Publications
Meat and Muscle Biology
Asmus AE, Belk KE, Noyes NR.
Genome Research
Shaw J, Boucher C, Yu YY, Noyes NR, Li H.
Exploring the phylogenetic diversity and antimicrobial activity of non-aureus staphylococci and mammaliicocci isolated from teat apices of organic dairy cows
Frontiers in Microbiology
Peña-Mosca F, Gaire TN, Dean C, Ferm P, Manriquez D, Pinedo P, Noyes NR, Caixeta L.
Associations between hyperketonemia and the rumen metagenome and metabolome in Holstein cows during the first 2 weeks postpartum
Animal microbiome
Gaire TN, Young J, Wehri T, Schwartz M, Singer R, Pieters M, Noyes NR.
Temporality and genetic relatedness of Salmonella in a pork processing facility
Journal of Food Protection
Asmus AE, Heimer KM, Davis KW, Ferm PM, Belk KE, Singer RS, Johnson TJ, Noyes NR.
Fresh pork microbiota is temporally dynamic and compositionally diverse across meat, contact surfaces, and processing lines in a pork processing facility
Applied Environmental Microbiology
Asmus AE, Gaire TN, Heimer KM, Belk KE, Singer RS, Johnson TJ, Noyes NR.
The gut microbiome and resistome of yellow perch (Perca flavescens) living in Minnesota lakes under varying anthropogenic pressure
One Health
Jimenez-Lopez O, Ray T, Dean C, Slizovskiy I, Deere J, Wolf T, Moore S, Primus A, Høy-Petersen J, Finstad S, Mo J, Sørum H, Noyes N.
The teat skin microbiota of organic primiparous dairy cows is dynamic during the transition period
Preventive Veterinary Medicine
Dean CJ, Ray T, Pena-Mosca F, Wehri TJ, Sharpe K, Antunes AM, Doster E, Fernandes L, Calles VF, Bauman C, Heins B, Pinedo P, Machado V, Caixeta LS, Noyes NR.
Influence of rainfall on size-resolved bioaerosols around a livestock farm
Science of The Total Environment
Kwak N, Tsameret S, Gaire TN, Mendoza KM, Cortus EL, Cardona C, Noyes NR, Li J.
Slaughtering processes impact microbial communities and antimicrobial resistance genes of pig carcasses
Science of The Total Environment
Gaire TN, Odland CA, Zhang B, Slizovskiy IB, Jorgenson B, Wehri T, Ferm PM, Schuld J, Hansen D, Singer J, Asmus A, Ray T, Dee S, Nerem J, Davies P, Noyes NR
Scalable de novo classification of antimicrobial resistance of Mycobacterium Tuberculosis
Bioinformatics
Serajian M, Marini S, Alanko JN, Noyes NR, Prosperi M and Boucher C.
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.
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.
Evaluating variations in metabolic profiles during the dry period related to the time of hyperketonemia onset in dairy cows
PLOS ONE
Rodriguez, Z., Picasso-Risso, C., Gaire, T., Nakagawa, K., Noyes, N., Cramer, G., & Caixeta, L.
The K-mer antibiotic resistance gene
variant analyzer (KARGVA)
Frontiers in Microbiology
Marini, S., Boucher, C., Noyes, N., & Prosperi, M.
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.
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.
Target-enriched long-read sequencing (TELSeq) contextualizes antimicrobial resistance genes in metagenomes
Microbiome
Slizovskiy, I., Oliva, M., Settle, J., Zyskina, L., Prosperi, M., Boucher, C., & Noyes, N.
The impacts of viral infection and subsequent antimicrobials on the microbiome-resistome of growing pigs
Microbiome
Gaire, T., Odland, C., Zhang, B., Ray, T., Doster, E., Nerem, J., Dee, S., Davies, P., & Noyes, N.R.
Syotti: Scalable bait design for DNA enrichment
Bioinformatics
Alanko, J., Slizovskiy, I., Lokshtanov, D., Gagle, T., Noyes, N., & Boucher, C.
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
Gigascience
Marini, S., Olivia, M., Slizovskiy, I. B., Das, R.A., Noyes, N. R., Kahveci, T., Boucher, C.A., & Prosperi, M.
Evaluation of the impact of
antimicrobial use protocols in PRRS virus infected swine on phenotypic
antimicrobial resistance
patterns
Applied and Environmental Microbiology
Odland, C., Elder R., Noyes, N.R., Dee, S., Nerem, J., & Davies, P.
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
Metagenome SNP calling via read dolored de Bruijn Graphs
Bioinformatics
Bahar Alipanahi, Martin D Muggli, Musa Jundi, Noelle R Noyes, Christina A Boucher
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
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.
Metagenomics of meat and poultry
Food Microbiology: Fundamentals and Frontiers, 5th Ed.
Weinroth MD, Noyes NR, Morley PS, Belk KE.
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
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
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.
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.
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.
Cell Report Methods
Bravo JE, Newsom KJ, Noyes NR, Boucher C.
Reducing skin microbiome exposure impacts through swine farm biosecurity
Gigascience
Slizovskiy IB, Gaire TN, Ferm PM, Odland CA, Dee SA, Nerem J, Bravo JE, Kimball AD, Boucher C, Noyes NR.
Assessment of a program for monitoring antimicrobial purchase and resistance
in Escherichia coli and Salmonella enterica on pig farms in the Midwestern United States from May 2020 through October 2023
Frontiers in Veterinary Science
Havas KA, Edler R, Ruesch L, Braun M, Ferm P, Noyes NR, Goodman LB, Scott HM, Nerem J, Spronk T, Dee SA.
The impact of pooling
on the observed microbiome profile of preweaned piglet feces
EMS Microbiology Ecology
Gaire TN, Young J, Wehri T, Schwartz M, Singer R, Pieters M, Noyes NR.
Microbiome characterization of
two fresh pork cuts during production in a pork fabrication facility
Microbiology Spectrum
Asmus AE, Gaire TN, Schweisthal KJ, Staben SM, Noyes NR.
Evaluation of antibiotic purchase data for ceftiofur and enrofloxacin and minimum inhibitory concentrations among Escherichia coli isolates from swine farms in the Midwestern United States using multiple statistical models
Preventive Veterinary Medicine
Havas KA, Edler R, Ruesch L, Braun M, Nerem J, Dee S, Spronk T, Goodman LB, Noyes N, Scott HM.
Factors impacting target-enriched long-read sequencing of resistomes and mobilomes
Genome Research
Slizovskiy IB, Bonin N, Bravo JE, Ferm PM, Singer J, Boucher CA, Noyes NR.
The TELCoMB protocol for
high-sensitivity detection of ARG-MGE colocalizations in complex microbial communities
Current Protocols
Bravo JE, Slizovskiy I, Bonin N, Oliva M, Noyes NR, Boucher C.
Using a multi-omics approach to explore potential associations with rumen content and serum of cows with different milk production levels based on genomic predicted transmitting ability for milk and
phenotypic milk production
PLoS ONE
Ravelo AD, Ferm P, Guo Y, Omontese BO, Morley PS, Chen C, Noyes NR
Analysis of the northern pitcher plant (Sarracenia purpurea L.) phytotelm bacteriome throughout a temperate region growing season
PLoS One
Melchior PP, Reiss E, Payne Z, Vuong N, Hovorka K, Lindsay HL, Diaz GR, Gaire T, Noyes NR.
The impact of kit, environmental and sampling contamination on the observed microbiome of bovine milk
mSystems
Dean CJ, Deng Y, Wehri TC, Pena-Mosca F, Ray T, Crooker BA, Godden SM, Caixeta LS, Noyes NR.
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.
Temporal dynamics of the fecal microbiome infemale pigs from early life through estrus, parturition, and weaning of the first litter of
piglets
Animal Microbiome
Gaire T.N., Scott H.M., Noyes N.R., Ericsson A.C., Tokach M.D., William H., Menegat M.B., Vinasco J., Nagaraja T.G., Volkova V.V.
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.
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.
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.
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.
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.
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.
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.
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
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
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
PLOS ONE
Noelle Noyes, Kyu-Chul Cho, Jacques Ravel, Larry J. Forney, Zaid Abdo
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
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
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
Antimicrobial resistance in Escherichia coli recovered from feedlot cattle and associations with antimicrobial se
PLOS ONE
Antimicrobial resistance in Escherichia coli recovered from feedlot cattle and associations with antimicrobial use
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.