Manuscripts

This page reflects manuscripts for the last 5 years. For a full list see Google Scholar, ResearchGate, Orcid, or ReseacherID

 

2023

  • van Heule, Machteld, Hossam El-Sheikh Ali, Cory Schlesener, Kirsten E Scoggin, Barry A Ball, Peter Daels, Bart C Weimer, Pouya Dini. 2023. The placental microbiome during nocardioform placentitis. Journal of Equine Veterinary Science 125:104789.
  • Gillian Carney, Bart C. Weimer, Marguerite Clyne and Tadhg Ó Cróinín. 2023. Different stages of the infection cycle are enriched for Campylobacterstrains with distinct phenotypes and levels of fluoroquinolone resistance. Microbiology 169:001349 (DOI:10.1099/mic.0.001349)
  • van Heule, Machteld, Hugo Fernando Monteiro, Ali Bazzazan, Kirsten Scoggin, Matthew Rolston, Hossam El-Sheikh Ali, Bart C. Weimer, Barry Ball, Peter Daels, Pouya Dini. 2023. Characterization of the Equine Placental Microbial Population in Healthy Pregnancies.  Theriogenology 206:60-70 (DOI:10.1016/j.theriogenology.2023.04.022)
  • Cunha, Lais, Hugo Monteiro, Igor Canisso, Rodrigo Bicalho, Felipe Cardoso,
    Bart C. Weimer, and Fabio Lima. 2023. Characterization of rumen microbiome and metabolome from an oro-esophageal probe and fluid, particulate and fluid-particulate fractions from rumen fistula in Holstein dairy cow. Sci reports 13:5854.
  • Worede, Dennis, Krystle L Reagan, Barbara A Byrne; Bart C Weimer, Steven E Epstein, Cory Lee Schlesener, Bihua C. Huang, Jane E Sykes. 2023. Characteristics of Extended-Spectrum β-Lactamase producing Enterobacterales isolated from dogs and cats, 2011-2021. Veterinary Sciences 10:178 (DOI:10.3390/vetsci10030178) (Special Issue Antimicrobial Use in Companion Animals).
  • Gonçalves-Oliveira, Jonathan, Ricardo Gutierrez, David A. Jaffe, Cory Lee Schlesener, Alvaro Aguilar-Setien, Henri-Jean Boulouis, Yaarit Nachum-Biala, B. Carol Huang,
    Bart C. Weimer, Bruno B. Chomel, Shimon Harrus. 2023. Genomic characterization of three novel Bartonella strains in rodents and bats from Mexico. Microorganisms 11:340 (DOI:10.3390/microorganisms11020340) (Special Issue Domestic Animals and Wildlife Zoonotic Microorganisms)
  • Mohamad-Fauzi, Nuradilla, Claire Shaw, Soraya H. Foutouhi, Matthias Hess, Nguyet Kong, Amir Kol, Dori Borjesson, Prerak Desai, Jigna Shah, James D. Murray, and
    Bart C. Weimer. 2023. Salmonella Enhances Osteogenic Differentiation in Adipose-Derived Mesenchymal Stem Cells. Frontiers in Cell and Developmental Biology 11:1077350 (DOI: 10.3389/fcell.2023.1077350) (Special Issue Membrane Traffic special issue)
  • Shetty, B. Dharmaveer, Noha Amaly, Bart C. Weimer, and Pramod Pandey. 2023. Predicting Escherichia coli levels in manure using machine learning in weeping wall and mechanical liquid-solid separation systems. Frontiers in Artificial Intelligence 5:921924 (DOI:10.3389/frai.2022.921924) (Special issue AI in Food, Agriculture and Water)

2022

  • Carey, M., et al. Kathryn E. Holt, et al., Bart C. Weimer. Global diversity and antimicrobial resistance of typhoid fever pathogens: insights from 13,000
    Salmonella Typhigenomes. 2022. MedRxiv (DOI:10.1101/2022.12.28.22283969).
  • Shaw, Claire, Matthias Hess, and Bart C. Weimer. 2022. Two-Component Systems Regulate Bacterial Virulence in Response to the Host Gastrointestinal Environment and Metabolic Cues. Virulence 13:1666–1680 (DOI:10.1080/21505594.2022.2127196; PMID: 36128741)
  • Pinho, Raquel M., Lydia C. Garas, B. Carol Huang, Bart C. Weimer, Elizabeth A. Maga. 2022.  Malnourishment affects gene expression along the length of the small intestine. Frontiers in Nutrition 2:1885 (DOI:10.3389/fnut.2022.894640).
  • Hurtado, Raquel; Debmalya Barh, Bart C. Weimer, Marcus Vinicius Canário Viana, Willi Quino, Renan Pedro Souza, Orson Mestanza, Rodrigo Profeta, Ronnie G. Gavilán, and Vasco Azevedo. 2022. WGS-based lineage and antimicrobial resistance pattern of
    Salmonella Typhimurium isolated during 2000-2017 in Peru. Antibiotics 11:1170(DOI:10.3390/antibiotics11091170)
  • da Cunha, Lais L., Hugo F. Monteiro, Igor F. Canisso, Rodrigo C. Bicalho, Felipe C. Cardoso, Bart C. Weimer, Fabio S. Lima. 2022. Characterization of rumen microbiome and metabolome from an oro-esophageal probe and fluid, particulate and fluid-particulate fractions from rumen fistula in Holstein dairy cows. BioRxiv (DOI:10.1101/2022.07.25.501495).
  • Chang, Ruixue, Pramod Pandey, Peja James, Prachi Pandey, Yanming Li, Ruihong Zhang, and Bart C. Weimer. 2022. Assessment Impacts of Ozone on Salmonella
    Typhimurium and Escherichia coli O157:H7 in Liquid Dairy Waste. Applied Sciences 12:6527. (DOI:10.3390/app12136527). (Special Issue New Trends in Waste Management Models).
  • Monteiro, H. F., Z. Zhou, M. S. Gomes, P. M. G. Peixoto, E. C. R. Bonsaglia, I. F. Canisso, B. C. Weimer, and F. S. Lima. 2022. Rumen and lower gut microbiomes relationship with feed efficiency and production traits throughout the lactation of Holstein dairy cows. Sci Report 12:4904. (DOI:10.1038/s41598-022-08761-5).
  • Aguilar-Zamora, Emmanuel, Bart C. Weimer, Roberto C. Torres, Alejandro Gomez-Delgado, Nayeli Ortiz-Olvera, Varenka Barbero-Becerro, Gerardo Aparicio-Ozores, Javier Torres, and Margarita Camorlinga-Ponce. 2022. Molecular epidemiology and antimicrobial resistance in hospitalized patients from Mexico. Frontiers in Microbiology 12:787451. (DOI:10.3389/fmicb.2021.787451).  
  • Weimer, B.C., 2022. Lactic Acid Bacteria: Physiology and Stress Responses. In: McSweeney, P.L.H., McNamara, J.P. (Eds.), Encyclopedia of Dairy Sciences (3rd edition), vol. 4. Academic Press, pp. 238–248. (DOI:10.1016/B978-0-12-818766-1.00377-9; ISBN: 9780128187661).

2021

  • Wang, Yi, Pramod K. Pandey, Colleen Chiu, Richard Jeannotte, Sundaram Kuppu, Ruihong Zhang, Richard Pereira, Bart C. Weimer, Nitin Nitin, Sharif Aly. 2021. Quantification of antibiotic resistance genes and mobile gene elements in manure from dairy farms in California. PeerJ 9:e12408 (DOI: 10.7717/peerj.12408).
  • Weimer, Bart C. 2021. Bacteria: A journal for the new developments and management of challenging area of microbiology. Bacteria 1:1-2 (DOI: 10.3390/bacteria1010001).
  • van Oosterhout, Cock, Jessica F. Stephenson, Bart C. Weimer, Hinh Ly, Neil Hall, Kevin M. Tyler.COVID-19 adaptive evolution during the pandemic – Implications of new SARS-CoV-2 variants on public health policies. Virulence 12:2013-2016 (DOI: 10.1080/21505594.2021.1960109).
  • Hernández-Juárez, Laura E., Margarita Camorlinga, Alfonso Méndez-Tenorio, Judith Flores Calderón, B. Carol Huang, DJ Darwin R. Bandoy, Bart C. Weimer, and Javier Torres. 2021. Analyses of publicly available Hungatella hathewayi genomes revealed genetic distances indicating they belong to more than one species. Virulence 12:1950-1964. (DOI:10.1080/21505594.2021.1950955).
  • Flores-Valdez, Mauricio, Miguel A. Ares, Roberto Rosales-Reyes, Javier Torres, Jorge A Girón, Bart C. Weimer, Alfonso Mendez Tenorio, and Miguel A. De la Cruz. 2021. Whole genome sequencing of pediatric Klebsiella pneumoniae strains reveals important insights into their virulence-associated traits. Frontiers in Microbiology 12:711577 (DOI: 10.3389/fmicb.2021.711577).
  • Weimer, Bart C., and DJ Darwin Bandoy. 2021. Where coronavirus variants emerge, surges follow – new research suggests how genomic surveillance can be an early warning system. TheConversation.com (https://theconversation.com/where-coronavirus-variants-emerge-surges-follow-new-research-suggests-how-genomic-surveillance-can-be-an-early-warning-system-158733)
  • Santos-Medellin, Christian, Zachary Liechty, Joseph Edwards, Bao Nguyen, Bihua Huang, Bart C. Weimer, and Venkatesan Sundaresan. 2021. Drought duration determines the recovery dynamics of rice root microbiomes. Nature Plants (DOI:10.1038/s41477-021-00967-1).
  • Borras, Eva, Leah Schrumpf, Noelle Stephens, Bart C. Weimer, Cristina E. Davis, and Edward S. Schelegle. 2021. Novel LC-MS methodology to detect and quantify ascorbic and uric acid simultaneously using different biological matrices. J. Chrom B:122588 (DOI:10.1016/j.jchromb.2021.122588).
  • Miller, John J.,Bart C. Weimer, Ruth Timme, Catharina Lüdeke, James Pettengill, DJ Darwin Bandoy, Allison Weis, James Kaufman, Bihua Huang, Justin Payne, Errol Strain, and Jessica Jones. 2021. Phylogenetic and biogeographic patterns of
    Vibrio parahaemolyticus from North America inferred from whole-genome sequence data. Appl. Environ. Microbiol. 87:e01403-20 (DOI:10.1128/AEM.01403-20; PMID: 33187991)
  • Bandoy, DJ Darwin, and Bart C. Weimer. 2021. Analysis of SARS-CoV-2 genomic epidemiology reveals disease transmission coupled to variant emergence and allelic variation. Nature Scientific Reports 11:7380-92 (DOI:10.1038/s41598-021-86265-4)
  • Hurley, Karyl, Caroline Mansfield, Ilze Matīse VanHoutan, Lauren Lacorcia, Karin Allenspach, Geoffrey Hebbard, Stanley L. Marks, Bob Poppenga, James H. Kaufman,
    Bart C. Weimer, Kevin Douglas Woolard,Joe Bielitzki,Derek Lulham, and Jerome Naar. 2021. A comparative analysis of two unrelated incidents of food-associated megaesophagus outbreaks in dogs: Latvia 2014-2016 and Australia 2017-2018. JAVMA 259:172-183. (DOI:10.2460/javma.259.2.172).
  • Beck, Kristen L., Niina Haiminen, David Chambliss, Stefan Edlund, Mark Kunitomi, Robert Baker, Peter Markwell, Bala Ganesan, Laxmi Parida, Ban Kawas, Matthew Davis, Robert Prill, Carol Huang, Nguyet Kong, Trey Marlowe, Steven Binder, Geraud Dubois, James Kaufman, and Bart C. Weimer. 2021. Characterizing the microbiome in factory ingredient samples using metatranscriptome deep sequencing data. npj Sci Food5. (DOI:10.1038/s41538-020-00083-y)

2020

  • Higdon, Shawn M., Tania Pozzo, Nguyet Kong, Bihua C. Huang, Mai Lee Yang, Richard Jeannotte, C. Titus Brown, Alan Bennett, and Bart C. Weimer. 2020. Genomic characterization of a diazotrophic microbiota associated with maize aerial root mucilage. PLoS One 15:e0239677 (DOI:10.1371/journal.pone.0239677)
  • Higdon, Shawn M., Bihua C. Huang, Alan B. Bennett, and Bart C. Weimer. 2020. Identification of nitrogen fixation genes in Lactococcus isolated from maize using population genomics and machine learning. Microorganisms8:2043 (DOI:10.3390/microorganisms8122043) (Special Issue – Plant microbe interactions)
  • Higdon, Shawn M., Tania Pozzo, Emily Tibbett, Colleen Chiu, Richard Jeannotte, Bart C. Weimer, and Alan B. Bennett. 2020. Diazotrophic bacteria from maize exhibit multifaceted plant growth promotion traits in multiple hosts. PLoS One 15:e0239081 (DOI:10.1371/journal.pone.0239081; PMID: 32925972)
  • Santos-Medellin, Christian, Zachary Liechty, Joseph Edwards, Bao Nguyen, Bihua Huang, Bart C. Weimer, Venkatesan Sundaresan. 2020. Drought duration determines the recovery dynamics of rice root microbiomes. BioRxiv (DOI:10.1101/2020.09.29.314781)
  • Nayfach, Stephen, Simon Roux, Rekha Seshadri, Daniel Udwary, Neha Varghese, Frederik Schulz, Dongying Wu, David Paez-Espino, I-Min Chen, Marcel Huntemann, Krishna Palaniappan, Joshua Ladau, Supratim Mukherjee, T.B.K. Reddy, Torben Nielsen, Edward Kirton, José P. Faria, Janaka N. Edirisinghe, Christopher S. Henry, Sean P. Jungbluth, Dylan Chivian, Paramvir Dehal, Elisha M. Wood-Charlson, Adam P. Arkin, Susannah Tringe, Axel Visel, IMG/M Data Consortium (Bart C. Weimer), Tanja Woyke, Nigel J. Mouncey, Natalia N. Ivanova, Nikos C. Kyrpides, Emiley A. Eloe-Fadrosh. 2020. A Genomic Catalogue of Earth’s Microbiomes. Nature Biotechnology (DOI:10.1038/s41587-020-0718-6
  • Chang, Ruixue, Pramod Pandey, Yanming Li, Chandrasekar Venkitasamy, Zhao Chen, Rodrigo Gallardo,Bart C. Weimer, Michele Jay-Russell. 2020. Assessment of Gaseous Ozone Treatment on Salmonella Typhimurium and Escherichia coli O157:H7. Reductions in Poultry Litter. Waste Management 117:42-47   DOI:10.1016/j.wasman.2020.07.039
  • Beck, Kristen L., Niina Haiminen, David Chambliss, Stefan Edlund, Mark Kunitomi, Robert Baker, Peter Markwell, Bala Ganesan, Laxmi Parida, Ban Kawas, Matthew Davis, Robert Prill, Carol Huang, Nguyet Kong, Trey Marlowe, Steven Binder, Geraud Dubois, James Kaufman, Bart C. Weimer. 2020. Characterizing the microbiome in factory ingredient samples using metatranscriptome deep sequencing data. BioRxiv (DOI:10.1101/2020.05.18.102574)
  • Higdon, Shawn M., Tania Pozzo, Emily Tibbett, Colleen Chiu, Richard Jeannotte, Bart C. Weimer, and Alan B. Bennett. 2020. Diazotrophic bacteria from maize exhibit multifaceted plant growth promotion traits and host adaptability. BioRxiv  (DOI: https://doi.org/10.1101/2020.04.27.064337)
  • Higdon, Shawn M., Tania Pozzo, Nguyet Kong, Bihua C. Huang, Mai Lee Yang, Richard Jeannotte, C. Titus Brown, Alan B. Bennett, Bart C. Weimer. 2020. Genomic characterization of a diazotrophic microbiota associated with maize aerial root mucilage. BioRxiv DOI:10.1101/2020.04.27.064337
  • Chen, Poyin, DJ Darwin Bandoy, Bart C. Weimer. 2020. Bacterial epigenomics: epigenetics in the age of population genomics. In The Pan-Genome – Diversity, Dynamics, and Evolution of Genomes. Ed.Duccio Medini and Hervé Tettelin. Springer, NYC, NY. ISBN 978-3-030-38281-0 (eBook); 978-3-030-38280-3 (hardback); DOI: 10.1007/978-3-030-38281-0
  • Pandey, Pramod, Sriram K Vidyarthi, Venkata Vaddella, Chandrasekar Venkitasamy, Maurice Pitesky, Bart C. Weimer, Alda F. A. Pires. 2020. Improving biosecurity procedures to minimize the risk of spreading pathogenic infections agents after carcass recycling. Front in Food Micro 11:623 DOI:10.3389/fmicb.2020.00623
  • Bandoy, DJ Darwin and Bart C. Weimer. 2020. Biological Machine Learning Combined with Campylobacter Population Genomics Reveals Virulence Gene Allelic Variants Cause Disease. DOI:10.3390/microorganisms8040549
  • Bandoy, DJ Darwin and Bart C. Weimer. 2020. Pandemic dynamics of COVID-19 using epidemic stage, instantaneous reproductive number, and pathogen genome identity (GENI) score: modeling molecular epidemiology. DOI:10.1101/2020.03.17.20037481
  •  Coolbear, T., Martin G. Wilkinson, Bart C. Weimer. 2020. Lactic Acid Bacteria in Flavor Development. DOI:10.1016/B978-0-12-818766-1.00019-2

2019

  • Foutouhi,Soraya H., Nuradilla Mohamad-Fauzi, Dylan Bobby Storey, Azarene A. Foutouhi, Nguyet Kong, Amir Kol, Dori Borjesson, Prerak Desai, Jigna Shah, James D. Murray, Bart C. Weimer. 2019. Salmonella Enhances Osteogenic Differentiation in Adipose-Derived Mesenchymal Stem Cells      (DOI: https://doi.org/10.1101/795617)
  • Bandoy, DJ Darwin R. and Bart C. Weimer.2019. Biological machine learning combined with bacterial population genomics reveals common and rare allelic variants of genes to cause disease BioRxiv    (DOI: https://doi.org/10.1101/739540)
  • Haiminen, Niina, Stefan Edlund, David Chambliss, Mark Kunitomi, Bart C. Weimer, Balasubramanian Ganesan, Robert Baker, Peter Markwell, Matthew Davis, B Carol Huang, Nguyet Kong, Robert Prill, Carl H Marlowe, André Quintanar, Sophie Pierre, Geraud Dubois, James Kaufman, Laxmi Parida, Kristen Beck. 2019. Food authentication from metagenome sequencing reads. Nature – Science of Food (DOI 10.1038/s41538-019-0056-6)
  • Kaufman, James H., Christopher A. Elkins, Matthew Davis, Allison M. Weis, Bihua C. Huang, Mark K. Mammel, Isha R. Patel, Kristen L. Beck, Stefan Edlund, David Chambliss, Judith Douglas, Simone Bianco, Mark Kunitomi, Bart C. Weimer. 2019. Insular Microbiogeography. In “Microbial Ecology: Current Advances from Genomics, Metagenomics and Other Omics”, pp. 45-64. Edited by Diana Marco. Caister Academic Press, Poole, UK. (ISBN: 978-1-912530-02-1) (https://doi.org/10.21775/9781912530021; chapter: https://doi.org/10.21775/9781912530021.04)
  • Gerst, Michelle, Emily Campbell, Carol Huang, Nguyet Kong, Bart C. Weimer, and Ahmed E. Yousef. 2018. Draft genome of Bacillus velezensis CE2 which genetically encodes a novel multi-component lantibiotic. Microbiology Resource Announcements (DOI 10.1128/MRA.01420-18)
  • Bandoy, DJ Darwin R., B Carol Huang, and Bart C. Weimer. 2019. Misclassification of a whole-genome sequence reference defined by the Human Microbiome Project: a detrimental carryover effect to microbiome studies. MedRxiv 19000489 (doi.org/10.1101/19000489).

2018

  • Kaufman, James, Ed Seabolt, Mark Kunitomi, Akshay Agarwal, Kristen Beck, Harsha Krishnareddy and Bart C. Weimer. 2018. Exploiting Functional Context in Biology: Reconsidering Classification of Bacterial Life. IEEE Computer Science 9:17-20. (DOI 10.1109/ICDEW.2018.00009)
  • Harness, E. Bart C. Weimer, JD Murray. 2018. Characterization of pig mesenchymal stromal cells for investigation of bacterial association and modification of stem cell function. Transgenic Research 27:485-485.
  • Van Deynze, Allen, Pablo Zamora, Pierre-Marc Delaux, Cristobal Heitmann, Dhileepkumar Jayaraman, Shanmugam Rajasekar, Junko Maeda, Srijak Bhatnagar, Guillaume Jospin, Danielle Graham, Richard Jeannotte, Donald Gibson, Aaron Darling, Kevin D. Schwartz, Alison M. Berry, Javier Lopez, Bart C. Weimer, Jonathan A. Eisen, Howard-Yana Shapiro, Jean-Michel Ané, and Alan B. Bennett. 2018. Nitrogen fixation in a landrace of maize is supported by a mucilage-associated diazotrophic microbiota. PLOS Biology. 16(8): e2006352. (https://doi.org/10.1371/journal.pbio.2006352).
  • Weimer, Bart C., Poyin Chen, Prerak T. Desai, Dong Chen, and Jigna Shah. 2018. Whole cell cross-linking to discover host-microbe protein cognate receptor/ligand pairs. Frontiers in Microbiology 9:1585. (doi: 10.3389/fmicb.2018.01585)
  • Arabyan, Narine and Bart C. Weimer. 2018. Glycosyide Hydrolases: Novel virulence factors during Salmonella infection Atlas of Science. In press.
  • Lawton, Samantha, Allison M. Weis, Barbara A. Byrne, Heather Fritz, Conor Taff, Andrea Townsend, Bart C. Weimer, Asli Mete, Sarah Wheeler, Walter M. Boyce. 2018. Comparative analysis of Campylobacter isolates from wild birds and chickens using MALDI-TOF, biochemical testing, and sequence analysis. Journal of Veterinary Diagnostic Investigation. (PMID: 29528812) (doi.org/10.1177/1040638718762562)
  • Zamuruyev, Konstantin O, Eva Borras, Dayna R Pettit, Alexander A Aksenov, Jason D Simmons, Bart C. Weimer, Michael Schivo, Nicholas J Kenyon, Jean-Pierre Delplanque, Cristina Davis. 2018. Effect of collection temperature on metabolite content in exhaled breath condensate. Analytica Chimica Acta.1006:49-60 https://doi.org/10.1016/j.aca.2017.12.025