Microbiology Doctoral Training Program

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 2023 authored by MDTP students.

  1. Alexander, L.M., & van Pijkeren, J.P. (2023). Modes of therapeutic delivery in synthetic microbiology. Trends in microbiology, 31(2), 197-211.
  2. Arellano, A.A., Sommer, A.J., & Coon, K.L. (2023). Beyond canonical models: why a broader understanding of Diptera-microbiota interactions is essential for vector-borne disease control. Evolutionary ecology, 37(1), 165-88.
  3. Bhatnagar, S., Cowley, E.S., Kopf, S.H., Castro, S.P., Kearney, S., Dawson, S.C., … & Ruff, S.E. (2023). Author Correction: Microbial community dynamics and coexistence in a sulfide-driven phototrophic bloom. Environmental microbiome, 18(1), 27.
  4. Cruz, E., Haeberle, A.L., Westerman, T.L., Durham, M.E., Suyemoto, M.M., Knodler, L.A., & Elfenbein, J.R. (2023). Nonredundant Dimethyl Sulfoxide Reductases Influence Salmonella enterica Serotype Typhimurium Anaerobic Growth and Virulence. Infection and immunity, 91(2), e0057822.
  5. Cuevas-Zuviría, B., Fer, E., Adam, Z.R., & Kaçar, B. (2023). The modular biochemical reaction network structure of cellular translation. NPJ systems biology and applications, 9(1), 52.
  6. Hromada, S., & Venturelli, O.S. (2023). Gut microbiota interspecies interactions shape the response of Clostridioides difficile to clinically relevant antibiotics. PLoS biology, 21(5), e3002100.
  7. Hugon, A.M., Deblois, C.L., Simmons, H.A., Mejia, A., Schotzo, M.L., Czuprynski, C.J., … & Golos, T.G.(in press). Listeria monocytogenes infection in pregnant macaques alters the maternal gut microbiome. Biology of reproduction. doi:10.1093/biolre/ioad104
  8. Huss, P., Chen, J., & Raman, S. (2023). High-throughput approaches to understand and engineer bacteriophages. Trends in biochemical sciences, 48(2), 187-97.
  9. Hutchison, E.R., Kasahara, K., Zhang, Q., Vivas, E.I., Cross, T.L., & Rey, F.E. (2023). Dissecting the impact of dietary fiber type on atherosclerosis in mice colonized with different gut microbial communities. NPJ biofilms and microbiomes, 9(1), 31.
  10. Ji, M., Xu, X., Xu, Q., Hsiao, Y.C., Martin, C., Ukraintseva, S., … & Li, X. (2023). Methionine restriction-induced sulfur deficiency impairs antitumour immunity partially through gut microbiota. Nature metabolism, 5(9), 1526-43.
  11. Khana, D.B., Tatli, M., Rivera Vazquez, J., Weraduwage, S.M., Stern, N., Hebert, A.S., … & Amador-Noguez, D. (2023). Systematic Analysis of Metabolic Bottlenecks in the Methylerythritol 4-Phosphate (MEP) Pathway of Zymomonas mobilis. mSystems, 8(2), e0009223.
  12. Kim, M.S., Chang, H., Zheng, L., Yan, Q., Pfleger, B.F., Klier, J., … & Huber, G.W. (2023). A Review of Biodegradable Plastics: Chemistry, Applications, Properties, and Future Research Needs. Chemical reviews, 123(16), 9915-39.
  13. Kosmopoulos, J.C., & Anantharaman, K.(in press). To cull or kill. Nature ecology & evolution. doi:10.1038/s41559-023-02210-w
  14. Kosmopoulos, J.C., Campbell, D.E., Whitaker, R.J., & Wilbanks, E.G. (2023). Horizontal Gene Transfer and CRISPR Targeting Drive Phage-Bacterial Host Interactions and Coevolution in “Pink Berry” Marine Microbial Aggregates. Applied and environmental microbiology, 89(7), e0017723.
  15. Lan, F., Saba, J., Qian, Y., Ross, T., Landick, R., & Venturelli, O.S. (2023). Single-cell analysis of multiple invertible promoters reveals differential inversion rates as a strong determinant of bacterial population heterogeneity. Science advances, 9(31), eadg5476.
  16. Mendoza Cavazos, C., Heredia, M.Y., Owens, L.A., & Knoll, L.J. (2023). Using Entamoeba muris To Model Fecal-Oral Transmission of Entamoeba in Mice. mBio, 14(1), e0300822.
  17. Nikodemova, M., Holzhausen, E.A., Deblois, C.L., Barnet, J.H., Peppard, P.E., Suen, G., & Malecki, K.M. (2023). The effect of low-abundance OTU filtering methods on the reliability and variability of microbial composition assessed by 16S rRNA amplicon sequencing. Frontiers in cellular and infection microbiology, 13, 1165295.
  18. Olaitan, A.O., Dureja, C., Youngblom, M.A., Topf, M.A., Shen, W.J., Gonzales-Luna, A.J., … & Hurdle, J.G. (2023). Decoding a cryptic mechanism of metronidazole resistance among globally disseminated fluoroquinolone-resistant Clostridioides difficile. Nature communications, 14(1), 4130.
  19. Olmsted, C.N., Ort, R., Tran, P.Q., McDaniel, E.A., Roden, E.E., Bond, D.R., … & McMahon, K.D. (2023). Environmental predictors of electroactive bacterioplankton in small boreal lakes. Environmental microbiology, 25(3), 705-20.
  20. Pensinger, D.A., Fisher, A.T., Dobrila, H.A., Van Treuren, W., Gardner, J.O., Higginbottom, S.K., … & Hryckowian, A.J. (2023). Butyrate Differentiates Permissiveness to Clostridioides difficile Infection and Influences Growth of Diverse C. difficile Isolates. Infection and immunity, 91(2), e0057022.
  21. Pensinger, D.A., Gutierrez, K.V., Smith, H.B., Vincent, W.J.B., Stevenson, D.S., Black, K.A., … & Sauer, J.D. (2023). Listeria monocytogenes GlmR Is an Accessory Uridyltransferase Essential for Cytosolic Survival and Virulence. mBio, 14(2), e0007323.
  22. Romero, S., Unchwaniwala, N., Evans, E.L., Eliceiri, K.W., Loeb, D.D., & Sherer, N.M. (2023). Live Cell Imaging Reveals HBV Capsid Translocation from the Nucleus To the Cytoplasm Enabled by Cell Division. mBio, 14(2), e0330322.
  23. Salamzade, R., Cheong, J.Z.A., Sandstrom, S., Swaney, M.H., Stubbendieck, R.M., Starr, N.L., … & Kalan, L.R. (2023). Evolutionary investigations of the biosynthetic diversity in the skin microbiome using lsaBGC. Microbial genomics, 9(4), mgen000988.
  24. Salamzade, R., Swaney, M.H., & Kalan, L.R. (2023). Comparative Genomic and Metagenomic Investigations of the Corynebacterium tuberculostearicum Species Complex Reveals Potential Mechanisms Underlying Associations To Skin Health and Disease. Microbiology spectrum, 11(1), e0357822.
  25. Schoen, T.J., Calise, D.G., Bok, J.W., Giese, M.A., Nwagwu, C.D., Zarnowski, R., … & Keller, N.P. (2023). Aspergillus fumigatus transcription factor ZfpA regulates hyphal development and alters susceptibility to antifungals and neutrophil killing during infection. PLoS pathogens, 19(5), e1011152.
  26. Stubbendieck, R.M., Dissanayake, E., Burnham, P.M., Zelasko, S.E., Temkin, M.I., Wisdorf, S.S., … & Currie, C.R. (2023). Rothia from the Human Nose Inhibit Moraxella catarrhalis Colonization with a Secreted Peptidoglycan Endopeptidase. mBio, 14(2), e0046423.
  27. Swaney, M.H., Nelsen, A., Sandstrom, S., & Kalan, L.R. (2023). Sweat and Sebum Preferences of the Human Skin Microbiota. Microbiology spectrum, 11(1), e0418022.
  28. Townsend, E.C., & Kalan, L.R. (2023). The dynamic balance of the skin microbiome across the lifespan. Biochemical Society transactions, 51(1), 71-86.
  29. Tran, P.Q., Bachand, S.C., Hotvedt, J.C., Kieft, K., McDaniel, E.A., McMahon, K.D., & Anantharaman, K. (2023). Physiological and genomic evidence of cysteine degradation and aerobic hydrogen sulfide production in freshwater bacteria. mSystems, 8(3), e0020123.
  30. Truchon, A.N., Dalsing, B.L., Khokhani, D., MacIntyre, A., McDonald, B.R., Ailloud, F., … & Allen, C. (2023). Plant-Pathogenic Ralstonia Phylotypes Evolved Divergent Respiratory Strategies and Behaviors To Thrive in Xylem. mBio, 14(1), e0318822.
  31. Williams, M., Cowley, E.S., Valley, T.M., Farooque, A., Shultz, Z., Godecker, A., … & Jacques, L. (2023). An online alternative: a qualitative study of virtual abortion values clarification workshops. Medical education online, 28(1), 2258004.
  32. Yan, Q., Jacobson, T.B., Ye, Z., Cortés-Pena, Y.R., Bhagwat, S.S., Hubbard, S., … & Pfleger, B.F. (2023). Evaluation of 1,2-diacyl-3-acetyl triacylglycerol production in Yarrowia lipolytica. Metabolic engineering, 76, 18-28.
  33. Youngblom, M.A., Shockey, A.C., Callaghan, M.M., Dillard, J.P., & Pepperell, C.S. (2023). The Gonococcal Genetic Island defines distinct sub-populations of Neisseria gonorrhoeae. Microbial genomics, 9(5), mgen000985.
  34. Zhou, Z., Tran, P.Q., Adams, A.M., Kieft, K., Breier, J.A., Fortunato, C.S., … & Anantharaman, K. (2023). Sulfur cycling connects microbiomes and biogeochemistry in deep-sea hydrothermal plumes. The ISME journal, 17(8), 1194-207.
  35. Zuke, J.D., Erickson, R., Hummels, K.R., & Burton, B.M. (2023). Visualizing dynamic competence pili and DNA capture throughout the long axis of Bacillus subtilis. Journal of bacteriology, 205(9), e0015623.
  36. Zuniga-Chaves, I., Eggers, S., Kates, A.E., Safdar, N., Suen, G., & Malecki, K.M.C. (2023). Neighborhood socioeconomic status is associated with low diversity gut microbiomes and multi-drug resistant microorganism colonization. NPJ biofilms and microbiomes, 9(1), 61.