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.
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- Kieft, K., & Anantharaman, K. (2022b). Deciphering Active Prophages from Metagenomes. MSystems, 7(2), e0008422. https://doi.org/10.1128/msystems.00084-22
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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