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 during the academic year 2020-21 authored by MDTP students.

*Bold – Student; Underlined – PI

  1. Agarwal, H., Nyffeler, K.E., Blackwell, H.E., Lynn, D.M., 2021a. Fabrication of Slippery Liquid-Infused Coatings in Flexible Narrow-Bore Tubing. ACS Appl Mater Interfaces. https://doi.org/10.1021/acsami.1c14662
  2. Agarwal, H., Nyffeler, K.E., Manna, U., Blackwell, H.E., Lynn, D.M., 2021b. Liquid Crystal-Infused Porous Polymer Surfaces: A “Slippery” Soft Material Platform for the Naked-Eye Detection and Discrimination of Amphiphilic Species. ACS Appl Mater Interfaces 13, 33652–33663. https://doi.org/10.1021/acsami.1c08170
  3. Anderson, B.W., Fung, D.K., Wang, J.D., Regulatory Themes and Variations by the Stress-Signaling Nucleotide Alarmones (p)ppGpp in Bacteria. Annu Rev Genet. https://doi.org/10.1146/annurev-genet-021821-025827
  4. Ausderau, K., Kabakov, S., Razo, E., Mitzey, A.M., Bach, K.M., Crooks, C.M., Dulaney, N., Keding, L., Salas-Quinchucua, C., Medina-Magües, L.G., Weiler, A.M., Bliss, M., Eickhoff, J., Simmons, H.A., Mejia, A., Antony, K.M., Morgan, T., Capuano, S., Schneider, M.L., Aliota, M.T., Friedrich, T.C., O’Connor, D.H., Golos, T.G., Mohr, E.L., 2021. Neonatal Development in Prenatally Zika Virus-Exposed Infant Macaques with Dengue Immunity. Viruses 13, 1878. https://doi.org/10.3390/v13091878
  5. 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., Perturbing HIV-1 ribosomal frameshifting frequency reveals a cis preference for Gag-Pol incorporation into assembling virions. J Virol JVI0134921. https://doi.org/10.1128/JVI.01349-21
  6. Callaghan, M.M., Klimowicz, A.K., Shockey, A.C., Kane, J., Pepperell, C.S., Dillard, J.P., Transcriptional and Translational Responsiveness of the Neisseria gonorrhoeae Type IV Secretion System to Conditions of Host Infections. Infect Immun 89, e0051921. https://doi.org/10.1128/IAI.00519-21
  7. Clark, R.L., Connors, B.M., Stevenson, D.M., Hromada, S.E., Hamilton, J.J., Amador-Noguez, D., Venturelli, O.S., Design of synthetic human gut microbiome assembly and butyrate production. Nat Commun 12, 3254. https://doi.org/10.1038/s41467-021-22938-y
  8. Cook, T.B., Jacobson, T.B., Venkataraman, M.V., Hofstetter, H., Amador-Noguez, D., Thomas, M.G., Pfleger, B.F., 2021. Stepwise genetic engineering of Pseudomonas putida enables robust heterologous production of prodigiosin and glidobactin A. Metab Eng 67, 112–124. https://doi.org/10.1016/j.ymben.2021.06.004
  9. Cox, M.S., Deblois, C.L., Suen, G., Assessing the Response of Ruminal Bacterial and Fungal Microbiota to Whole-Rumen Contents Exchange in Dairy Cows. Front Microbiol 12, 665776. https://doi.org/10.3389/fmicb.2021.665776
  10. Crooks, C.M., Weiler, A.M., Rybarczyk, S.L., Bliss, M., Jaeger, A.S., Murphy, M.E., Simmons, H.A., Mejia, A., Fritsch, M.K., Hayes, J.M., Eickhoff, J.C., Mitzey, A.M., Razo, E., Braun, K.M., Brown, E.A., Yamamoto, K., Shepherd, P.M., Possell, A., Weaver, K., Antony, K.M., Morgan, T.K., Zeng, X., Dudley, D.M., Peterson, E., Schultz-Darken, N., O’Connor, D.H., Mohr, E.L., Golos, T.G., Aliota, M.T., Friedrich, T.C., African-Lineage Zika Virus Replication Dynamics and Maternal-Fetal Interface Infection in Pregnant Rhesus Macaques. J Virol 95, e0222020. https://doi.org/10.1128/JVI.02220-20
  11. Crooks, C.M., Weiler, A.M., Rybarczyk, S.L., Bliss, M.I., Jaeger, A.S., Murphy, M.E., Simmons, H.A., Mejia, A., Fritsch, M.K., Hayes, J.M., Eickhoff, J.C., Mitzey, A.M., Razo, E., Braun, K.M., Brown, E.A., Yamamoto, K., Shepherd, P.M., Possell, A., Weaver, K., Antony, K.M., Morgan, T.K., Newman, C.M., Dudley, D.M., Schultz-Darken, N., Peterson, E., Katzelnick, L.C., Balmaseda, A., Harris, E., O’Connor, D.H., Mohr, E.L., Golos, T.G., Friedrich, T.C., Aliota, M.T., 2021b. Previous exposure to dengue virus is associated with increased Zika virus burden at the maternal-fetal interface in rhesus macaques. PLoS Negl Trop Dis 15, e0009641. https://doi.org/10.1371/journal.pntd.0009641
  12. de Campos, J.L., Kates, A., Steinberger, A., Sethi, A., Suen, G., Shutske, J., Safdar, N., Goldberg, T., Ruegg, P.L., 2021. Quantification of antimicrobial usage in adult cows and preweaned calves on 40 large Wisconsin dairy farms using dose-based and mass-based metrics. J Dairy Sci 104, 4727–4745. https://doi.org/10.3168/jds.2020-19315
  13. Francoeur, C.B., Khadempour, L., Moreira-Soto, R.D., Gotting, K., Book, A.J., Pinto-Tomas, A.A., Keefover-Ring, K., Currie, C.R., Erratum for Francoeur et al., “Bacteria Contribute to Plant Secondary Compound Degradation in a Generalist Herbivore System.” mBio 12, e0182721. https://doi.org/10.1128/mBio.01827-21
  14. Francoeur, C.B., May, D.S., Thairu, M.W., Hoang, D.Q., Panthofer, O., Bugni, T.S., Pupo, M.T., Clardy, J., Pinto-Tomás, A.A., Currie, C.R., Burkholderia from Fungus Gardens of Fungus-Growing Ants Produces Antifungals That Inhibit the Specialized Parasite Escovopsis. Appl Environ Microbiol 87, e0017821. https://doi.org/10.1128/AEM.00178-21
  15. Gall, A.R., Hsueh, B.Y., Siletti, C., Waters, C.M., Huynh, T.N., NrnA is a linear dinucleotide phosphodiesterase with limited function in cyclic dinucleotide metabolism in Listeria monocytogenes. J Bacteriol JB0020621. https://doi.org/10.1128/JB.00206-21
  16. Gregory, A.L., Pensinger, D.A., Hryckowian, A.J., 2021. A short chain fatty acid-centric view of Clostridioides difficile pathogenesis. PLoS Pathog 17, e1009959. https://doi.org/10.1371/journal.ppat.1009959
  17. Grunwald, D.J., Zapotocny, R.W., Ozer, S., Diers, B.W., Bent, A.F., Detection of rare nematode resistance Rhg1 haplotypes in Glycine soja and a novel Rhg1 α-SNAP. Plant Genome e20152. https://doi.org/10.1002/tpg2.20152
  18. Hamilton, C.D., Steidl, O.R., MacIntyre, A.M., Hendrich, C.G., Allen, C., Ralstonia solanacearum Depends on Catabolism of Myo-Inositol, Sucrose, and Trehalose for Virulence in an Infection Stage-Dependent Manner. Mol Plant Microbe Interact 34, 669–679. https://doi.org/10.1094/MPMI-10-20-0298-R
  19. Henry, K.K., Ross, W., Gourse, R.L., Rhodobacter sphaeroides CarD Negatively Regulates Its Own Promoter. J Bacteriol 203, e0021021. https://doi.org/10.1128/JB.00210-21
  20. Hess, N.J., S Bharadwaj, N., Bobeck, E.A., McDougal, C.E., Ma, S., Sauer, J.-D., Hudson, A.W., Gumperz, J.E., iNKT cells coordinate immune pathways to enable engraftment in nonconditioned hosts. Life Sci Alliance 4, e202000999. https://doi.org/10.26508/lsa.202000999
  21. Horton, M.V., Johnson, C.J., Zarnowski, R., Andes, B.D., Schoen, T.J., Kernien, J.F., Lowman, D., Kruppa, M.D., Ma, Z., Williams, D.L., Huttenlocher, A., Nett, J.E., Candida auris Cell Wall Mannosylation Contributes to Neutrophil Evasion through Pathways Divergent from Candida albicans and Candida glabrata. mSphere 6, e0040621. https://doi.org/10.1128/mSphere.00406-21
  22. Hromada, S., Qian, Y., Jacobson, T.B., Clark, R.L., Watson, L., Safdar, N., Amador-Noguez, D., Venturelli, O.S., Negative interactions determine Clostridioides difficile growth in synthetic human gut communities. Mol Syst Biol 17, e10355. https://doi.org/10.15252/msb.202110355
  23. Hromada, S., Qian, Y., Jacobson, T.B., Clark, R.L., Watson, L., Safdar, N., Amador-Noguez, D., Venturelli, O.S., 2021b. Negative interactions determine Clostridioides difficile growth in synthetic human gut communities. Mol Syst Biol 17, e10355. https://doi.org/10.15252/msb.202110355
  24. Ingle, A.T., Fortney, N.W., Walters, K.A., Donohue, T.J., Noguera, D.R., 2021. Mixed Acid Fermentation of Carbohydrate-Rich Dairy Manure Hydrolysate. Front Bioeng Biotechnol 9, 724304. https://doi.org/10.3389/fbioe.2021.724304
  25. Jackson-Litteken, C.D., Ratliff, C.T., Kneubehl, A.R., Siletti, C., Pack, L., Lan, R., Huynh, T.N., Lopez, J.E., Blevins, J.S., 2021. The Diadenylate Cyclase CdaA Is Critical for Borrelia turicatae Virulence and Physiology. Infect Immun 89, e00787-20. https://doi.org/10.1128/IAI.00787-20
  26. Jacobson, T.B., Callaghan, M.M., Amador-Noguez, D., Hostile Takeover: How Viruses Reprogram Prokaryotic Metabolism. Annu Rev Microbiol 75, 515–539. https://doi.org/10.1146/annurev-micro-060621-043448
  27. Johnson, C.J., Eix, E.F., Lam, B.C., Wartman, K.M., Meudt, J.J., Shanmuganayagam, D., Nett, J.E., Augmenting the Activity of Chlorhexidine for Decolonization of Candida auris from Porcine skin. J Fungi (Basel) 7, 804. https://doi.org/10.3390/jof7100804
  28. Kieft, K., Breister, A.M., Huss, P., Linz, A.M., Zanetakos, E., Zhou, Z., Rahlff, J., Esser, S.P., Probst, A.J., Raman, S., Roux, S., Anantharaman, K., Virus-associated organosulfur metabolism in human and environmental systems. Cell Rep 36, 109471. https://doi.org/10.1016/j.celrep.2021.109471
  29. Kieft, K., Zhou, Z., Anderson, R.E., Buchan, A., Campbell, B.J., Hallam, S.J., Hess, M., Sullivan, M.B., Walsh, D.A., Roux, S., Anantharaman, K., 2021b. Ecology of inorganic sulfur auxiliary metabolism in widespread bacteriophages. Nat Commun 12, 3503. https://doi.org/10.1038/s41467-021-23698-5
  30. Knoener, R., Evans, E., Becker, J.T., Scalf, M., Benner, B., Sherer, N.M., Smith, L.M., 2021. Identification of host proteins differentially associated with HIV-1 RNA splice variants. Elife 10, e62470. https://doi.org/10.7554/eLife.62470
  31. Lawson, C.E., Mundinger, A.B., Koch, H., Jacobson, T.B., Weathersby, C.A., Jetten, M.S.M., Pabst, M., Amador-Noguez, D., Noguera, D.R., McMahon, K., Lücker, S., 2021a. Investigating the Chemolithoautotrophic and Formate Metabolism of Nitrospira moscoviensis by Constraint-Based Metabolic Modeling and 13C-Tracer Analysis. mSystems 6, e0017321. https://doi.org/10.1128/mSystems.00173-21
  32. Lawson, C.E., Nuijten, G.H.L., de Graaf, R.M., Jacobson, T.B., Pabst, M., Stevenson, D.M., Jetten, M.S.M., Noguera, D.R., McMahon, K.D., Amador-Noguez, D., Lücker, S., 2021b. Autotrophic and mixotrophic metabolism of an anammox bacterium revealed by in vivo 13C and 2H metabolic network mapping. ISME J 15, 673–687. https://doi.org/10.1038/s41396-020-00805-w
  33. Leggieri, P.A., Liu, Y., Hayes, M., Connors, B., Seppälä, S., O’Malley, M.A., Venturelli, O.S., Integrating Systems and Synthetic Biology to Understand and Engineer Microbiomes. Annu Rev Biomed Eng 23, 169–201. https://doi.org/10.1146/annurev-bioeng-082120-022836
  34. Li, H., Young, S.E., Poulsen, M., Currie, C.R., 2021. Symbiont-Mediated Digestion of Plant Biomass in Fungus-Farming Insects. Annu Rev Entomol 66, 297–316. https://doi.org/10.1146/annurev-ento-040920-061140
  35. Lucas, L.N., Barrett, K., Kerby, R.L., Zhang, Q., Cattaneo, L.E., Stevenson, D., Rey, F.E., Amador-Noguez, D., Dominant Bacterial Phyla from the Human Gut Show Widespread Ability To Transform and Conjugate Bile Acids. mSystems e0080521. https://doi.org/10.1128/mSystems.00805-21
  36. Ludvik, D.A., Bultman, K.M., Mandel, M.J., Hybrid Histidine Kinase BinK Represses Vibrio fischeri Biofilm Signaling at Multiple Developmental Stages. J Bacteriol 203, e0015521. https://doi.org/10.1128/JB.00155-21
  37. Mangalea, M.R., Paez-Espino, D., Kieft, K., Chatterjee, A., Chriswell, M.E., Seifert, J.A., Feser, M.L., Demoruelle, M.K., Sakatos, A., Anantharaman, K., Deane, K.D., Kuhn, K.A., Holers, V.M., Duerkop, B.A., 2021. Individuals at risk for rheumatoid arthritis harbor differential intestinal bacteriophage communities with distinct metabolic potential. Cell Host Microbe 29, 726-739.e5. https://doi.org/10.1016/j.chom.2021.03.020
  38. Martien, J.I., Trujillo, E.A., Jacobson, T.B., Tatli, M., Hebert, A.S., Stevenson, D.M., Coon, J.J., Amador-Noguez, D., Metabolic Remodeling during Nitrogen Fixation in Zymomonas mobilis. mSystems e0098721. https://doi.org/10.1128/mSystems.00987-21
  39. McDougal, C.E., Morrow, Z.T., Christopher, T., Kim, S., Carter, D., Stevenson, D.M., Amador-Noguez, D., Miller, M.J., Sauer, J.-D., Phagocytes produce prostaglandin E2 in response to cytosolic Listeria monocytogenes. PLoS Pathog 17, e1009493. https://doi.org/10.1371/journal.ppat.1009493
  40. Murga-Garrido, S.M., Hong, Q., Cross, T.-W.L., Hutchison, E.R., Han, J., Thomas, S.P., Vivas, E.I., Denu, J., Ceschin, D.G., Tang, Z.-Z., Rey, F.E., Gut microbiome variation modulates the effects of dietary fiber on host metabolism. Microbiome 9, 117. https://doi.org/10.1186/s40168-021-01061-6
  41. Newman, C.M., Ramuta, M.D., McLaughlin, M.T., Wiseman, R.W., Karl, J.A., Dudley, D.M., Stauss, M.R., Maddox, R.J., Weiler, A.M., Bliss, M.I., Fauser, K.N., Haddock, L.A., Shortreed, C.G., Haj, A.K., Accola, M.A., Heffron, A.S., Bussan, H.E., Reynolds, M.R., Harwood, O.E., Moriarty, R.V., Stewart, L.M., Crooks, C.M., Prall, T.M., Neumann, E.K., Somsen, E.D., Burmeister, C.B., Hall, K.L., Rehrauer, W.M., Friedrich, T.C., O’Connor, S.L., O’Connor, D.H., Initial evaluation of a mobile SARS-CoV-2 RT-LAMP testing strategy. medRxiv 2020.07.28.20164038. https://doi.org/10.1101/2020.07.28.20164038
  42. Owens, L.A., Colitti, B., Hirji, I., Pizarro, A., Jaffe, J.E., Moittié, S., Bishop-Lilly, K.A., Estrella, L.A., Voegtly, L.J., Kuhn, J.H., Suen, G., Deblois, C.L., Dunn, C.D., Juan-Sallés, C., Goldberg, T.L., 2021a. A Sarcina bacterium linked to lethal disease in sanctuary chimpanzees in Sierra Leone. Nat Commun 12, 763. https://doi.org/10.1038/s41467-021-21012-x
  43. Pilch, H.E., Steinberger, A.J., Sockett, D.C., Aulik, N., Suen, G., Czuprynski, C.J., 2021. Assessing the microbiota of recycled bedding sand on a Wisconsin dairy farm. J Anim Sci Biotechnol 12, 114. https://doi.org/10.1186/s40104-021-00635-6
  44. Prall, T.M., Neumann, E.K., Karl, J.A., Shortreed, C.G., Baker, D.A., Bussan, H.E., Wiseman, R.W., O’Connor, D.H., Consistent ultra-long DNA sequencing with automated slow pipetting. BMC Genomics 22, 182. https://doi.org/10.1186/s12864-021-07500-w
  45. Raabis, S.M., Quick, A.E., Skarlupka, J.H., Suen, G., Ollivett, T.L., 2021. The nasopharyngeal microbiota of preweaned dairy calves with and without ultrasonographic lung lesions. J Dairy Sci 104, 3386–3402. https://doi.org/10.3168/jds.2020-19096
  46. Raffa, N., Won, T.H., Sukowaty, A., Candor, K., Cui, C., Halder, S., Dai, M., Landero-Figueroa, J.A., Schroeder, F.C., Keller, N.P., 2021. Dual-purpose isocyanides produced by Aspergillus fumigatus contribute to cellular copper sufficiency and exhibit antimicrobial activity. Proc Natl Acad Sci U S A 118, e2015224118. https://doi.org/10.1073/pnas.2015224118
  47. Riemersma, K.K., Jaeger, A.S., Crooks, C.M., Braun, K.M., Weger-Lucarelli, J., Ebel, G.D., Friedrich, T.C., Aliota, M.T., 2021. Rapid evolution of enhanced Zika virus virulence during direct vertebrate transmission chains. J Virol JVI.02218-20. https://doi.org/10.1128/JVI.02218-20
  48. Robinson, D., Place, M., Hose, J., Jochem, A., Gasch, A.P., Natural variation in the consequences of gene overexpression and its implications for evolutionary trajectories. Elife 10, e70564. https://doi.org/10.7554/eLife.70564
  49. Roman-Reyna, V., Truchon, A., Sharma, P., Hand, F.P., Mazloom, R., Vinatzer, B.A., Jacobs, J.M., Allen, C., Genome Resource: Ralstonia solanacearum Phylotype II Sequevar 1 (Race 3 Biovar 2) Strain UW848 From the 2020 U.S. Geranium Introduction. Plant Dis 105, 207–208. https://doi.org/10.1094/PDIS-06-20-1269-A
  50. Saba, J., Cao, X., Landick, R., Bacterial Transcription Continues to Surprise: Activation by Alarmone-Mediated σ-Factor Tethering. Mol Cell 81, 8–9. https://doi.org/10.1016/j.molcel.2020.12.031
  51. Speare, L., Woo, M., Bultman, K.M., Mandel, M.J., Wollenberg, M.S., Septer, A.N., 2021. Host-Like Conditions Are Required for T6SS-Mediated Competition among Vibrio fischeri Light Organ Symbionts. mSphere 6, e0128820. https://doi.org/10.1128/mSphere.01288-20
  52. Steidl, O.R., Truchon, A.N., Hayes, M.M., Allen, C., Complete Genome Resources for Ralstonia Bacterial Wilt Strains UW763 (Phylotype I); Rs5 and UW700 (Phylotype II); and UW386, RUN2474, and RUN2279 (Phylotype III). Mol Plant Microbe Interact MPMI04210086A. https://doi.org/10.1094/MPMI-04-21-0086-A
  53. Stubbendieck, R.M., Zelasko, S.E., Safdar, N., Currie, C.R., Biogeography of Bacterial Communities and Specialized Metabolism in Human Aerodigestive Tract Microbiomes. Microbiol Spectr 9, e0166921. https://doi.org/10.1128/Spectrum.01669-21
  54. Swaney, M.H., Kalan, L.R., Living in Your Skin: Microbes, Molecules, and Mechanisms. Infect Immun 89, e00695-20. https://doi.org/10.1128/IAI.00695-20
  55. Wahlig, T.A., Stanton, E., Godfrey, J.J., Stasic, A.J., Wong, A.C.L., Kaspar, C.W., A Single Nucleotide Polymorphism in lptG Increases Tolerance to Bile Salts, Acid, and Staining of Calcofluor-Binding Polysaccharides in Salmonella enterica Serovar Typhimurium E40. Front Microbiol 12, 671453. https://doi.org/10.3389/fmicb.2021.671453
  56. Weng, Y.-M., Francoeur, C.B., Currie, C.R., Kavanaugh, D.H., Schoville, S.D., 2021. A high-quality carabid genome assembly provides insights into beetle genome evolution and cold adaptation. Mol Ecol Resour 21, 2145–2165. https://doi.org/10.1111/1755-0998.13409
  57. Wu, M.-Y., Mead, M.E., Lee, M.-K., Neuhaus, G.F., Adpressa, D.A., Martien, J.I., Son, Y.-E., Moon, H., Amador-Noguez, D., Han, K.-H., Rokas, A., Loesgen, S., Yu, J.-H., Park, H.-S., 2021. Transcriptomic, Protein-DNA Interaction, and Metabolomic Studies of VosA, VelB, and WetA in Aspergillus nidulans Asexual Spores. mBio 12, e03128-20. https://doi.org/10.1128/mBio.03128-20