Publications

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Evaluation of the impact of
antimicrobial use protocols in PRRS virus infected swine on phenotypic
antimicrobial resistance
patterns.

 

Applied and Environmental Microbiology

Noyes NR, Slizovskiy IB, Singer RS

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Beyond Antimicrobial Use: A Framework for Prioritizing Antimicrobial Resistance Interventions

 

Annual Review of Animal Biosciences

Noyes NR, Slizovskiy IB, Singer RS

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Investigating the cow skin and teat canal microbiomes of the bovine udder using different sampling and sequencing approaches
 

Journal of Dairy Science

C.J.Dean, I.B.Slizovskiy, K.K.Crone, A.X.Pfennig, B.J.Heins, L.S.Caixeta, N.R.Noyes

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Metagenome SNP Calling via Read Colored de Bruijn Graphs

 

Bioinformatics

Bahar Alipanahi, Martin D Muggli, Musa Jundi, Noelle R Noyes, Christina A Boucher

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A Cautionary Report for Pathogen Identification Using Shotgun Metagenomics; A Comparison to Aerobic Culture and Polymerase Chain Reaction for Salmonella enterica Identification
 

Frontiers in Microbiology

Doster E, Rovira P, Noyes NR, Burgess BA, Yang X, Weinroth MD, Linke L, Magnuson R, Boucher CA, Belk KE, Morley PS.

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Characterization of the Microbial Resistome in Conventional and “Raised Without Antibiotics” Beef and Dairy Production Systems
 

Frontiers in Microbiology

Rovira, P, McAllister TA, Lakin SM, Cook SR, Doster E, Noyes NR, Weinroth MD, Yang X, Parker JK, Boucher CA, Booker CW, Woerner DR, Belk KE, Morley PS.

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PrPC knockdown by liposome-siRNA-peptide complexes (LSPCs) prolongs survival and normal behavior of prion-infected mice immunotolerant to treatment

PLOS ONE

Heather Bender, Noelle Noyes, Jessica L. Annis, Amanda Hitpas, Luke Mollnow, Kendra Croak, Sarah Kane, Kaitlyn Wagner, Steven Dow, Mark Zabel

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Circulation of plasmids harboring resistance genes to quinolones and/or extended spectrum cephalosporins in multiple Salmonella enterica serotypes from swine in the United States

Antimicrobial Agents and Chemotherapy

Elnekave E, Hong SL, Lim S, Hayer SS, Boxrud D, Taylor AJ, Lappi V, Noyes NR, Johnson TJ, Rovira A, Davies P, Perez A, Alvarez J

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Investigating effects of tulathromycin metaphylaxis on the fecal resistome and microbiome of feedlot cattle early in the feeding period using shotgun metagenomic sequencing

Frontiers in Microbiology

Doster E*, Rovira P, Noyes NR*, Burgess BA, Yang X, Weinroth MD, Lakin SM, Dean CJ, Linke L, Magnuson R, Jones KI, Boucher C, Ruiz J, Belk KE**, Morley PS**. *,** Authors contributed equally.

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Impact of sequencing depth on the characterization of the microbiome and resistome

Scientific Reports

Rahat Zaheer, Noelle Noyes, Rodrigo Ortega Polo, Shaun R. Cook, Eric Marinier, Gary Van Domselaar, Keith E. Belk, Paul S. Morley & Tim A. McAllister

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Enrichment allows identification of diverse, rare elements in metagenomic resistome-virulome sequencing

Microbiome

Noelle R. Noyes, Maggie D. Weinroth, Jennifer K. Parker, Chris J. Dean, Steven M. Lakin, Robert A. Raymond, Pablo Rovira, Enrique Doster, Zaid Abdo, Jennifer N. Martin, Kenneth L. Jones, Jaime Ruiz, Christina A. Boucher, Keith E. Belk, and Paul S. Morley

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Succinct Colored de Bruijn Graphs


 

Bioinformatics

Martin D. Muggli, Alexander Bowe, Noelle R. Noyes, Paul S. Morley, Keith E. Belk, Robert Raymond, Travis Gagie, Simon J. Puglisi, Christina Boucher

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Characterization of the resistome in manure, soil and wastewater from dairy and beef production systems
 

Scientific Reports

Noelle R. Noyes, Xiang Yang, Lyndsey M. Linke, Roberta J. Magnuson, Shaun R. Cook, Rahat Zaheer, Hua Yang, Dale R. Woerner, Ifigenia Geornaras, Jessica A. McArt, Sheryl P. Gow, Jaime Ruiz, Kenneth L. Jones, Christina A. Boucher, Tim A. McAllister, Keith E. Belk & Paul S. Morley

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Mannheimia haemolytica in Feedlot Cattle: Prevalence of Recovery and Associations with Antimicrobial Use, Resistance, and Health Outcomes
 

Journal of Veterinary Internal Medicine

Noyes, N. R., Benedict, K. M., Gow, S. P., Booker, C. W., Hannon, S. J., McAllister, T. A., & Morley, P. S. 

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Antimicrobial Resistance in Escherichia coli Recovered from Feedlot Cattle and Associations with Antimicrobial Use
 

PLOS ONE

Benedict, K.M., Gow, S.P., McAllister, T.A., Booker, C.W., Hannon, S.J., Checkley, S.L., Noyes, N.R., & Morley, P.S.

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Effect of subclinical mastitis
detected in the first month of lactation on somatic cell count linear scores, milk yield, fertility, and culling of dairy cows
in certified organic herds.

 

Journal of Dairy Science

Fernandes LM, Guimaraes I, Noyes NR, Caixeta L, Machado, V.

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Exploring Prediction of Antimicrobial
Resistance Based on Protein Solvent Accessibility Variation


 

Frontiers in Genetics

Marini S, Slizovskiy IB, Noyes NR, Boucher C, Prosperi M.

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Mobilization of Antibiotic Resistance: Are Current Approaches for Colocalizing Resistomes and Mobilomes Useful?
 

Frontiers in Microbiology

Ilya B. Slizovskiy, Kingshuk Mukherjee, Christopher J. Dean, Christina Boucher, Noelle R. Noyes

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MEGARes 2.0: a database for classification of antimicrobial drug, biocide and metal resistance determinants in metagenomic sequence data
 

Nucleic Acids Research

Enrique Doster, Steven M. Lakin, Christopher J. Dean, Cory Wolfe, Jared G. Young, Christina Boucher, Keith E Belk, Noelle R Noyes, Paul S Morley

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Genome sequence of Listeria innocua
strain MEZLIS26 isolated from a goat in South Africa


 

Microbiology Resource Announcements

Zowalaty ME, Hickman R, Zishiri O, Noyes NR, Järhult J.

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Metagenomics of Meat and Poultry

 

Food Microbiology: Fundamentals and Frontiers, 5th Ed.

Weinroth MD, Noyes NR, Morley PS, Belk KE.

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Hierarchical Hidden Markov models enable accurate and diverse detection of antimicrobial resistance sequences

 

Communications Biology

Lakin SM, Kuhnle A, Alipanahi B, Noyes NR, Dean C, Martin M, Raymond RE, Zaid A, Prosperi

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A Comparative Study of Serum Biochemistry, Metabolome and Microbiome Parameters of Clinically Healthy, Normal Weight, Overweight, and Obese Companion Dogs

Topics in Companion Animal Medicine

Forster GM, Stockman J, Noyes NR, Heuberger AL, Broeckling CD, Bantle CM, Ryan EP.

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Effects of Ceftiofur and Chlortetracycline on the Resistome of Feedlot Cattle
 

Applied and Environmental Microbiology

Margaret D. Weinroth, H. Morgan Scott, Bo Norby, Guy H. Loneragan, Noelle R. Noyes, Pablo Rovira, Enrique Doster, Xiang Yang, Dale R. Woerner, Paul S. Morley and Keith E. Belk

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Associations between sexual habits, menstrual hygiene practices, demographics and the vaginal microbiome as revealed by Bayesian network analysis

PLOS ONE

Noelle Noyes, Kyu-Chul Cho, Jacques Ravel, Larry J. Forney, Zaid Abdo

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Whole-Genome Sequencing and Concordance Between Antimicrobial Susceptibility Genotypes and Phenotypes of Bacterial Isolates Associated with Bovine Respiratory Disease

G3

Owen JR, Noyes N, Young AE, Prince DJ, Blanchard PC, Lehenbauer TW, Aly SS, Davis JH, O'Rourke SM, Abdo Z, Belk K, Miller MR, Morley P, Van Eenennaam AL

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MEGARes: an antimicrobial resistance database for high throughput sequencing

 

Nucleic Acids Research

Steven M. Lakin, Chris Dean, Noelle R. Noyes, Adam Dettenwanger, Anne Spencer Ross, Enrique Doster, Pablo Rovira, Zaid Abdo, Kenneth L. Jones, Jaime Ruiz, Keith E. Belk, Paul S. Morley, Christina Boucher

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Resistome diversity in cattle and the environment decreases during beef production
 

eLife

Noelle R Noyes, Xiang Yang, Lyndsey M Linke, Roberta J Magnuson, Adam Dettenwanger, Shaun Cook, Ifigenia Geornaras, Dale E Woerner, Sheryl P Gow, Tim A McAllister, Hua Yang, Jaime Ruiz, Kenneth L Jones, Christina A Boucher, Paul S Morley, Keith E Belk

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Modelling considerations in the analysis of associations between antimicrobial use and resistance in beef feedlot cattle
 

Epidemiology and Infection

Noyes, N. R., Benedict, K. M., Gow, S. P.,  Waldner, C.L., Reid-Smith, R.J., Booker, C. W., McAllister, T. A., & Morley, P. S.