740; PMCID: PMC11870506. |
| Qiu X, Bailey AL. Two mutations in NS2B are responsible for attenuation of the yellow fever virus (YFV) vaccine strain 17D. PLoS Pathog. 2025 Jul 31;21(7):e1013373. doi: 10.1371/journal.ppat.1013373. PMID: 40743291; PMCID: PMC12312905. |
| Thomazella MV, Qiu X, Silveira CGT, Correia CA, Marmorato MP, Sanson E, Norton A, Sharobim M, Ho YL, Dolhnikoff M, Matkovic E, Kallas EG, Duarte-Neto AN, Bailey AL. Mesenteric ischemia and bacterial translocation precipitate the intoxication phase of yellow fever. J Infect Dis. 2025 Sep 22:jiaf483. doi: 10.1093/infdis/jiaf483. Epub ahead of print. PMID: 40982533. |
| Riel M, Johannsen EC. LMP2A-The Other EBV Oncogene. Curr Top Microbiol Immunol. 2025 Oct 8. doi: 10.1007/82_2025_330. Epub ahead of print. PMID: 41055744. |
| Sommer AJ, Worley TK, Sapountzis P, Coon KL. Phylogenetic intermixing reveals stable fly-mediated circulation of mastitis-associated bacteria in dairy settings. mSystems. 2025 Sep 23;10(9):e0021525. doi: 10.1128/msystems.00215-25. Epub 2025 Aug 1. PMID: 40748061; PMCID: PMC12455971. |
| Sommer AJ, Skarlupka JH, Teseo S, Otani S, Suen G, Coon KL, Sapountzis P. Genomic evidence for flies as carriers of zoonotic pathogens on dairy farms. NPJ Biofilms Microbiomes. 2025 Jun 19;11(1):111. doi: 10.1038/s41522-025-00685-y. PMID: 40537478; PMCID: PMC12179284. |
| Sommer AJ, Kettner JE, Worley TK, Petrick J, Haynie C, Coon KL. Prevalence of antimicrobial resistance phenotypes and genes in stable fly- and manure-derived bacterial isolates from clinically relevant taxa in dairy settings. J Appl Microbiol. 2025 Feb 3;136(2):lxaf025. doi: 10.1093/jambio/lxaf025. PMID: 39886877. |
| Zhao SY, Sommer AJ, Bartlett D, Harbison JE, Irwin P, Coon KL. Microbiota Composition Associates With Mosquito Productivity Outcomes in Belowground Larval Habitats. Mol Ecol. 2025 Jan;34(2):e17614. doi: 10.1111/mec.17614. Epub 2024 Dec 13. PMID: 39673091; PMCID: PMC11701876. |
| Sommer AJ, Worley TK, Kettner JE, Coon KL. A bacterial culture collection from stable flies and manure relevant to bovine mastitis. Microbiol Resour Announc. 2025 Oct 20:e0080525. doi: 10.1128/mra.00805-25. Epub ahead of print. PMID: 41114520. |
| Khana DB, Jen A, Shishkova E, Fisher K, Thusoo E, Williams J, Henkel A, Stevenson DM, Coon JJ, Amador-Noguez D. Thermodynamics shapes the in vivo enzyme burden of glycolytic pathways. mBio. 2025 Oct 8;16(10):e0183725. doi: 10.1128/mbio.01837-25. Epub 2025 Sep 16. PMID: 40956114; PMCID: PMC12506098. |
| Khana DB, Jen A, Shishkova E, Thusoo E, Williams J, Henkel A, Stevenson DM, Coon JJ, Amador-Noguez D. Thermodynamics shape the in vivo enzyme burden of glycolytic pathways. bioRxiv [Preprint]. 2025 Feb 6:2025.01.31.635972. doi: 10.1101/2025.01.31.635972. Update in: mBio. 2025 Oct 8;16(10):e0183725. doi: 10.1128/mbio.01837-25. PMID: 39974948; PMCID: PMC11838459. |