Publications
A randomized controlled trial evaluating the efficacy of systemic ceftiofur administration for metritis therapy in dairy cows and the effect of metritis cure on economically important outcomes
Journal of Dairy Science
Menta, P., Fernandes, L., Prim, J., De Oliveria, E., Lima, F., Galvao, K., Noyes, N., Ballou, M., & Machado, V.
Exploring associations between the teat apex microbiome and Staphylococcus aureus intramammary infection risk in primiparous cows under organic directives using shotgun metagenomics and bacterial culture.
Applied and Environmental Microbiology
Dean, C., Pena-Mosca, F., Ray, T., Wheri, T., Sharpe, K., Junior, A., Doster, E., Fernandes, L., Calles V., Bauman, C., Godden, S., Heins, B., Pinedo, P., Machado, V., Caixeta, L., & Noyes, N.
Associations between early lactation intramammary infections and udder health and performance during the first 180 days in milk in first-lactation organic dairy cows
Journal of Dairy Science
Pena-Mosca, F., Dean, C., Fernandes, L., Doster, E., Sharpe, K., Ray, T., Feijoo, V., Antunes, A., Baumann, C., Wehri, T., Pinedo, P., Machado, V., Noyes, N., & Caixeta, L.
Investigation of intramammary infections in primiparous cows during early lactation on organic dairy farms
Journal of Dairy Science
Pena-Mosca, F., Dean, C., Machado, V., Fernandes, L., Pinedo, P., Doster, E., Heins, B., Sharpe, K., Ray, T., Feijoo, V., Antunes, A., Baumann, C., Wehri, T., Noyes, N., & Caixeta, L.
MEGARes and AMR++, v3.0 an updated comprehensive database of antimicrobial resistance determinants and an improved software pipeline for classification using high-throughput sequencing
Nucleic Acid Research
Bonin, N., Doster, E., Worley, H., Pinnel, L., Bravo, J., Ferm, P., Marini, S., Prosperi, M., Noyes, N., Morley, P., & Boucher, C.
Evaluating the effects of antimicrobial drug use on the ecology of antimicrobial resistance and microbial community structure in beef feedlot cattle
Microbiology
Doster, E., Pinnell, L., Noyes, N., Parker, J., Anderson, C., Booker, C., Hannon, S.J., McAllister, T.A., Gow, S.P,, Belk K.E., & . Morley, P.
Considerations and best practices for animal science 16S ribosomal RNA gene sequencing microbiome studies
Journal of Animal Science
Weinroth, M.D., Belk, A.D., Dean, C.J., Noyes, N.R., Dittoe, D.K., Rothrock, M.J., Jr., Rickie, S.C., Myer, P.R., Henniger, M.T., Ramirez, G.A., Oakley, B.B., Summers, K.L., Miles, A.M., Ault-Seay, T.B., Yu, Z., Metcalf, J., & Wells, J.
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
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
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
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
Advancing antimicrobial resistance monitoring in surface waters with metagenomic and quasimetagenomic methods
PLOS Water
Ottesen, A., Kocurek, B., Ramachandran, P., Reed, E., Commichaux, S., Engelbach, G., Nannekm M., Fleurant, S.S., Zhao, S., Kabera, C., Merrill, A., Bonin, N., Worley, H., Noyes, N.R., Boucher, C., McDermott, P., & Strain, E.
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
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.
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.
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
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.
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
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
Use of metagenomic shotgun sequencing technology to detect foodborne pathogens within the microbiome of the beef production chain
Applied and Environmental Microbiology
Yang, X., Noyes, N., Doster, E., Martin, J., Linke, L., Magnuson, R., Yang, H., Geornaras, I., Woener, D., Jones, K.L., Boucher, C., Morley, P.S., & Belk, K.