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 2024 authored by MDTP students.
Alas I, Braun DR, Ericksen SS, Salamzade R, Kalan L, Rajski SR, Bugni TS. Micromonosporaceae biosynthetic gene cluster diversity highlights the need for broad-spectrum investigations. Microb Genom. 2024 Jan;10(1):001167. doi: 10.1099/mgen.0.001167. PMID: 38175683; PMCID: PMC10868606.
Arellano AA, Young EB, Coon KL. An inquiline mosquito modulates microbial diversity and function in an aquatic microecosystem. Mol Ecol. 2024 Apr;33(7):e17314. doi: 10.1111/mec.17314. Epub 2024 Mar 5. PMID: 38441172; PMCID: PMC10989397.
Atuahene D, Zuniga-Chaves I, Martello E, Stefanon B, Suen G, Balouei F, Meineri G. The Canine Gut Health: The Impact of a New Feed Supplement on Microbiota Composition. Animals (Basel). 2024 Apr 15;14(8):1189. doi: 10.3390/ani14081189. PMID: 38672336; PMCID: PMC11047554.
Bacon EE, Tran JS, Nadig N, Peters JM. Modular, inducible, and titratable expression systems for Escherichia coli and Acinetobacter baumannii. Microbiol Spectr. 2024 Sep 20:e0130624. doi: 10.1128/spectrum.01306-24. Epub ahead of print. PMID: 39302127.
Banta AB, Myers KS, Ward RD, Cuellar RA, Place M, Freeh CC, Bacon EE, Peters JM. A Targeted Genome-scale Overexpression Platform for Proteobacteria. bioRxiv [Preprint]. 2024 Mar 4:2024.03.01.582922. doi: 10.1101/2024.03.01.582922. PMID: 38496613; PMCID: PMC10942329.
Calise DG, Park SC, Bok JW, Goldman GH, Keller NP. An oxylipin signal confers protection against antifungal echinocandins in pathogenic aspergilli. Nat Commun. 2024 May 4;15(1):3770. doi: 10.1038/s41467-024-48231-2. PMID: 38704366; PMCID: PMC11069582.
Chen J, Nilsen ED, Chitboonthavisuk C, Mo CY, Raman S. Systematic, high-throughput characterization of bacteriophage gene essentiality on diverse hosts. bioRxiv [Preprint]. 2024 Oct 11:2024.10.10.617714. doi: 10.1101/2024.10.10.617714. PMID: 39416107; PMCID: PMC11482910.
Chitboonthavisuk C, Martin C, Huss P, Peters JM, Anantharaman K, Raman S. Systematic genome-wide discovery of host factors governing bacteriophage infectivity. bioRxiv [Preprint]. 2024 Apr 21:2024.04.20.590424. doi: 10.1101/2024.04.20.590424. PMID: 38659955; PMCID: PMC11042327.
De La Cruz KF, Townsend EC, Alex Cheong JZ, Salamzade R, Liu A, Sandstrom S, Davila E, Huang L, Xu KH, Wu SY, Meudt JJ, Shanmuganayagam D, Gibson ALF, Kalan LR. The porcine skin microbiome exhibits broad fungal antagonism. Fungal Genet Biol. 2024 Aug;173:103898. doi: 10.1016/j.fgb.2024.103898. Epub 2024 May 28. PMID: 38815692.
Desorcy-Scherer K, Zuniga-Chaves I, Reisner MA, Suen G, Hernandez LL. Investigating the influence of perinatal fluoxetine exposure on murine gut microbial communities during pregnancy and lactation. Sci Rep. 2024 Jun 14;14(1):13762. doi: 10.1038/s41598-024-62224-7. PMID: 38877103; PMCID: PMC11178873.
Dieppa-Colón E, Martin C, Anantharaman K. Prophage-DB: A comprehensive database to explore diversity, distribution, and ecology of prophages. bioRxiv [Preprint]. 2024 Jul 16:2024.07.11.603044. doi: 10.1101/2024.07.11.603044. PMID: 39071402; PMCID: PMC11275716.
Dixon MH, Nellore D, Zaacks SC, Barak JD. Time of arrival during plant disease progression and humidity additively influence Salmonella enterica colonization of lettuce. Appl Environ Microbiol. 2024 Sep 18;90(9):e0131124. doi: 10.1128/aem.01311-24. Epub 2024 Aug 29. PMID: 39207142; PMCID: PMC11409676.
Dor S, Nudel K, Eagan JL, Cohen R, Hull CM, Keller NP, Prusky D, Afriat-Jurnou L. Bacterial-fungal crosstalk is defined by a fungal lactone mycotoxin and its degradation by a bacterial lactonase. Appl Environ Microbiol. 2024 Jun 18;90(6):e0029924. doi: 10.1128/aem.00299-24. Epub 2024 May 24. PMID: 38786360; PMCID: PMC11218642.
Eagan JL, Digman ER, Boon MD, Regalado R, Rawa MSA, Hull CM, Keller NP. Patulin inhibition of specific apple microbiome members uncovers Hanseniaspora uvarum as a potential biocontrol agent. Phytopathology. 2024 Oct 7. doi: 10.1094/PHYTO-06-24-0189-R. Epub ahead of print. PMID: 39373615.
Enright AL, Heelan WJ, Ward RD, Peters JM. CRISPRi functional genomics in bacteria and its application to medical and industrial research. Microbiol Mol Biol Rev. 2024 Jun 27;88(2):e0017022. doi: 10.1128/mmbr.00170-22. Epub 2024 May 29. PMID: 38809084; PMCID: PMC11332340.
Finn JP 4th, Luzinski C, Burton BM. Differential expression of the yfj operon in a Bacillus subtilis biofilm. Appl Environ Microbiol. 2024 Oct 22:e0136224. doi: 10.1128/aem.01362-24. Epub ahead of print. PMID: 39436054.
Garcia EM, Klimowicz AK, Edupuganti L, Topf MA, Bhide SR, Slusser DJ, Leib SM, Coddington CL, Matveyev A, Buck GA, Jefferson KK, Pepperell CS, Dillard JP. Phase variable colony variants are conserved across Gardnerella spp. and exhibit different virulence-associated phenotypes. mSphere. 2024 Jul 30;9(7):e0045024. doi: 10.1128/msphere.00450-24. Epub 2024 Jun 27. PMID: 38926904; PMCID: PMC11287997.
Grunst MW, Gil HM, Grandea AG 3rd, Snow BJ, Andrabi R, Nedellec R, Burton I, Clark NM, Janaka SK, Keles NK, Moriarty RV, Weiler AM, Capuano S 3rd, Fennessey CM, Friedrich TC, O’Connor SL, O’Connor DH, Broman AT, Keele BF, Lifson JD, Hangartner L, Burton DR, Evans DT. Potent antibody-dependent cellular cytotoxicity of a V2-specific antibody is not sufficient for protection of macaques against SIV challenge. PLoS Pathog. 2024 Jan 22;20(1):e1011819. doi: 10.1371/journal.ppat.1011819. PMID: 38252675; PMCID: PMC10833561.
Hellenbrand CN, Stevenson DM, Gromek KA, Amador-Noguez D, Hershey DM. A deoxynucleoside triphosphate triphosphohydrolase promotes cell cycle progression in Caulobacter crescentus. bioRxiv [Preprint]. 2024 Apr 26:2024.04.25.591158. doi: 10.1101/2024.04.25.591158. PMID: 38712277; PMCID: PMC11071499.
Holt AM, Nett JE. Innate immune response to Candida auris. Curr Opin Microbiol. 2024 Aug;80:102510. doi: 10.1016/j.mib.2024.102510. Epub 2024 Jul 3. PMID: 38964276; PMCID: PMC11323126.
Horton MV, Eix EF, Johnson CJ, Dean MEB, Andes BD, Wartman KM, Nett JE. Impact of Micafungin on Candida auris β-glucan Masking and Neutrophil Interactions. J Infect Dis. 2024 Sep 23;230(3):763-767. doi: 10.1093/infdis/jiae043. PMID: 38330449; PMCID: PMC11420706.
Klein JA, Predeus AV, Greissl AR, Clark-Herrera MM, Cruz E, Cundiff JA, Haeberle AL, Howell M, Lele A, Robinson DJ, Westerman TL, Wrande M, Wright SJ, Green NM, Vallance BA, McClelland M, Mejia A, Goodman AG, Elfenbein JR, Knodler LA. Pathogenic diversification of the gut commensal Providencia alcalifaciens via acquisition of a second type III secretion system. Infect Immun. 2024 Oct 15;92(10):e0031424. doi: 10.1128/iai.00314-24. Epub 2024 Sep 10. PMID: 39254346; PMCID: PMC11477908.
Klier KM, Martin C, Langwig MV, Anantharaman K. Evolutionary history and origins of Dsr-mediated sulfur oxidation. ISME J. 2024 Jan 8;18(1):wrae167. doi: 10.1093/ismejo/wrae167. PMID: 39206688; PMCID: PMC11406059.
Kosmopoulos JC, Klier KM, Langwig MV, Tran PQ, Anantharaman K. Viromes vs. mixed community metagenomes: choice of method dictates interpretation of viral community ecology. Microbiome. 2024 Oct 7;12(1):195. doi: 10.1186/s40168-024-01905-x. PMID: 39375774; PMCID: PMC11460016.
Lan F, Saba J, Ross TD, Zhou Z, Krauska K, Anantharaman K, Landick R, Venturelli OS. Massively parallel single-cell sequencing of diverse microbial populations. Nat Methods. 2024 Feb;21(2):228-235. doi: 10.1038/s41592-023-02157-7. Epub 2024 Jan 17. PMID: 38233503; PMCID: PMC11089590.
Lane Starr NM, Al-Rayyan N, Smith JM, Sandstrom S, Swaney MH, Salamzade R, Steidl O, Kalan LR, Singh AM. Combined metagenomic- and culture-based approaches to investigate bacterial strain-level associations with medication-controlled mild-moderate atopic dermatitis. J Allergy Clin Immunol Glob. 2024 Apr 15;3(3):100259. doi: 10.1016/j.jacig.2024.100259. PMID: 38779310; PMCID: PMC11109885.
Ling J, Hryckowian AJ. Re-framing the importance of Group B Streptococcus as a gut-resident pathobiont. Infect Immun. 2024 Sep 10;92(9):e0047823. doi: 10.1128/iai.00478-23. Epub 2024 Mar 4. PMID: 38436256; PMCID: PMC11392526.
Liu A, Cheong JZA, Hassan S, Wielgat MB, Meudt JJ, Townsend EC, Shanmuganayagam D, Kalan LR, Gibson A. The effect of anatomic location on porcine models of burn injury and wound healing. Wound Repair Regen. 2024 May 22. doi: 10.1111/wrr.13190. Epub ahead of print. PMID: 38775411.
Liu HY, Li Z, Reindl T, He Z, Qiu X, Golden RP, Donovan KA, Bailey A, Fischer ES, Zhang T, Gray NS, Yang PL. Broad-spectrum activity against mosquito-borne flaviviruses achieved by a targeted protein degradation mechanism. Nat Commun. 2024 Jun 19;15(1):5179. doi: 10.1038/s41467-024-49161-9. PMID: 38898037; PMCID: PMC11187112.
Magesh S, Hurley AI, Nepper JF, Chevrette MG, Schrope JH, Li C, Beebe DJ, Handelsman J. Surface colonization by Flavobacterium johnsoniae promotes its survival in a model microbial community. mBio. 2024 Mar 13;15(3):e0342823. doi: 10.1128/mbio.03428-23. Epub 2024 Feb 8. PMID: 38329367; PMCID: PMC10936215.
Magesh S, Schrope JH, Soto NM, Li C, Hurley AI, Huttenlocher A, Beebe DJ, Handelsman J. Co-zorbs: Motile, multispecies biofilms aid transport of diverse bacterial species. bioRxiv [Preprint]. 2024 Aug 29:2024.08.29.607786. doi: 10.1101/2024.08.29.607786. PMID: 39257784; PMCID: PMC11383685.
Martin C, Gitter A, Anantharaman K. Protein Set Transformer: A protein-based genome language model to power high diversity viromics. Res Sq [Preprint]. 2024 Sep 23:rs.3.rs-4844047. doi: 10.21203/rs.3.rs-4844047/v1. PMID: 39399683; PMCID: PMC11469463.
McGrath KM, Russell SJ, Fer E, Garmendia E, Hosgel A, Baltrus DA, Kaçar B. Fitness benefits of a synonymous substitution in an ancient EF-Tu gene depend on the genetic background. J Bacteriol. 2024 Feb 22;206(2):e0032923. doi: 10.1128/jb.00329-23. Epub 2024 Jan 30. PMID: 38289064; PMCID: PMC10882980.
Mooney RA, Zhu J, Saba J, Landick R. NusG-Spt5 Transcription Factors: Universal, Dynamic Modulators of Gene Expression. J Mol Biol. 2024 Oct 5:168814. doi: 10.1016/j.jmb.2024.168814. Epub ahead of print. PMID: 39374889.
Nikodemova M, Holzhausen EA, Deblois CL, Barnet JH, Peppard PE, Suen G, Malecki KM. Corrigendum: The effect of low-abundance OTU filtering methods on the reliability and variability of microbial composition assessed by 16S rRNA amplicon sequencing. Front Cell Infect Microbiol. 2024 Jun 13;14:1419131. doi: 10.3389/fcimb.2024.1419131. Erratum for: Front Cell Infect Microbiol. 2023 Jun 12;13:1165295. doi: 10.3389/fcimb.2023.1165295. PMID: 38938881; PMCID: PMC11208917.
Pensinger DA, Dobrila HA, Stevenson DM, Hryckowian ND, Amador-Noguez D, Hryckowian AJ. Exogenous butyrate inhibits butyrogenic metabolism and alters virulence phenotypes in Clostridioides difficile. mBio. 2024 Mar 13;15(3):e0253523. doi: 10.1128/mbio.02535-23. Epub 2024 Jan 30. PMID: 38289141; PMCID: PMC10936429.
Raabis SM, Westerman TL, Cruz E, Deblois CL, Suen G, Elfenbein JR. Sensitivity of dairy calf Salmonella enterica serotype Cerro isolates to infection-relevant stressors. Microbiol Spectr. 2024 Oct 3;12(10):e0021224. doi: 10.1128/spectrum.00212-24. Epub 2024 Aug 15. PMID: 39145636; PMCID: PMC11448428.
Rivera Vazquez J, Trujillo E, Williams J, She F, Getahun F, Callaghan MM, Coon JJ, Amador-Noguez D. Lipid membrane remodeling and metabolic response during isobutanol and ethanol exposure in Zymomonas mobilis. Biotechnol Biofuels Bioprod. 2024 Jan 28;17(1):14. doi: 10.1186/s13068-023-02450-9. PMID: 38281959; PMCID: PMC10823705.
Rivera-Kohr DA, Rodriguez-Ramos D, Tanner L, Vo P, Thalpur NA, Nielsen-Fox HC, Shatara FJ, Bingman CA, Hou L, Fox BG, Majumder EL-W. Draft genome of the caprolactam-degrading Paenarthrobacter sp. CAP02 isolated from a landfill. Microbiol Resour Announc. 2024 Oct 10;13(10):e0065024. doi: 10.1128/mra.00650-24. Epub 2024 Aug 29. PMID: 39206955; PMCID: PMC11465857.
Saba J, Flores K, Marshall B, Engstrom MD, Peng Y, Garje AS, Comstock L, Landick R. Bacteroides expand the functional versatility of a universal transcription factor and transcribed DNA to program capsule diversity. bioRxiv [Preprint]. 2024 Jun 21:2024.06.21.599965. doi: 10.1101/2024.06.21.599965. PMID: 38948710; PMCID: PMC11213015.
Salamzade R, Tran PQ, Martin C, Manson AL, Gilmore MS, Earl AM, Anantharaman K, Kalan LR. zol & fai: large-scale targeted detection and evolutionary investigation of gene clusters. bioRxiv [Preprint]. 2024 Sep 12:2023.06.07.544063. doi: 10.1101/2023.06.07.544063. PMID: 37333121; PMCID: PMC10274777.
Shaw TM, Huey D, Mousa-Makky M, Compaleo J, Nennig K, Shah AP, Jiang F, Qiu X, Klipsic D, Rowland RRR, Slukvin II, Sullender ME, Baldridge MT, Li H, Warren CJ, Bailey AL. The neonatal Fc receptor (FcRn) is a pan-arterivirus receptor. Nat Commun. 2024 Aug 7;15(1):6726. doi: 10.1038/s41467-024-51142-x. PMID: 39112502; PMCID: PMC11306234.
Siletti C, Freeman M, Tu Z, Stevenson DM, Amador-Noguez D, Sauer JD, Huynh TN. C-di-AMP accumulation disrupts glutathione metabolism and inhibits virulence program expression in Listeria monocytogenes. bioRxiv [Preprint]. 2024 Jan 18:2024.01.18.576247. doi: 10.1101/2024.01.18.576247. PMID: 38293011; PMCID: PMC10827153.
Singh P, Zhu L, Shipley MA, Ye ZA, Neumann DM. The HSV-1 encoded CCCTC-binding factor, CTRL2, impacts the nature of viral chromatin during HSV-1 lytic infection. PLoS Pathog. 2024 Oct 7;20(10):e1012621. doi: 10.1371/journal.ppat.1012621. PMID: 39374265; PMCID: PMC11486355.
Skarlupka JH, Cox MS, Steinberger AJ, Sbardellati DL, McClure JC, Bickhart DM, Scheftgen AJ, Zuniga-Chaves I, Wolfe LA, Paget E, Skadron C, Attipetty N, Suen G. Oral swabs as a proxy for direct ruminal microbiome sampling in Holstein dairy cows is correlated with sample color. Front Microbiol. 2024 Sep 17;15:1466375. doi: 10.3389/fmicb.2024.1466375. PMID: 39355424; PMCID: PMC11443345.
Snow BJ, Keles NK, Grunst MW, Janaka SK, Behrens RT, Evans DT. Potent broadly neutralizing antibodies mediate efficient antibody-dependent phagocytosis of HIV-infected cells. PLoS Pathog. 2024 Oct 28;20(10):e1012665. doi: 10.1371/journal.ppat.1012665. Epub ahead of print. PMID: 39466835.
Sommer AJ, Kettner JE, Coon KL. Stable flies are bona fide carriers of mastitis-associated bacteria. mSphere. 2024 Jul 30;9(7):e0033624. doi: 10.1128/msphere.00336-24. Epub 2024 Jun 26. PMID: 38920390; PMCID: PMC11288000.
Spurgeon ME, Townsend EC, Blaine-Sauer S, McGregor SM, Horswill M, den Boon JA, Ahlquist P, Kalan L, Lambert PF. Key aspects of papillomavirus infection influence the host cervicovaginal microbiome in a preclinical murine papillomavirus (MmuPV1) infection model. mBio. 2024 Jun 12;15(6):e0093324. doi: 10.1128/mbio.00933-24. Epub 2024 May 14. PMID: 38742830; PMCID: PMC11237646.
Townsend EC, Cheong JZA, Radzietza M, Fritz B, Malone M, Bjarnsholt T, Ousey K, Swanson T, Schultz G, Gibson ALF, Kalan LR. What is slough? Defining the proteomic and microbial composition of slough and its implications for wound healing. Wound Repair Regen. 2024 Apr 1:10.1111/wrr.13170. doi: 10.1111/wrr.13170. Epub ahead of print. PMID: 38558438; PMCID: PMC11442687.
Vander Griend JA, Isenberg RY, Kotla KR, Mandel MJ. Transcriptional pathways across colony biofilm models in the symbiont Vibrio fischeri. mSystems. 2024 Jan 23;9(1):e0081523. doi: 10.1128/msystems.00815-23. Epub 2023 Dec 21. PMID: 38126773; PMCID: PMC10804989.
Walters KA, Myers KS, Donohue TJ, Noguera DR. Metagenome-assembled genomes from microbiomes fermenting dairy coproducts. Microbiol Resour Announc. 2024 Jul 18;13(7):e0017324. doi: 10.1128/mra.00173-24. Epub 2024 May 31. PMID: 38819152; PMCID: PMC11256825.
Ward RD, Tran JS, Banta AB, Bacon EE, Rose WE, Peters JM. Essential gene knockdowns reveal genetic vulnerabilities and antibiotic sensitivities in Acinetobacter baumannii. mBio. 2024 Feb 14;15(2):e0205123. doi: 10.1128/mbio.02051-23. Epub 2023 Dec 21. PMID: 38126769; PMCID: PMC10865783.
Zelasko S, Swaney MH, Sandstrom S, Davenport TC, Seroogy CM, Gern JE, Kalan LR, Currie CR. Upper respiratory microbial communities of healthy populations are shaped by niche and age. Microbiome. 2024 Oct 18;12(1):206. doi: 10.1186/s40168-024-01940-8. PMID: 39425237; PMCID: PMC11490146.
Zelasko S, Swaney MH, Suh WS, Sandstrom S, Carlson C, Cagnazzo J, Golfinos A, Fossen J, Andes D, Kalan LR, Safdar N, Currie CR. Altered oral microbiota of drug-resistant organism carriers exhibit impaired gram-negative pathogen inhibition. bioRxiv [Preprint]. 2024 Sep 25:2024.09.24.614756. doi: 10.1101/2024.09.24.614756. PMID: 39386697; PMCID: PMC11463450.