Our publications can also be found here: Davies Lab publications.
Preprints
2024
Kulikova AV, Parker JK, Davies BW, Wilke CO. Semantic search using protein large language models detects class II microcins in bacterial genomes. mSystems. 2024 Sep 18:e0104424. doi: 10.1128/msystems.01044-24.
Kim SY, Randall JR, Gu R, Nguyen QD, Davies BW. Antibacterial action, proteolytic immunity, and in vivo activity of a Vibrio cholerae microcin. Cell Host Microbe. 2024 Aug 30;. doi: 10.1016/j.chom.2024.08.012. [Epub ahead of print] PubMed PMID: 39260372.
Randall JR, Vieira LC, Wilke CO, Davies BW. Deep mutational scanning and machine learning uncover antimicrobial peptide features driving membrane selectivity. Nature Biomedical Engineering. 2024 Jul 31. doi: 10.1038/s41551-024-01243-1.
Groover KE, Randall JR, Davies BW. Development of a Selective and Stable Antimicrobial Peptide. ACS Infect Dis. 2024 May 7. doi: 10.1021/acsinfecdis.4c00142.
2023
Shipley A, Frampton G, Davies BW, Umlauf BJ. Generating Shigella that internalize into glioblastoma cells. Front Oncol. 2023 Nov 23;13:1229747. doi: 10.3389/fonc.2023.1229747.
Randall JR, Groover KE, O’Donnell AC, Garza JM, Cole TJ, Davies BW. Adapting antibacterial display to identify serum active macrocyclic peptide antibiotics. PNAS Nexus. 2023 Aug 17;2(8):pgad270. doi: 10.1093/pnasnexus/pgad270.
Randall JR, Wang X, Groover KE, O’Donnell AC, Davies BW. Using display technologies to identify macrocyclic peptide antibiotics. Biochim Biophys Acta Mol Cell Res. 2023 Jun;1870(5):119473. doi: 10.1016/j.bbamcr.2023.119473.
Knauf GA, Groover KE, O’Donnell AC, Davies BW. Generation of Synthetic Acinetobacter baumannii-Specific Nanobodies. ACS Infect Dis. 2023 May 10;. doi: 10.1021/acsinfecdis.3c00024.
Kim SY, Parker JK, Gonzalez-Magaldi M, Telford MS, Leahy DJ, Davies BW. Export of Diverse and Bioactive Small Proteins through a Type I Secretion System. Appl Environ Microbiol. 2023 Apr 20;:e0033523. doi: 10.1128/aem.00335-23.
Parker JK, Gu R, Estrera GA, Kirkpatrick B, Rose DT, Mavridou DAI, Mondy KE, Davies BW. Carbapenem-Resistant and ESBL-Producing Enterobacterales Emerging in Central Texas. Infect Drug Resist. 2023;16:1249-1261. doi: 10.2147/IDR.S403448.
Fleeman RM, Mikesh M, Davies BW. Investigating Klebsiella pneumoniae biofilm preservation for scanning electron microscopy. Access Microbiol. 2023;5(2). doi: 10.1099/acmi.0.000470.v3.
Randall JR, DuPai CD, Cole TJ, Davidson G, Groover KE, Slater SL, Mavridou DAI, Wilke CO, Davies BW. Designing and identifying β-hairpin peptide macrocycles with antibiotic potential. Sci Adv. 2023 Jan 13;9(2):eade0008. doi: 10.1126/sciadv.ade0008.
2022
Cole TJ, Parker JK, Feller AL, Wilke CO, Davies BW. Evidence for Widespread Class II Microcins in Enterobacterales Genomes. Appl Environ Microbiol. 2022 Dec 13;88(23):e0148622. doi: 10.1128/aem.01486-22.
Macias LA, Wang X, Davies BW, Brodbelt JS. Mapping paratopes of nanobodies using native mass spectrometry and ultraviolet photodissociation. Chem Sci. 2022 Jun 7;13(22):6610-6618. doi: 10.1039/d2sc01536f.
Fleeman RM, Davies BW. Polyproline Peptide Aggregation with Klebsiella pneumoniae Extracellular Polysaccharides Exposes Biofilm Associated Bacteria. Microbiol Spectr. 2022 Apr 27;10(2):e0202721.
Parker JK, Davies BW. Microcins reveal natural mechanisms of bacterial manipulation to inform therapeutic development. Microbiology (Reading). 2022 Apr;168(4). doi: 10.1099/mic.0.001175.
Knauf GA, Powers MJ, Herrera CM, Trent MS, Davies BW. Acinetobactin-Mediated Inhibition of Commensal Bacteria by Acinetobacter baumannii. mSphere. 2022 Feb 23;7(1):e0001622. doi: 10.1128/msphere.00016-22.
Randall JR, Davidson G, Fleeman RM, Acosta SA, Riddington IM, Cole TJ, DuPai CD, Davies BW. Synthetic antibacterial discovery of symbah-1, a macrocyclic β-hairpin peptide antibiotic. iScience. 2022 Jan 21;25(1):103611. doi: 10.1016/j.isci.2021.103611.
Randall JR, DuPai CD, Davies BW. Discovery of Antimicrobial Peptide Macrocycles Through Bacterial Display. Methods Mol Biol. 2022;2371:287-298. doi: 10.1007/978-1-0716-1689-5_15.
2021
Randall JR, Davies BW. Mining for novel antibiotics. Curr Opin Microbiol. 2021 Oct;63:66-69. doi: 10.1016/j.mib.2021.06.001.
Cunningham AL, Esarte Palomero O, Voss BJ, Trent MS, Davies BW. Irritable Bowel Syndrome Therapeutic Has Broad-Spectrum Antimicrobial Activity. Antimicrob Agents Chemother. 2021 Sep 17;65(10):e0044321. doi: 10.1128/AAC.00443-21.
DuPai CD, Davies BW, Wilke CO. A systematic analysis of the beta hairpin motif in the Protein Data Bank. Protein Sci. 2021 Mar;30(3):613-623. doi: 10.1002/pro.4020.
Esarte Palomero O, Cunningham AL, Davies BW*, Jones RA*. Antibacterial Thiamine inspired silver (I) and gold (I) N-heterocyclic carbene compounds. Inorganica Chim Acta. 2021 Mar 1;517. doi: 10.1016/j.ica.2020.120152. *co-corresponding.
Butz HA, Mey AR, Ciosek AL, Crofts AA, Davies BW, Payne SM. Regulatory Effects of CsrA in Vibrio cholerae. mBio. 2021 Feb 2;12(1). doi: 10.1128/mBio.03380-20.
2020
DuPai CD, Cunningham AL, Conrado AR, Wilke CO, Davies BW. TsrA Regulates Virulence and Intestinal Colonization in Vibrio cholerae. mSphere. 2020 Dec 9;5(6). doi: 10.1128/mSphere.01014-20.
Fleeman RM, Macias LA, Brodbelt JS, Davies BW. Defining principles that influence antimicrobial peptide activity against capsulated Klebsiella pneumoniae. Proc Natl Acad Sci U S A. 2020 Nov 3;117(44):27620-27626. doi: 10.1073/pnas.2007036117.
DuPai CD, Wilke CO, Davies BW. A Comprehensive Coexpression Network Analysis in Vibrio cholerae. mSystems. 2020 Jul 7;5(4). doi: 10.1128/mSystems.00550-20.
Wang X, Cole CG, DuPai CD, Davies BW. Protein Aggregation is Associated with Acinetobacter baumannii Desiccation Tolerance. Microorganisms. 2020 Feb 28;8(3). doi: 10.3390/microorganisms8030343.
Leonard SP, Powell JE, Perutka J, Geng P, Heckmann LC, Horak RD, Davies BW, Ellington AD, Barrick JE, Moran NA. Engineered symbionts activate honey bee immunity and limit pathogens. Science. 2020 Jan 31;367(6477):573-576. doi: 10.1126/science.aax9039.
2019
Powers MJ, Herrera CM, Tucker AT, Davies BW, Trent MS. Isolation of Lipid Cell Envelope Components from Acinetobacter baumannii. Methods Mol Biol. 2019;1946:233-252. doi: 10.1007/978-1-4939-9118-1_22.
Wang X, Trent MS, Davies BW. Desiccation Tolerance Assays for Acinetobacter baumannii. Methods Mol Biol. 2019;1946:189-194. doi: 10.1007/978-1-4939-9118-1_18.
Tucker AT, Powers MJ, Trent MS, Davies BW. RecET-Mediated Recombineering in Acinetobacter baumannii. Methods Mol Biol. 2019;1946:107-113. doi: 10.1007/978-1-4939-9118-1_11.
2018
Crofts AA, Giovanetti SM, Rubin EJ, Poly FM, Gutiérrez RL, Talaat KR, Porter CK, Riddle MS, DeNearing B, Brubaker J, Maciel M Jr, Alcala AN, Chakraborty S, Prouty MG, Savarino SJ, Davies BW, Trent MS. Enterotoxigenic E. coli virulence gene regulation in human infections. Proc Natl Acad Sci U S A. 2018 Sep 18;115(38):E8968-E8976. doi: 10.1073/pnas.1808982115.
Leonard SP, Perutka J, Powell JE, Geng P, Richhart DD, Byrom M, Kar S, Davies BW, Ellington AD, Moran NA, Barrick JE. Genetic Engineering of Bee Gut Microbiome Bacteria with a Toolkit for Modular Assembly of Broad-Host-Range Plasmids. ACS Synth Biol. 2018 May 18;7(5):1279-1290. doi: 10.1021/acssynbio.7b00399.
Crofts AA, Poly FM, Ewing CP, Kuroiwa JM, Rimmer JE, Harro C, Sack D, Talaat KR, Porter CK, Gutierrez RL, DeNearing B, Brubaker J, Laird RM, Maue AC, Jaep K, Alcala A, Tribble DR, Riddle MS, Ramakrishnan A, McCoy AJ, Davies BW, Guerry P, Trent MS. Campylobacter jejuni transcriptional and genetic adaptation during human infection. Nat Microbiol. 2018 Apr;3(4):494-502. doi: 10.1038/s41564-018-0133-7.
Reuther JF, Goodrich AC, Escamilla PR, Lu TA, Del Rio V, Davies BW, Anslyn EV. A Versatile Approach to Noncanonical, Dynamic Covalent Single- and Multi-Loop Peptide Macrocycles for Enhancing Antimicrobial Activity. J Am Chem Soc. 2018 Mar 14;140(10):3768-3774. doi: 10.1021/jacs.8b00046.
Knauf GA, Cunningham AL, Kazi MI, Riddington IM, Crofts AA, Cattoir V, Trent MS, Davies BW. Exploring the Antimicrobial Action of Quaternary Amines against Acinetobacter baumannii. mBio. 2018 Feb 6;9(1). doi: 10.1128/mBio.02394-17.
Tucker AT, Leonard SP, DuBois CD, Knauf GA, Cunningham AL, Wilke CO, Trent MS, Davies BW. Discovery of Next-Generation Antimicrobials through Bacterial Self-Screening of Surface-Displayed Peptide Libraries. Cell. 2018 Jan 25;172(3):618-628.e13. doi: 10.1016/j.cell.2017.12.009.
2017
Sinel C, Cacaci M, Meignen P, Guérin F, Davies BW, Sanguinetti M, Giard JC, Cattoir V. Subinhibitory Concentrations of Ciprofloxacin Enhance Antimicrobial Resistance and Pathogenicity of Enterococcus faecium. Antimicrob Agents Chemother. 2017 May;61(5). doi: 10.1128/AAC.02763-16.
Luna BM, Ulhaq A, Yan J, Pantapalangkoor P, Nielsen TB, Davies BW, Actis LA, Spellberg B. Selectable Markers for Use in Genetic Manipulation of Extensively Drug-Resistant (XDR) Acinetobacter baumannii HUMC1. mSphere. 2017 Mar-Apr;2(2). doi: 10.1128/mSphere.00140-17.
Ghosal A, Köhrer C, Babu VMP, Yamanaka K, Davies BW, Jacob AI, Ferullo DJ, Gruber CC, Vercruysse M, Walker GC. C21orf57 is a human homologue of bacterial YbeY proteins. Biochem Biophys Res Commun. 2017 Mar 11;484(3):612-617. doi: 10.1016/j.bbrc.2017.01.149.
2016
Vercruysse M, Köhrer C, Shen Y, Proulx S, Ghosal A, Davies BW, RajBhandary UL, Walker GC. Identification of YbeY-Protein Interactions Involved in 16S rRNA Maturation and Stress Regulation in Escherichia coli. mBio. 2016 Nov 8;7(6). doi: 10.1128/mBio.01785-16.
Boll JM, Crofts AA, Peters K, Cattoir V, Vollmer W, Davies BW, Trent MS. A penicillin-binding protein inhibits selection of colistin-resistant, lipooligosaccharide-deficient Acinetobacter baumannii. Proc Natl Acad Sci U S A. 2016 Oct 11;113(41):E6228-E6237. doi: 10.1073/pnas.1611594113.
Kazi MI, Conrado AR, Mey AR, Payne SM, Davies BW. ToxR Antagonizes H-NS Regulation of Horizontally Acquired Genes to Drive Host Colonization. PLoS Pathog. 2016 Apr;12(4):e1005570. doi: 10.1371/journal.ppat.1005570.
2015
Boll JM, Tucker AT, Klein DR, Beltran AM, Brodbelt JS, Davies BW, Trent MS. Reinforcing Lipid A Acylation on the Cell Surface of Acinetobacter baumannii Promotes Cationic Antimicrobial Peptide Resistance and Desiccation Survival. mBio. 2015 May 19;6(3):e00478-15. doi: 10.1128/mBio.00478-15.
Herrera CM, Crofts AA, Henderson JC, Pingali SC, Davies BW, Trent MS. Correction for Herrera et al., The Vibrio cholerae VprA-VprB two-component system controls virulence through endotoxin modification. mBio. 2015 Mar 3;6(2):e00155. doi: 10.1128/mBio.00155-15.
Herrera CM, Crofts AA, Henderson JC, Pingali SC, Davies BW, Trent MS. The Vibrio cholerae VprA-VprB two-component system controls virulence through endotoxin modification. mBio. 2014 Dec 23;5(6). doi: 10.1128/mBio.02283-14.
2014
Tucker AT, Nowicki EM, Boll JM, Knauf GA, Burdis NC, Trent MS, Davies BW. Defining gene-phenotype relationships in Acinetobacter baumannii through one-step chromosomal gene inactivation. mBio. 2014 Aug 5;5(4):e01313-14. doi: 10.1128/mBio.01313-14.
Vercruysse M, Köhrer C, Davies BW, Arnold MF, Mekalanos JJ, RajBhandary UL, Walker GC. The highly conserved bacterial RNase YbeY is essential in Vibrio cholerae, playing a critical role in virulence, stress regulation, and RNA processing. PLoS Pathog. 2014 Jun;10(6):e1004175. doi: 10.1371/journal.ppat.1004175.
Graduate and Postdoctoral
Jacob AI, Köhrer C, Davies BW, RajBhandary UL, Walker GC. Conserved bacterial RNase YbeY plays key roles in 70S ribosome quality control and 16S rRNA maturation. Mol Cell. 2013 Feb 7;49(3):427-38. doi: 10.1016/j.molcel.2012.11.025.
Bogard RW, Davies BW, Mekalanos JJ. MetR-regulated Vibrio cholerae metabolism is required for virulence. mBio. 2012;3(5). doi: 10.1128/mBio.00236-12.
Davies BW, Bogard RW, Young TS, Mekalanos JJ. Coordinated regulation of accessory genetic elements produces cyclic di-nucleotides for V. cholerae virulence. Cell. 2012 Apr 13;149(2):358-70. doi: 10.1016/j.cell.2012.01.053.
Davies BW, Bogard RW, Mekalanos JJ. Mapping the regulon of Vibrio cholerae ferric uptake regulator expands its known network of gene regulation. Proc Natl Acad Sci U S A. 2011 Jul 26;108(30):12467-72. doi: 10.1073/pnas.1107894108.
Davies BW, Bogard RW, Dupes NM, Gerstenfeld TA, Simmons LA, Mekalanos JJ. DNA damage and reactive nitrogen species are barriers to Vibrio cholerae colonization of the infant mouse intestine. PLoS Pathog. 2011 Feb;7(2):e1001295. doi: 10.1371/journal.ppat.1001295.
Davies BW, Köhrer C, Jacob AI, Simmons LA, Zhu J, Aleman LM, Rajbhandary UL, Walker GC. Role of Escherichia coli YbeY, a highly conserved protein, in rRNA processing. Mol Microbiol. 2010 Oct;78(2):506-18. doi: 10.1111/j.1365-2958.2010.07351.x.
Davies BW, Kohanski MA, Simmons LA, Winkler JA, Collins JJ, Walker GC. Hydroxyurea induces hydroxyl radical-mediated cell death in Escherichia coli. Mol Cell. 2009 Dec 11;36(5):845-60. doi: 10.1016/j.molcel.2009.11.024.
Simmons LA, Goranov AI, Kobayashi H, Davies BW, Yuan DS, Grossman AD, Walker GC. Comparison of responses to double-strand breaks between Escherichia coli and Bacillus subtilis reveals different requirements for SOS induction. J Bacteriol. 2009 Feb;191(4):1152-61. doi: 10.1128/JB.01292-08.
Simmons LA, Davies BW, Grossman AD, Walker GC. Beta clamp directs localization of mismatch repair in Bacillus subtilis. Mol Cell. 2008 Feb 15;29(3):291-301. doi: 10.1016/j.molcel.2007.10.036.
Davies BW, Walker GC. A highly conserved protein of unknown function is required by Sinorhizobium meliloti for symbiosis and environmental stress protection. J Bacteriol. 2008 Feb;190(3):1118-23. doi: 10.1128/JB.01521-07.
Jones KM, Kobayashi H, Davies BW, Taga ME, Walker GC. How rhizobial symbionts invade plants: the Sinorhizobium-Medicago model. Nat Rev Microbiol. 2007 Aug;5(8):619-33. doi: 10.1038/nrmicro1705.
Davies BW, Walker GC. Disruption of sitA compromises Sinorhizobium meliloti for manganese uptake required for protection against oxidative stress. J Bacteriol. 2007 Mar;189(5):2101-9. doi: 10.1128/JB.01377-06.
Davies BW, Walker GC. Identification of novel Sinorhizobium meliloti mutants compromised for oxidative stress protection and symbiosis. J Bacteriol. 2007 Mar;189(5):2110-3. doi: 10.1128/JB.01802-06.
McBurney MW, Lau S, Jardine K, Yang X, Davies B. Reexpression of a cluster of silenced transgenes is associated with their rearrangement. Genes Chromosomes Cancer. 2001 Dec;32(4):311-23. doi: 10.1002/gcc.1196.