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Micro Student Publications

Publication in peer-reviewed journals is a very important part of graduate training. Publications by Molecular Microbiology students over the past five years are listed below. The names of student authors are in bold font.


Flowers LJ, Hu S, Shrestha A, Martinot AJ, Leong JM, Osburne MS. 2021. Citrobacter rodentium lysogenized with a Shiga toxin-producing phage: A murine model for shiga toxin-producing E. coli infection. Methods Mol Biol. 2291:381-397. doi: 10.1007/978-1-0716-1339-9_19. Abstract

Levene RE, Shrestha SD, Gaglia MM. 2021. The influenza A virus host shutoff factor PA-X is rapidly turned over in a strain-specific manner. J Virol. 27:JVI.02312-20. doi: 10.1128/JVI.02312-20. Abstract

Lim ANW, Yen M, Seed KD, Lazinski DW, Camilli A . 2021. A tail fiber protein and a receptor-binding protein mediate ICP2 bacteriophage interactions with Vibrio cholerae OmpU. J Bacteriol. Apr 19:JB.00141-21. doi: 10.1128/JB.00141-21. Abstract

Markey L, Pugliese A, Tian T, Roy F, Lee K, Kumamoto CA. 2021. Decreased ecological resistance of the gut microbiota in response to clindamycin challenge in mice colonized with the fungus Candida albicans. mSphere. 6: e00982-20. doi: 10.1128/mSphere.00982-20. Abstract


Anand IS, Choi WY, Isberg RR. 2020. Components of the endocytic and recycling trafficking pathways interfere with the integrity of the Legionella-containing vacuole. Cell Microbiol. 15:e13151. doi: 10.1111/cmi.13151. Abstract

Anand I, Choi W, Isberg RR. 2020. The vacuole guard hypothesis: how intravacuolar pathogens fight to maintain the integrity of their beloved home. Curr Opin Microbiol. 54: 51-58. Abstract

Barrasso K, Watve S, Simpson CA, Geyman LJ, van Kessel JC, Ng WL. 2020. Dual-function quorum-sensing systems in bacterial pathogens and symbionts. PLoS Pathog. 16:e1008934. doi: 10.1371/journal.ppat.1008934. Abstract

Bernard Q, Phelan JP, Hu LT. 2020. Controlling Lyme disease: New paradigms for targeting the tick-pathogen-reservoir axis on the horizon. Front Cell Infect Microbiol. 10:607170. doi: 10.3389/fcimb.2020.607170. Abstract

Bhalla M, Simmons SR, Abamonte A, Herring SE, Roggensack SE, Bou Ghanem EN. 2020. Extracellular adenosine signaling reverses the age-driven decline in the ability of neutrophils to kill Streptococcus pneumoniae. Aging Cell 13:e13218. Abstract

Bourgeois J, Lazinski DW, Camilli A. 2020. Identification of spacer and protospacer sequence requirements in the Vibrio cholerae Type I-E CRISPR/Cas System. mSphere 5(6):e00813-20. doi: 10.1128/mSphere.00813-20. Abstract

Bulow U, Govindan R, Munro JB. 2020. Acidic pH triggers lipid mixing mediated by Lassa virus GP. Viruses 12(7) pii: E716. doi: 10.3390/v12070716. Abstract

Clark SA, Thibault D, Shull LM, Davis KM, Aunins E, van Opijnen T, Isberg R. 2020. Topologically correct synthetic reconstruction of pathogen social behavior found during Yersinia growth in deep tissue sites. Elife. 9. pii: e58106. doi: 10.7554/eLife.58106. Abstract

Cornacchione LP, Hu LT. 2020. Hydrogen peroxide-producing pyruvate oxidase from Lactobacillus delbrueckii is catalytically activated by phosphotidylethanolamine. BMC Microbiol. 20(1):128. doi: 10.1186/s12866-020-01788-6. Abstract

Das DK, Bulow U, Diehl WE, Durham ND, Senjobe F, Chandran K, Luban J, Munro JB. 2020. Conformational changes in the Ebola virus membrane fusion machine induced by pH, Ca2+, and receptor binding. PLoS Biol. 18(2):e3000626. doi: 10.1371/journal.pbio.3000626. Abstract

de la Puebla HB, Giacalone D, Cooper A, Shen A. 2020. Role of SpoIVA ATPase motifs during Clostridioides difficile sporulation. J Bacteriol. 17:JB.00387-20. Abstract

Donnelly ML, Forster ER, Rohlfing AE, Shen A. 2020. Differential effects of "resurrecting" Csp pseudoproteases during Clostridioides difficile spore germination. Biochem J. pii: BCJ20190875. doi: 10.1042/BCJ20190875. Abstract

Durham ND, Howard AR, Govindan R, Senjobe F, Fels JM, Diehl WE, Luban J, Chandran K, Munro JB. 2020. Real-time analysis of individual Ebola virus glycoproteins reveals pre-fusion, entry-relevant conformational dynamics. Viruses. 12(1). pii: E103. doi: 10.3390/v12010103. Abstract

Koenigsberg AL, Pitts JD, Heldwein EE. 2020. Identification of buffer conditions for optimal thermostability and solubility of herpesviral protein UL37 using the thermofluor assay. Bio Protoc. 10(12):e3662. doi: 10.21769/BioProtoc.3662.. Abstract

Markey L, Hooper A, Melon LC, Baglot S, Hill MN, Maguire J, Kumamoto CA. 2020. Colonization with the commensal fungus Candida albicans perturbs the gut-brain axis through dysregulation of endocannabinoid signaling. Psychoneuroendocrinology 121: 104808. Abstract

Metrick CM, Koenigsberg AL, Heldwein EE. 2020. Conserved outer tegument component UL11 from herpes simplex virus 1 is an intrinsically disordered, RNA-binding protein. mBio. 11: pii: e00810-20. doi: 10.1128/mBio.00810-20. Abstract

Nguyen GT, Shaban L, Mack M, Swanson KD, Bunnell SC, Sykes DB, Mecsas J. 2020. SKAP2 is required for defense against K. pneumoniae infection and neutrophil respiratory burst. Elife pii: e56656. doi: 10.7554/eLife.56656. Abstract

Oliveira PH, Ribis JW, Garrett EM, Trzilova D, Kim A, Sekulovic O, Mead EA, Pak T, Zhu S, Deikus G, Touchon M, Lewis-Sandari M, Beckford C, Zeitouni NE, Altman DR, Webster E, Oussenko I, Bunyavanich S, Aggarwal AK, Bashir A, Patel G, Wallach F, Hamula C, Huprikar S, Schadt EE, Sebra R, van Bakel H, Kasarskis A, Tamayo R, Shen A, Fang G. 2020. Epigenomic characterization of Clostridioides difficile finds a conserved DNA methyltransferase that mediates sporulation and pathogenesis. Nat Microbiol. 5(1):166-180. Abstract

Romo JA, Markey L, Kumamoto CA. 2020. Lipid species in the GI tract are increased by the commensal fungus Candida albicans and decrease the virulence of Clostridioides difficile. J Fungi pii: E100. doi: 10.3390/jof6030100. Abstract

Shaban L, Nguyen GT, Mecsas-Faxon BD, Swanson KD, Tan S, Mecsas J. 2020. Yersinia pseudotuberculosis YopH targets SKAP2-dependent and independent signaling pathways to block neutrophil antimicrobial mechanisms during infection. PLoS Pathog. 16: e1008576. Abstract

Siwapornchai N, Lee JN, Tchalla EYI, Bhalla M, Yeoh JH, Roggensack SE, Leong JM, Bou Ghanem EN. 2020. Extracellular adenosine enhances the ability of PMNs to kill Streptococcus pneumoniae by inhibiting IL-10 production. J Leukoc Biol. doi: 10.1002/JLB.4MA0120-115RR. Abstract

Smith TC 2nd, Pullen KM, Olson MC, McNellis ME, Richardson I, Hu S, Larkins-Ford J, Wang X, Freundlich JS, Ando DM, Aldridge BB. 2020. Morphological profiling of tubercle bacilli identifies drug pathways of action. Proc Natl Acad Sci USA Jul 17:202002738. doi: 10.1073/pnas.2002738117.Jul 17:202002738. doi: 10.1073/pnas.2002738117. Abstract

Watve S, Barrasso K, Jung SA, Davis KJ, Hawver LA, Khataokar A, Palaganas RG, Neiditch MB, Perez LJ, Ng WL. 2020. Parallel quorum-sensing system in Vibrio cholerae prevents signal interference inside the host. PLoS Pathog. 16:(2):e1008313. doi: 10.1371/journal.ppat.1008313. Abstract

Yang X, Forster ER, Darabedian N, Kim AT, Pratt MR, Shen A, Hang HC. 2020. Translation of microbiota short-chain fatty acid mechanisms affords anti-infective acyl-salicylic acid derivatives. ACS Chem Biol. 15(5):1141-1147.Abstract


Burgain A, Pic É, Markey L, Tebbji F, Kumamoto CA, Sellam A. 2019. A novel genetic circuitry governing hypoxic metabolic flexibility, commensalism and virulence in the fungal pathogen Candida albicans. PLos Pathog. 15: e1007823. Abstract

Cornacchione LP, Klein BA, Duncan MJ, Hu LT. 2019. Interspecies inhibition of Porphyromonas gingivalis by yogurt-derived Lactobacillus delbrueckii require active pyruvate oxidase. Appl Environ Microbiol. Epub ahead of print. Abstract

Davis KM, Krupp J, Clark S, Isberg RR. 2019. Iron-sulfur cluster repair contributes to Y. pseudotuberculosis survival within deep tissues. Infect Immun. Epub ahead of print. Abstract

Gaucherand L, Porter BK, Levene RE, Price EL, Schmaling SK, Rycroft CH, Kevorkian Y, McCormick C, Khaperskyy DA, Gaglia MM. 2019. The Influenza A virus endoribonuclease PA-X usurps host mRNA processing machinery to limit host gene expression. Cell Rep. 27: 776-792. Abstract

Geisinger E, Huo W, Hernandez-Bird J, Isberg RR. 2019. Acinetobacter baumannii: Envelope determinants that control drug resistance, virulence, and surface variability. Annu Rev Microbiol. Epub ahead of print. Abstract

Holloway JR, Williams ZH, Freeman MM, Bulow U, Coffin JM. 2019. Gorillas have been infected with the HERV-K (HML-2) endogenous retrovirus much more recently than humans and chimpanzees. Proc Natl Acad Sci USA. 116: 1337-1346.. Abstract

MacGilvary NJ, Kevorkian YL, Tan S. 2019. Potassium response and homeostasis in Mycobacterium tuberculosis modulates environmental adaptation and is important for host colonization. PLoS Pathog. 15(2):e1007591. Abstract

Phelan JP, Kern A, Ramsey ME, Lundt ME, Sharma B, Lin T, Gao L, Norris SJ, Hyde JA, Skare JT, Hu LT. 2019. Genome-wide screen identifies novel genes required for Borrelia burgdorferi survival in its Ixodes tick vector. PLoS Pathog. 15: e1007644. Abstract

Sekulovic O, Bourgeois J, Shen A, Camilli A. 2019. Expanding the repertoire of conservative site-specific recombination in Clostridioides difficile. Anaerobe Epub ahead of print. Abstract

Silver RJ, Paczosa MK, McCabe AL, Balada-Llasat JM, Baleja JD, Mecsas J. 2019. Amino acid biosynthetic pathways are required for Klebsiella pneumoniae growth in immunocompromised lungs and are druggable targets during infection. Antimicrob Agents Chemother. Epub ahead of print. Abstract

Sol A, Lipo E, de Jesús-Díaz DA, Murphy C, Devereux M, Isberg RR. 2019. Legionella pneumophila translocated translation inhibitors are required for bacterial-induced host cell cycle arrest. Proc Natl Acad Sci USA. 116: 3221-3228. Abstract

Thibault D, Jensen PA, Wood S, Qabar C, Clark S, Shainheit MG, Isberg RR, van Opijnen T. 2019. Droplet Tn-Seq combines microfluidics with Tn-Seq for identifying complex single-cell phenotypes. Nat Commun. 10(1)5729 doi: 10.1038/s41467-019-13719-9. Abstract

Tscherner M, Giessen TW, Markey L, Kumamoto CA, Silver PA. 2019. A synthetic system that senses Candida albicans and inhibits virulence factors. ACS Synth Biol. 8: 434-444. Abstract


Duncan MC, Forbes JC, Nguyen Y, Shull LM, Gillette RK, Lazinski DW, Ali A, Shanks RMQ, Kadouri DE, Camilli A. 2018. Vibrio cholerae motility exerts drag force to impede attack by the bacterial predator Bdellovibrio bacteriovorus. Nat Commun. 9: 4757. Abstract

Koenigsberg AL, Heldwein E. 2018. The dynamic nature of the conserved tegument protein UL37 of herpesviruses. J Biol Chem. 293: 15927-15839. Abstract

Logsdon MM, Aldridge BB. 2018. Stable regulation of cell cycle events in Mycobacteria: Insights from inherently heterogeneous bacterial populations. Front Microbiol. 9:541. Abstract

Markey L, Shaban L, Green ER, Lemon KP, Mecsas J, Kumamoto CA. 2018. Pre-colonization with the commensal fungus Candida albicans reduces murine susceptibility to Clostridium difficile infection. Gut Microbes 9: 497-509. Abstract

Montesion M, Williams ZH, Subramanian RP, Kuperwasser C, Coffin JM. 2018. Promoter expression of HERV-K (HML-2) provirus-derived sequences is related to LTR sequence variation and polymorphic transcription factor binding sites. Retrovirology 15: 57. Abstract

Ribis JW, Fimlaid KA, Shen A. 2018. Differential requirements for conserved peptidoglycan remodeling enzymes during Clostridioides difficile spore formation. Mol Microbiol. 110: 370-389. Abstract

Sekulovic O, Mathias Garrett E, Bourgeois J, Tamayo R, Shen A, Camilli A. Genome-wide detection of conservative site-specific recombination in bacteria. PLoS Genet. 14: e10007332. Abstract

Severin GB, Ramliden MS, Hawver LA, Wang K, Pell ME, Kieninger AK, Khataokar A, O'Hara BJ, Behrmann LV, Neiditch MB, Benning C, Waters CM, Ng WL. 2018. Direct activation of a phospholipase by cyclic GMP-AMP in El Tor Vibrio cholerae. Proc Natl Acad Sci USA 115: E6048-E6055. Abstract

Shaban L, Chen Y, Fasciano AC, Lin Y, Kaplan DL, Kumamoto CA, Mecsas J. 2018. A 3D intestinal tissue model supports Clostridioides difficile germination, colonization, toxin production and epithelial damage. Anaerobe 50: 85-92. Abstract

Shull LM, Camilli A. 2018. Transposon sequencing of Vibrio cholerae in the infant rabbit model of cholera. Methods Mol Biol. 1839: 103-116. Abstract


Bhowmick R, Clark S, Bonventre JV, Leong JM, McCormick BA 2017. Cytosolic phospholipase A2α promotes pulmonary inflammation and systemic disease during Streptococcus pneumoniae infection. Infect Immun. 85: e00280-17. Abstract

Cokol M, Kuru N, Bicak E, Larkins-Ford J, Aldridge BB. 2017. Efficient measurement and factorization of high-order drug interactions in Mycobacterium tuberculosis. Sci Adv. 3:e1701881. Abstract

de Jesús-Díaz DA, Murphy C, Sol A, Dorer M, Isberg RR. 2017. Host cell S phase restricts Legionella pneumophila intracellular replication by destabilizing the membrane-bound replication compartment. MBio 8: e02345-16. Abstract

Herwald SE, Zucchi PC, Tan S, Kumamoto CA.n 2017. The two transmembrane regions of Candida albicans Dfi1 contribute to its biogenesis. Biochem Biophys Res Commun. 488: 153-158. Abstract

Klein BA, Cornacchione LP, Collins M, Malamy MH, Duncan MJ, Hu LT. 2017. Using Tn-seq to identify pigmentation related genes of Porphyromonas gingivalis: Characterization of the role of a putative glycosyltransferase. J Bacteriol. 199: e00832-16.  Abstract

Koenigsberg AL, Heldwein EE. 2017. Crystal structure of the N-terminal half of the traffic controller UL37 from Herpes Simplex virus Type 1. J Virol. 91: e01244-17. Abstract

Logsdon MM, Ho PY, Papavinasasundaram K, Richardson K, Cokol M, Sassetti CM, Amir A, Aldridge BB. 2017. A parallel adder coordinates Mycobacterial cell-cycle progression and cell-size homeostasis in the context of asymmetric growth and organization. Curr Biol. 27: 3367-3374. Abstract

Mann KM, Huang DL, Hooppaw AJ, Logsdon MM, Richardson K, Lee HJ, Kimmey JM, Aldridge BB, Stallings CL. 2017. Rv0004 is a new essential member of the mycobacterial DNA replication machinery. PloS Genet. 13: e1007115. Abstract

Montesion M, Bhardwaj N, Williams ZH, Kuperwasser C, Coffin JM. 2018. Mechanisms of HERV-K (HML-2) transcription during human mammary epithelial cell transformation. J Virol. J Virol 92: e01258-17.  Abstract

Nguyen GT, Green ER, Mecsas J. 2017. Neutrophils to the ROScue: Mechanisms of NADPH oxidase activation and bacterial resistance. Front Cell Infect Microbiol. 7:373. Abstract

Richards AL, Sollars PJ, Pitts JD, Stults AM, Heldwein EE, Pickard GE, Smith GA. 2017. The pUL37 tegument protein guides alpha-herpesvirus retrograde axonal transport to promote neuroinvasion. PLoS Pathog. 13: e1006741. Abstract

Yen M, Cairns LS, Camilli A. 2017. A cocktail of three virulent bacteriophages prevents Vibrio cholerae infection in animal models. Nat Commun. 8: 14187. Abstract


Curtis A, Blackburn JK, Smiley SL, Yen M, Camilli A, Alam MT, Ali A, Morris JG. 2016. Mapping to support fine scale epidemiological cholera investigations: A case study of spatial video in Haiti. Int J Environ Res Public Health 13 (2).  Abstract

Fleming E, Camilli A. 2016. ManLMN is a glucose transporter and central metabolic regulator in Streptococcus pneumoniae. Mol Microbiol. 102: 467-487.  Abstract

Flowers LJ, Bou Ghanem EN, Leong JM. 2016. Synchronous disease kinetics in a murine model for enterohemorrhagic E. coli infection using food-borne inoculation. Front Cell Infect Microbiol. 6:138.  Abstract

Green ER, Clark S, Crimmins GT, Mack M, Kumamoto CA, Mecsas J. 2016. Fis is essential for Yersinia pseudotuberculosis virulence and protects against reactive oxygen species produced by phagocytic cells during infection. PLoS Pathog. 12: e1005898.   Abstract

Hawver LA, Jung SA, Ng WL. 2016. Specificity and complexity in bacterial quorum-sensing systems. FEMS Microbiol Rev. 40: 738-752. Abstract

Jung SA, Hawver LA, Ng WL. 2016. Parallel quorum sensing signaling pathways in Vibrio cholerae. Curr Genet. 62: 255-260. Abstract

Khaperskyy DA, Schmaling S, Larkins-Ford J, McCormick C, Gaglia MM. 2016. Selective degradation of host RNA polymerase II transcripts by influenza A virus PA-X host shutoff protein. PLoS Pathog. 12: e1005427.  Abstract

Kotewicz KM, Ramabhadran V, Sjoblom N, Vogel JP, Haenssler E, Zhang M, Behringer J, Scheck RA, Isberg RR. 2016. A single Legionella effector catalyzes a multistep ubiquitination pathway to rearrange tubular endoplasmic reticulum for replication. Cell Host Microbe. 21: 169-181. Abstract

McDonough E, Kamp H, Camilli A. 2016. Vibrio cholerae phosphatases required for the utilization of nucleotides and extracellular DNA as phosphate sources. Mol Microbiol. 99: 453-469.  Abstract

Tyc KM, Herwald SE, Hogan JA, Pierce JV, Klipp E, Kumamoto CA. 2016. The game theory of Candida albicans colonization dynamics reveals host status-responsive gene expression. BMC Syst Biol. 10: 20.   Abstract

Wildschutte JH*, Williams ZH*, Montesion M, Subramanian RP, Kidd JM, Coffin JM. 2016. Discovery of unfixed endogenous retrovirus insertions in diverse human populations. Proc Natl Acad Sci USA 113: E2326-E2334. (* equal contribution) Abstract