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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.

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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.

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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.

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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.

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Age influences the temporal dynamics of microbiome and antimicrobial resistance genes among fecal bacteria in a cohort of production pigs

Animal Microbiome

Gaire, T., Scott, H., Noyes, N., Ericsson, A., Tokach, M., Menegat, M., Vinasco, J., Roenne, B., Ray, T., Nagaraja, T.G., & Volkova, V.

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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.

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Evaluating the effects of antimicrobial drug use on the ecology of antimicrobial resistance and microbial community structure in beef feedlot cattle


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.

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Factors influencing usage of antimicrobial drugs among pastoralists in Kenya

Tropical Animal Health and Production 

Makau, D., Slizovskiy, I., Obanda, V., Noyes, N., Johnson, J., Oakes, M., Travis, D., VanderWaal, K., & Omondi, G.

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A longitudinal investigation of the effects of age, dietary fiber type and level, and injectable antimicrobials on the fecal microbiome and antimicrobial resistance of finisher pigs

Journal of Animal Science

Gaire, T., Noyes, N.R., Scott, H.M., Nagaraja, T.G., & Volkova, V.


Evaluation of contamination in milk samples pooled from independently collected quarters within a laboratory setting 

Frontiers in Microbiology

Dean, C., Fernandes, L.M., Mosca, F., Caixeta, L., Machado, V., & Noyes, N.R.

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Challenges in large-scale life science projects and implications for training


Humanities and Social Sciences Communication

Morrison-Smith, S., Noyes, N.R., Boucher, C.A., & Ruiz, J.


The microbiome of common bedding materials before and after use on commercial dairy farms

Animal Microbiome

Ray, T., Gaire, T.N., Dean, C.J., Rowe, S., Godden, S.W., & Noyes, N.R.


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.

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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.


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


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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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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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.


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


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

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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.


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


Whole-genome sequencing and concordance between antimicrobial susceptibility genotypes and phenotypes of bacterial isolates associated with bovine respiratory disease


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


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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Antimicrobial resistance in Escherichia coli recovered from feedlot cattle and associations with antimicrobial Use



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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Mannheimia haemolytica in heedlot 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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Predictive models for metritis cure using farm-collected data, metabolic and inflammation biomarkers, and hemogram variables measured at diagnosis

Journal of Dairy Science

Menta, P., Prim, J., de Oliveria, E., Lima, F., Klibs, G., Noyes, N.,

Ballou, M., & Machado, V.

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Effect of castration timing and weaning strategy on the rumen metagenome of beef calves

Animal Microbiome

Diaz, G., Gaire, T., Ferm, P., Case, L., Caixeta, L., Goldsmith, T.,

Armstrong, J., & Noyes, N.

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Evaluating variations in metabolic profiles during the dry period related to the time of hyperketonemia onset in dairy cows


Rodriguez, Z., Picasso-Risso, C., Gaire, T., Nakagawa, K., Noyes, N., Cramer, G., & Caixeta, L.

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The K-mer antibiotic resistance gene
variant analyzer (KARGVA)


Frontiers in Microbiology

Marini, S., Boucher, C., Noyes, N., & Prosperi, M.

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Elucidation of genomic conjugative features and associated cargo genes across bacterial genera using genus-genus mobilization networks

Frontiers in Genetics

Nayar, G., Terrizzano, I., Seabolt, E., Agarwal, A., Boucher, C., Ruiz, J., Slizovskiy, I., Kaufman, J., & Noyes, N.

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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. 

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Target-enriched long-read sequencing (TELSeq) contextualizes antimicrobial resistance genes in metagenomes


Slizovskiy, I., Oliva, M., Settle, J., Zyskina, L., Prosperi, M., Boucher, C., & Noyes, N.

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The impacts of viral infection and subsequent antimicrobials on the microbiome-resistome of growing pigs



Gaire, T., Odland, C., Zhang, B., Ray, T., Doster, E., Nerem, J., Dee, S., Davies, P., & Noyes, N.R.

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Syotti: Scalable bait design for DNA enrichment


Alanko, J., Slizovskiy, I., Lokshtanov, D., Gagle, T., Noyes, N., & Boucher, C. 

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Cow-related factors associated with intramammary infections during the 1st week postpartum in primiparous dairy cows in certified organic herds

The Veterinary Journal

Fernandes, L., Celestino, M.L., Menta, P.R., Silva, T.H., Paiva, D., Ribeiro, T.L., Caixeta, L.S., Noyes, N.R., & Machado, V.S.


Towards routine employment of computational tools for antimicrobial resistance determination via high-throughput sequencing

Briefings in Bioinformatics

Marini, S.,  Mora, R., Boucher, C., Noyes, N.R., & Prosperi, M.


AMR-meta: a k-mer and metafeature approach to classify antimicrobial resistance from high-throughput short-read metagenomics data


Marini, S., Olivia, M., Slizovskiy, I. B., Das, R.A., Noyes, N. R., Kahveci, T., Boucher, C.A., & Prosperi, M.

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


Applied and Environmental Microbiology

Odland, C., Elder R., Noyes, N.R., Dee, S., Nerem, J., & Davies, P.

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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


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 dolored de Bruijn Graphs



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

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


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


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.

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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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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.


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


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


Succinct colored de Bruijn Graphs


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


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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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.

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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. 

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Rapid Salmonella detection in experimentally inoculated equine faecal and veterinary hospital environmental samples using commercially available lateral flow immunoassays

Equine Veterinary Journal

Burgess, B. A., Noyes, N. R., Bolte, D. S., Hyatt, D. R., van Metre, D. C., & Morley, P. S.

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