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-September 2022 authored by MDTP students.

 

  1. Amato, K. A., Haddock, L. A., Braun, K. M., Meliopoulos, V., Livingston, B., Honce, R., Schaack, G. A., Boehm, E., Higgins, C. A., Barry, G. L., Koelle, K., Schultz-Cherry, S., Friedrich, T. C., & Mehle, A. (2022). Influenza A virus undergoes compartmentalized replication in vivo dominated by stochastic bottlenecks. Nature Communications, 13(1), 3416. https://doi.org/10.1038/s41467-022-31147-0
  2. Anderson, B. W., Schumacher, M. A., Yang, J., Turdiev, A., Turdiev, H., Schroeder, J. W., He, Q., Lee, V. T., Brennan, R. G., & Wang, J. D. (2022). The nucleotide messenger (p)ppGpp is an anti-inducer of the purine synthesis transcription regulator PurR in Bacillus. Nucleic Acids Research, 50(2), 847–866. https://doi.org/10.1093/nar/gkab1281
  3. Arellano, A. A., & Coon, K. L. (2022). Bacterial communities in carnivorous pitcher plants colonize and persist in inquiline mosquitoes. Animal Microbiome, 4(1), 13. https://doi.org/10.1186/s42523-022-00164-1
  4. Benner, B. E., Bruce, J. W., Kentala, J. R., Murray, M., Becker, J. T., Garcia-Miranda, P., Ahlquist, P., Butcher, S. E., & Sherer, N. M. (2022). Perturbing HIV-1 Ribosomal Frameshifting Frequency Reveals a cis Preference for Gag-Pol Incorporation into Assembling Virions. Journal of Virology, 96(1), e0134921. https://doi.org/10.1128/JVI.01349-21
  5. Cao, Y., Aquino-Martinez, R., Hutchison, E., Allayee, H., Lusis, A. J., & Rey, F. E. (2022). Role of gut microbe-derived metabolites in cardiometabolic diseases: Systems based approach. Molecular Metabolism, 64, 101557. https://doi.org/10.1016/j.molmet.2022.101557
  6. Chelluboina, B., Kieft, K., Breister, A., Anantharaman, K., & Vemuganti, R. (2022). Gut virome dysbiosis following focal cerebral ischemia in mice. Journal of Cerebral Blood Flow and Metabolism: Official Journal of the International Society of Cerebral Blood Flow and Metabolism, 42(9), 1597–1602. https://doi.org/10.1177/0271678X221107702
  7. Cheong, J. Z. A., Irvine, J. M., Roesemann, S., Nora, A., Morgan, C. E., Daniele, C., Kalan, L. R., & Brennan, M. B. (2022). Ankle brachial indices and anaerobes: Is peripheral arterial disease associated with anaerobic bacteria in diabetic foot ulcers? Therapeutic Advances in Endocrinology and Metabolism, 13, 20420188221118748. https://doi.org/10.1177/20420188221118747
  8. Chiang, E., Deblois, C. L., Carey, H. V., & Suen, G. (2022). Characterization of captive and wild 13-lined ground squirrel cecal microbiotas using Illumina-based sequencing. Animal Microbiome, 4(1), 1. https://doi.org/10.1186/s42523-021-00154-9
  9. Chitboonthavisuk, C., Luo, C. H., Huss, P., Fernholz, M., & Raman, S. (2022). Engineering a Dynamic Controllable Infectivity Switch in Bacteriophage T7. ACS Synthetic Biology, 11(1), 286–296. https://doi.org/10.1021/acssynbio.1c00414
  10. Debédat, J., Le Roy, T., Voland, L., Belda, E., Alili, R., Adriouch, S., Bel Lassen, P., Kasahara, K., Hutchison, E., Genser, L., Torres, L., Gamblin, C., Rouault, C., Zucker, J.-D., Kapel, N., Poitou, C., Marcelin, G., Rey, F. E., Aron-Wisnewsky, J., & Clément, K. (2022). The human gut microbiota contributes to type-2 diabetes non-resolution 5-years after Roux-en-Y gastric bypass. Gut Microbes, 14(1), 2050635. https://doi.org/10.1080/19490976.2022.2050635
  11. Eix, E. F., Johnson, C. J., Wartman, K. M., Kernien, J. F., Meudt, J. J., Shanmuganayagam, D., Gibson, A. L. F., & Nett, J. E. (2022). Ex Vivo Human and Porcine Skin Effectively Model Candida auris Colonization, Differentiating Robust and Poor Fungal Colonizers. The Journal of Infectious Diseases, 225(10), 1791–1795. https://doi.org/10.1093/infdis/jiac094
  12. Fortney, N. W., Myers, K. S., Ingle, A. T., Walters, K. A., Scarborough, M. J., Donohue, T. J., & Noguera, D. R. (2022). Metagenomes and Metagenome-Assembled Genomes from Microbiomes Metabolizing Thin Stillage from an Ethanol Biorefinery. Microbiology Resource Announcements, 11(8), e0029022. https://doi.org/10.1128/mra.00290-22
  13. Foster, C., Boorla, V. S., Dash, S., Gopalakrishnan, S., Jacobson, T. B., Olson, D. G., Amador-Noguez, D., Lynd, L. R., & Maranas, C. D. (2022). Assessing the impact of substrate-level enzyme regulations limiting ethanol titer in Clostridium thermocellum using a core kinetic model. Metabolic Engineering, 69, 286–301. https://doi.org/10.1016/j.ymben.2021.12.012
  14. Gall, A. R., Hsueh, B. Y., Siletti, C., Waters, C. M., & Huynh, T. N. (2022). NrnA Is a Linear Dinucleotide Phosphodiesterase with Limited Function in Cyclic Dinucleotide Metabolism in Listeria monocytogenes. Journal of Bacteriology, 204(1), e0020621. https://doi.org/10.1128/JB.00206-21
  15. Gambacorta, F. V., Wagner, E. R., Jacobson, T. B., Tremaine, M., Muehlbauer, L. K., McGee, M. A., Baerwald, J. J., Wrobel, R. L., Wolters, J. F., Place, M., Dietrich, J. J., Xie, D., Serate, J., Gajbhiye, S., Liu, L., Vang-Smith, M., Coon, J. J., Zhang, Y., Gasch, A. P., … Pfleger, B. F. (2022). Comparative functional genomics identifies an iron-limited bottleneck in a Saccharomyces cerevisiae strain with a cytosolic-localized isobutanol pathway. Synthetic and Systems Biotechnology, 7(2), 738–749. https://doi.org/10.1016/j.synbio.2022.02.007
  16. Grunwald, D. J., Zapotocny, R. W., Ozer, S., Diers, B. W., & Bent, A. F. (2022). Detection of rare nematode resistance Rhg1 haplotypes in Glycine soja and a novel Rhg1 α-SNAP. The Plant Genome, 15(1), e20152. https://doi.org/10.1002/tpg2.20152
  17. Hurley, A., Chevrette, M. G., Rosario-Meléndez, N., & Handelsman, J. (2022). THOR’s Hammer: The Antibiotic Koreenceine Drives Gene Expression in a Model Microbial Community. MBio, 13(3), e0248621. https://doi.org/10.1128/mbio.02486-21
  18. Ingle, A. T., Fortney, N. W., Myers, K. S., Walters, K. A., Scarborough, M. J., Donohue, T. J., & Noguera, D. R. (2022). Metagenome-Assembled Genomes from a Microbiome Grown in Dairy Manure Hydrolysate. Microbiology Resource Announcements, 11(8), e0029222. https://doi.org/10.1128/mra.00292-22
  19. Isenberg, R. Y., Christensen, D. G., Visick, K. L., & Mandel, M. J. (2022). High Levels of Cyclic Diguanylate Interfere with Beneficial Bacterial Colonization. MBio, 13(4), e0167122. https://doi.org/10.1128/mbio.01671-22
  20. Janaka, S. K., Snow, B. J., Behrens, R. T., & Evans, D. T. (2022). Substitutions in Nef That Uncouple Tetherin and SERINC5 Antagonism Impair Simian Immunodeficiency Virus Replication in Primary Rhesus Macaque Lymphocytes. Journal of Virology, 96(11), e0017622. https://doi.org/10.1128/jvi.00176-22
  21. Kates, A., Keating, J., Baubie, K., Putman-Buehler, N., Watson, L., Godfrey, J., Deblois, C. L., Suen, G., Cook, D. B., Rabago, D., Gangnon, R., & Safdar, N. (2022). Examining the association between the gastrointestinal microbiota and Gulf War illness: A prospective cohort study. PloS One, 17(7), e0268479. https://doi.org/10.1371/journal.pone.0268479
  22. Khana, D. B., Callaghan, M. M., & Amador-Noguez, D. (2022). Novel computational and experimental approaches for investigating the thermodynamics of metabolic networks. Current Opinion in Microbiology, 66, 21–31. https://doi.org/10.1016/j.mib.2021.11.007
  23. Kieft, K., Adams, A., Salamzade, R., Kalan, L., & Anantharaman, K. (2022). VRhyme enables binning of viral genomes from metagenomes. Nucleic Acids Research, 50(14), e83. https://doi.org/10.1093/nar/gkac341
  24. Kieft, K., & Anantharaman, K. (2022a). Virus genomics: What is being overlooked? Current Opinion in Virology, 53, 101200. https://doi.org/10.1016/j.coviro.2022.101200
  25. Kieft, K., & Anantharaman, K. (2022b). Deciphering Active Prophages from Metagenomes. MSystems, 7(2), e0008422. https://doi.org/10.1128/msystems.00084-22
  26. MacIntyre, A. M., Meline, V., Gorman, Z., Augustine, S. P., Dye, C. J., Hamilton, C. D., Iyer-Pascuzzi, A. S., Kolomiets, M. V., McCulloh, K. A., & Allen, C. (2022). Trehalose increases tomato drought tolerance, induces defenses, and increases resistance to bacterial wilt disease. PloS One, 17(4), e0266254. https://doi.org/10.1371/journal.pone.0266254
  27. Miller, R. M., Knoener, R. A., Benner, B. E., Frey, B. L., Scalf, M., Shortreed, M. R., Sherer, N. M., & Smith, L. M. (2022). Discovery of Dehydroamino Acid Residues in the Capsid and Matrix Structural Proteins of HIV-1. Journal of Proteome Research, 21(4), 993–1001. https://doi.org/10.1021/acs.jproteome.1c00867
  28. Miskolci, V., Tweed, K. E., Lasarev, M. R., Britt, E. C., Walsh, A. J., Zimmerman, L. J., McDougal, C. E., Cronan, M. R., Fan, J., Sauer, J.-D., Skala, M. C., & Huttenlocher, A. (2022). In vivo fluorescence lifetime imaging of macrophage intracellular metabolism during wound responses in zebrafish. ELife, 11, e66080. https://doi.org/10.7554/eLife.66080
  29. Mote, R. S., Hill, N. S., Skarlupka, J. H., Carpenter, J. M., Lourenco, J. M., Callaway, T. R., Tran, V. T., Liu, K., Smith, M. R., Jones, D. P., Suen, G., & Filipov, N. M. (2022). Integrative interactomics applied to bovine fescue toxicosis. Scientific Reports, 12(1), 4899. https://doi.org/10.1038/s41598-022-08540-2
  30. Polaske, T. J., Gahan, C. G., Nyffeler, K. E., Lynn, D. M., & Blackwell, H. E. (2022). Identification of small molecules that strongly inhibit bacterial quorum sensing using a high-throughput lipid vesicle lysis assay. Cell Chemical Biology, 29(4), 605-614.e4. https://doi.org/10.1016/j.chembiol.2021.12.005
  31. Raabis, S. M., Holschbach, C. L., Skarlupka, J. H., Suen, G., & Ollivett, T. L. (2022). Assessing the effects of experimental bacterial challenge with Pasteurella multocida and ampicillin on the respiratory microbiota of pre-weaned Holstein calves. Veterinary Microbiology, 269, 109428. https://doi.org/10.1016/j.vetmic.2022.109428
  32. Raasch, L. E., Yamamoto, K., Newman, C. M., Rosinski, J. R., Shepherd, P. M., Razo, E., Crooks, C. M., Bliss, M. I., Breitbach, M. E., Sneed, E. L., Weiler, A. M., Zeng, X., Noguchi, K. K., Morgan, T. K., Fuhler, N. A., Bohm, E. K., Alberts, A. J., Havlicek, S. J., Kabakov, S., … Dudley, D. M. (2022). Fetal loss in pregnant rhesus macaques infected with high-dose African-lineage Zika virus. PLoS Neglected Tropical Diseases, 16(8), e0010623. https://doi.org/10.1371/journal.pntd.0010623
  33. Regan, M. D., Chiang, E., Liu, Y., Tonelli, M., Verdoorn, K. M., Gugel, S. R., Suen, G., Carey, H. V., & Assadi-Porter, F. M. (2022). Nitrogen recycling via gut symbionts increases in ground squirrels over the hibernation season. Science (New York, N.Y.), 375(6579), 460–463. https://doi.org/10.1126/science.abh2950
  34. Sephus, C. D., Fer, E., Garcia, A. K., Adam, Z. R., Schwieterman, E. W., & Kacar, B. (2022). Earliest Photic Zone Niches Probed by Ancestral Microbial Rhodopsins. Molecular Biology and Evolution, 39(5), msac100. https://doi.org/10.1093/molbev/msac100
  35. Singh, P., Collins, M. F., Johns, R. N., Manuel, K. A., Ye, Z. A., Bloom, D. C., & Neumann, D. M. (2022). Deletion of the CTRL2 Insulator in HSV-1 Results in the Decreased Expression of Genes Involved in Axonal Transport and Attenuates Reactivation In Vivo. Viruses, 14(5), 909. https://doi.org/10.3390/v14050909
  36. Smith, T. M., Youngblom, M. A., Kernien, J. F., Mohamed, M. A., Fry, S. S., Bohr, L. L., Mortimer, T. D., O’Neill, M. B., & Pepperell, C. S. (2022). Rapid adaptation of a complex trait during experimental evolution of Mycobacterium tuberculosis. ELife, 11, e78454. https://doi.org/10.7554/eLife.78454
  37. Swaney, M. H., & Kalan, L. R. (2022). Two-for-one: Dual host-microbe functions of S. epidermidis Sph. Cell Host & Microbe, 30(3), 279–280. https://doi.org/10.1016/j.chom.2022.02.011
  38. Swaney, M. H., Sandstrom, S., & Kalan, L. R. (2022). Cobamide Sharing Is Predicted in the Human Skin Microbiome. MSystems, e0067722. https://doi.org/10.1128/msystems.00677-22
  39. Thrikawala, S., Niu, M., Keller, N. P., & Rosowski, E. E. (2022). Cyclooxygenase production of PGE2 promotes phagocyte control of A. fumigatus hyphal growth in larval zebrafish. PLoS Pathogens, 18(3), e1010040. https://doi.org/10.1371/journal.ppat.1010040
  40. Truchon, A. N., Hendrich, C. G., Bigott, A. F., Dalsing, B. L., & Allen, C. (2022). NorA, HmpX, and NorB Cooperate to Reduce NO Toxicity during Denitrification and Plant Pathogenesis in Ralstonia solanacearum. Microbiology Spectrum, 10(2), e0026422. https://doi.org/10.1128/spectrum.00264-22
  41. Trujillo, E. A., Hebert, A. S., Rivera Vazquez, J. C., Brademan, D. R., Tatli, M., Amador-Noguez, D., Meyer, J. G., & Coon, J. J. (2022). Rapid Targeted Quantitation of Protein Overexpression with Direct Infusion Shotgun Proteome Analysis (DISPA-PRM). Analytical Chemistry, 94(4), 1965–1973. https://doi.org/10.1021/acs.analchem.1c03243
  42. Venkatesh, N., Greco, C., Drott, M. T., Koss, M. J., Ludwikoski, I., Keller, N. M., & Keller, N. P. (2022). Bacterial hitchhikers derive benefits from fungal housing. Current Biology: CB, 32(7), 1523-1533.e6. https://doi.org/10.1016/j.cub.2022.02.017
  43. Walters, K. A., Myers, K. S., Wang, H., Fortney, N. W., Ingle, A. T., Scarborough, M. J., Donohue, T. J., & Noguera, D. R. (2022). Metagenomes and Metagenome-Assembled Genomes from Microbial Communities Fermenting Ultrafiltered Milk Permeate. Microbiology Resource Announcements, 11(7), e0029322. https://doi.org/10.1128/mra.00293-22
  44. Wijdeven, R. H., Cabukusta, B., Behr, F. M., Qiu, X., Amiri, D., Borras, D. M., Arens, R., Liang, Y., & Neefjes, J. (2022). CRISPR Activation Screening Identifies VGLL3-TEAD1-RUNX1/3 as a Transcriptional Complex for PD-L1 Expression. Journal of Immunology (Baltimore, Md.: 1950), ji2100917. https://doi.org/10.4049/jimmunol.2100917
  45. Wolf, P. G., Cowley, E. S., Breister, A., Matatov, S., Lucio, L., Polak, P., Ridlon, J. M., Gaskins, H. R., & Anantharaman, K. (2022). Diversity and distribution of sulfur metabolic genes in the human gut microbiome and their association with colorectal cancer. Microbiome, 10(1), 64. https://doi.org/10.1186/s40168-022-01242-x
  46. Zhou, Z., Tran, P. Q., Breister, A. M., Liu, Y., Kieft, K., Cowley, E. S., Karaoz, U., & Anantharaman, K. (2022). METABOLIC: High-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks. Microbiome, 10(1), 33. https://doi.org/10.1186/s40168-021-01213-8