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                    U.S. DEPARTMENT OF AGRICULTURE
 Egg and Poultry Production Safety Research Unit: Athens, GA
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ARS Home Southeast Area Athens, Georgia U.S. National Poultry Research Center Egg and Poultry Production Safety Research Unit People & Locations







Michael James Rothrock, Jr.

                                                                (PhD)
                        Egg and Poultry Production Safety Research Unit

                        




                        
                        Microbiologist
                        Phone: (706) 546-3072
                        
                        
                        Fax: (706) 546-3633(Employee information on this page comes from the REE Directory. Please contact your front office staff to update the REE Directory.)
                            ProjectsReduction of Foodborne Pathogens and Antimicrobial Resistance in Poultry Production Environments
                                                    In-House Appropriated
                                                                    (D)Accession Number: 438928Reduction of Foodborne Pathogens and Antimicrobial Resistance in Poultry Production Environments
                                                    Non-Assistance Cooperative Agreement
                                                                    (S)Accession Number: 444109Identify Environmental and Management Drivers of Foodborne Pathogen Ecology Under Pastured Poultry Rearing Systems
                                                    Non-Assistance Cooperative Agreement
                                                                    (S)Accession Number: 444742**Publications**
                                                (Clicking on the reprint icon
                                                    Reprint Icon
                                                    will take you to the publication reprint.)Alternative Additives for Organic and Natural Ready-to-Eat Meats to Control Spoilage and Maintain Shelf Life: Current Perspectives in the United States
                                                        

- (Peer Reviewed Journal)Bodie, A.R., Wythe, L.A., Dittoe, D.K., Rothrock Jr, M.J., Obryan, C.A., Ricke, S.C. 2024. Alternative Additives for Organic and Natural Ready-to-Eat Meats to Control Spoilage and Maintain Shelf Life: Current Perspectives in the United States. Foods. https://doi.org/10.3390/foods13030464.Relationship of the Poultry Microbiome to Pathogen Colonization, Farm Management, Poultry Production, and Foodborne Illness Risk Assessmen
                                                        

- (Peer Reviewed Journal)Xu, X., Rothrock Jr, M.J., Dev Kumar, G., Mishra, A. 2023. Relationship of the Poultry Microbiome to Pathogen Colonization, Farm Management, Poultry Production, and Foodborne Illness Risk Assessmen. Journal of Food Protection.  https://doi.org/10.1016/j.jfp.2023.100169.Listeria Occurrence in Conventional and Alternative Egg Production Systems
                                                        

- (Peer Reviewed Journal)Ricke, S.C., Obryan, C.A., Rothrock Jr, M.J. 2023. Listeria Occurrence in Conventional and Alternative Egg Production Systems. Microorganisms. https://doi.org/10.3390/microorganisms11092164.Predicting Foodborne Pathogens and Probiotics Taxa within Poultry-Related Microbiomes Using a Machine Learning Approach
                                                        

- (Peer Reviewed Journal)Ayoola, M., Pillai, N., Nanduri, B., Rothrock Jr, M.J., Ramkumar, M. 2023. Predicting Foodborne Pathogens and Probiotics Taxa within Poultry-Related Microbiomes Using a Machine Learning Approach. Animal Microbiome. https://doi.org/10.1186/s42523-023-00260-w.Assessing the risk of seasonal effects of Campylobacter contaminated broiler meat prepared in-home in the United States
                                                        

- (Peer Reviewed Journal)Xu, X., Rothrock Jr, M.J., Dev Kumar, G., Mishra, A. 2023. Assessing the risk of seasonal effects of Campylobacter contaminated broiler meat prepared in-home in the United States. Foods. https://doi.org/10.3390/feeds12132559.Towards Optimal Microbiome to Inhibit Multidrug Resistance
                                                        

- (Proceedings)Pillai, N., Nanduri, B., Rothrock Jr, M.J., Chen, Z., Ramkumar, M. 2023. Towards Optimal Microbiome to Inhibit Multidrug Resistance. IEEE/ACM Transactions on Computational Biology and Bioinformatics. https://doi.org/10.1109/CIBCB56990.2023.10264914.Tanshinone IIA-loaded nanoparticles and neural stem cell combination therapy improves gut homeostasis and recovery in a pig ishemic stroke model
                                                        

- (Peer Reviewed Journal)Jeon, J.H., Kaiser, E.E., Water, E.S., Yang, X., Lourenco, J.M., Fagan, M.M., Schuelin, K.M., Sneed, S.E., Shin, S.K., Kinder, H.A., Kumar, A., Platt, S., Anh, J., Duberstein, K.J., Rothrock Jr, M.J., Callaway, T.R., Xie, J., West, F.D., Park, H. 2023. Tanshinone IIA-loaded nanoparticles and neural stem cell combination therapy improves gut homeostasis and recovery in a pig ishemic stroke model. Nature Scientific Reports. https://doi.org/10.1038/s41598-023-29282-9.Serotype screening of salmonella enterica subspecies I by intergenic sequence ribotyping (ISR): Critical updates
                                                        

- (Peer Reviewed Journal)Guard, J.Y., Jones, D.R., Gast, R.K., Garcia, J.S., Rothrock Jr, M.J. 2022. Serotype screening of salmonella enterica subspecies I by intergenic sequence ribotyping (ISR): Critical updates. Microorganisms. 11(1):97. https://doi.org/10.3390/microorganisms11010097.An ensemble learning approach to identify pastured poultry farm practice variables and soil constituents that promote Salmonella prevalence
                                                        

- (Peer Reviewed Journal)Pillai, N., Ayoola, M.B., Nanduri, B., Rothrock Jr, M.J., Ramkumar, M. 2022. An ensemble learning approach to identify pastured poultry farm practice variables and soil constituents that promote Salmonella prevalence. Heliyon. 8(11):e11331. https://doi.org/10.1016/j.heliyon.2022.e11331.Preharvest Environmental and Management Drivers of Multidrug Resistance in Major Bacterial Zoonotic Pathogens in Pastured Poultry Flocks
                                                        

- (Peer Reviewed Journal)Ayoola, M.B., Pillai, N., Nanduri, B., Rothrock Jr, M.J., Ramkumar, M. 2022. Preharvest Environmental and Management Drivers of Multidrug Resistance in Major Bacterial Zoonotic Pathogens in Pastured Poultry Flocks. Microorganisms. v. 10 (9). https://doi.org/10.3390/microorganisms10091703.Comparison between LASSO and RT methods for prediction of generic E. coli concentration in pastured poultry farms
                                                        

- (Peer Reviewed Journal)Xu, K., Rothrock Jr, M.J., Reeves, J., Dev Kumar, G., Mishra, A. 2022. Comparison between LASSO and RT methods for prediction of generic E. coli concentration in pastured poultry farms. Food Research International. v.161, p.111860. https://doi.org/10.1016/j.foodres.2022.111860.Using E. coli populations to predict foodborne pathogens in pastured poultry farms.
                                                        

- (Peer Reviewed Journal)Xu, X., Rothrock Jr, M.J., Reeves, J., Mishra, A. 2022. Using E. coli populations to predict foodborne pathogens in pastured poultry farms. Food Microbiology. https://doi.org/10.1016/j.fm.2022.104092.Litter commensal bacteria can limit the horizontal gene transfer of antimicrobial resistance to Salmonella in chickens.

- (Peer Reviewed Journal)Oladeinde, A.A., Abdo, Z., Zwirzitz, B., Woyda, R., Lakin, S.M., Press, M.O., Cook, K.L., Cox Jr, N.A., Thomas, J.C., Looft, T.P., Rothrock Jr, M.J., Zock, G.S., Plumblee Lawrence, J.R., Cudnik, D., Ritz, C. 2022. Litter commensal bacteria can limit the horizontal gene transfer of antimicrobial resistance to Salmonella in chickens. Applied and Environmental Microbiology.88(9). https://doi.org/10.1128/aem.02517-21Communicating the utility of the microbiome and bioinformatics to small flock poultry producers
                                                        

- (Peer Reviewed Journal)Ricke, S.C., Dittoe, D.K., Tarcin, A.A., Rothrock Jr, M.J. 2022. Communicating the utility of the microbiome and bioinformatics to small flock poultry producers. Poultry Science. 101(5) https://doi.org/10.1016/j.psj.2022.101788.The impact of pre-slaughter fasting on the ruminal microbial population of commercial angus steers
                                                        

- (Peer Reviewed Journal)Welch, C.W., Lourenco, J.M., Seidel, D.S., Krause, T.R., Rothrock Jr, M.J., Pringle, T., Callaway, T.R. 2021. The impact of pre-slaughter fasting on the ruminal microbial population of commercial angus steers. Microorganisms. 9(12):2625. https://doi.org/10.3390/microorganisms9122625.Determination of bacterial pathogen diversity and prevalence in acidified re-used poultry litter during commercial live production

- (Abstract Only)Considerations and best practices in animal science 16S ribosomal RNA gene sequencing microbiome studies
                                                        

- (Review Article)Weinroth, M.D., Belk, A.D., Dean, C.J., Noyes, N.R., Dittoe, D.K., Rothrock Jr, M.J., Ricke, 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. 2022. Considerations and best practices in animal science 16S ribosomal RNA gene sequencing microbiome studies. Journal of Animal Science. 100:1018. https://doi.org/10.1093/jas/skab346.AT homopolymer strings in salmonella enterica subspecies I
contribute to speciation and serovar diversity
                                                        

- (Peer Reviewed Journal)Guard, J.Y., Rivers, A.R., Vaughn, J.N., Rothrock Jr, M.J., Oladeinde, A.A., Shah, D. 2021. AT homopolymer strings in salmonella enterica subspecies I contribute to speciation and serovar diversity. Microorganisms. 9(10):2075. https://doi.org/10.3390/microorganisms9102075.Salmonella diversity along the farm-to-fork continuum of pastured poultry flocks in the southeastern United States
                                                        

- (Peer Reviewed Journal)Rothrock Jr, M.J., Oladeinde, A.A., Guard, J.Y. 2021. Salmonella diversity along the farm-to-fork continuum of pastured poultry flocks in the southeastern United States. Frontiers in Animal Science. 2:761930. https://doi.org/10.3389/fanim.2021.761930.Detection of Campylobacter jejuni diversity by Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) from poultry sources
                                                        

- (Peer Reviewed Journal)Yeh, H., Awad, A., Rothrock Jr, M.J. 2021. Detection of Campylobacter jejuni diversity by Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) from poultry sources. Veterinary Medicine and Science. https://doi.org/10.1002/vms3.622.Horizontal gene transfer is the main driver of antimicrobial
resistance in broiler chicks infected with Salmonella enterica
Serovar Heidelberg
                                                        

- (Peer Reviewed Journal)Oladeinde, A.A., Abdo, Z., Press, M.O., Cook, K.L., Cox Jr, N.A., Zwirtzitz, B., Woyda, R., Lakin, S.M., Thomas Iv, J.C., Looft, T.P., Cosby, D.E., Hinton Jr, A., Guard, J.Y., Line, J.E., Rothrock Jr, M.J., Berrang, M.E., Herrington, K., Zock, G.S., Plumblee Lawrence, J.R., Cudnik, D., House, S.L., Ingram, K.D., Lariscy, L., Wagner, R., Aggrey, S.E., Chai, L., Ritz, C. 2021. Horizontal gene transfer is the main driver of antimicrobial resistance in broiler chicks infected with Salmonella enterica Serovar Heidelberg. mSystems. 6(4):e00729-21. https://doi.org/10.1128/mSystems.00729-21.Antibiotic resistance, antimicrobial residues and bacterial community diversity in pasture-raised poultry, swine and beef cattle manures
                                                        

- (Peer Reviewed Journal)Rothrock Jr, M.J., Min, B., Castleberry, B., Waldrip, H., Parker, D.B., Brauer, D.K., Pitta, D., Indugu, N. 2021. Antibiotic resistance, antimicrobial residues and bacterial community diversity in pasture-raised poultry, swine and beef cattle manures. Journal of Animal Science. https://doi.org/10.1093/jas/skab144Mapping foodborne pathogen contamination throughout the conventional and alternative poultry supply chains.
                                                        

- (Peer Reviewed Journal)Golden, C.E., Rothrock Jr, M.J., Abhinav, M. 2021. Mapping foodborne pathogen contamination throughout the conventional and alternative poultry supply chains. Poultry Science. https://doi.org/10.1016/j.psj.2021.101157.Using farm management practices to predict campylobacter prevalence in pastured poultry farm
                                                        

- (Peer Reviewed Journal)Xu, X., Rothrock Jr, M.J., Mohan, A., Kumar, G.D., Mishra, A. 2021. Using farm management practices to predict campylobacter prevalence in pastured poultry farm. Environmental Research. https://doi.org/10.1016/j.psj.2021.101122.The Effects of Feeding Antibiotic on the Intestinal Microbiota of Weanling Pigs.
                                                        

- (Peer Reviewed Journal)Lourenco, J.M., Hampton, R.S., Johnson, H.M., Callaway, T.R., Rothrock Jr, M.J., Azain, M.J. 2021. The Effects of Feeding Antibiotic on the Intestinal Microbiota of Weanling Pigs. Frontiers in Veterinary Science. https://doi.org/10.3389/fvets.2021.601394.Dynamic changes in the gut microbiome at the acute stage of ischemic stroke in a pig model
                                                        

- (Peer Reviewed Journal)Jeon, J., Lourenco, J., Kaiser, E.E., Waters, E.S., Scheulin, K.M., Fang, X., Kinder, H.A., Platt, S.R., Rothrock Jr, M.J., Callaway, T.R., West, F.D., Park, H. 2020. Dynamic changes in the gut microbiome at the acute stage of ischemic stroke in a pig model. PLoS ONE. https://doi.org/10.3389/fnins.2020.587986.The relationship between the rumen microbiome and carcass merit in Angus steers

- (Peer Reviewed Journal)Krause, T.R., Lourenco, J.M., Welch, C.B., Rothrock Jr, M.J., Callaway, T.R., Pringle, D.T. 2020. The relationship between the rumen microbiome and carcass merit in Angus steers. Journal of Animal Science. 98(9):1-12.Multidrug resistant Acinetobacter isolates release resistance determinants through contact-dependent killing and bacteriophage lysis

- (Peer Reviewed Journal)Crippen, C., Paltry, R.T., Rothrock Jr, M.J., Sanchez, S., Szymanski, C.M. 2020. Multidrug resistant Acinetobacter isolates release resistance determinants through contact-dependent killing and bacteriophage lysis. Frontiers in Microbiology. 11:1918.Prevalence of antibiotic resistance genes and bacterial community diversity from feces of pasture-raised broiler and layer chickens, swine, and beef cattle in the Southeastern USA

- (Abstract Only)Min, B., Castleberry, B., Rothrock Jr, M.J., Rutherford, L., Waldrip, H., Parker, D.B., Brauer, D.K., Pitta, D.W., Indugu, N. 2020. Prevalence of antibiotic resistance genes and bacterial community diversity from feces of pasture-raised broiler and layer chickens, swine, and beef cattle in the Southeastern USA [abstract]. 2020 ASAS-CSAS-WSASAS Virtual Annual Meeting and Trade Show. Paper No. PSXI-23.The impact of feed efficiency selection on the ruminal, cecal, and fecal microbiomes of Angus steers from a commercial feedlot

- (Peer Reviewed Journal)Welch, C.B., Lourenco, J.M., Davis, D.B., Krause, T.R., Carmichael, M.N., Rothrock Jr, M.J., Pringle, D.T., Callaway, T.R. 2020. The impact of feed efficiency selection on the ruminal, cecal, and fecal microbiomes of Angus steers from a commercial feedlot. Journal of Animal Science. 98(7):skaa230.Communicating bioinformatics to small poultry producers
                                                        

- (Abstract Only)Rothrock Jr, M.J. 2020. Communicating bioinformatics to small poultry producers. Poultry Science Association Meeting Abstract. v. 713. https://doi.org/10.1016/j.scitotenv.2019.136359.Farm management practices that affect the prevalence of Salmonella in pastured poultry farms.
                                                        

- (Peer Reviewed Journal)Hwang, D., Rothrock Jr, M.J., Pang, H., Kumar, G., Mishra, A. 2020. Farm management practices that affect the prevalence of Salmonella in pastured poultry farms. LWT - Food Science and Technology. v. 127. https://doi.org/10.1016/j.lwt.2020.109423.Assessment of a potential role of Dickeya dadantii DSM 18020 as a pectinase producer for utilization in poultry diets based on in silico analyses.

- (Peer Reviewed Journal)Dittoe, D.K., Barabite, R.D., Rothrock Jr, M.J., Ricke, S.C. 2020. Assessment of a potential role of Dickeya dadantii DSM 18020 as a pectinase producer for utilization in poultry diets based on in silico analyses. Frontiers in Microbiology. 11:751.Predicting Salmonella prevalence associated with meteorological factors in pastured poultry farms in southeastern United States
                                                        

- (Peer Reviewed Journal)Hwang, D., Rothrock Jr, M.J., Pang, H., Guo, M., Mishra, A. 2020. Predicting Salmonella prevalence associated with meteorological factors in pastured poultry farms in southeastern United States. Science of the Total Environment. 713. https://doi.org/10.1016/j.scitotenv.2019.136359.Low dose infection of hens in lay with Salmonella enterica serovar  Enteritidis from different genomic clades
                                                        

- (Peer Reviewed Journal)Guard, J.Y., Rothrock Jr, M.J., Jones, D.R., Gast, R.K. 2020. Low dose infection of hens in lay with Salmonella enterica serovar Enteritidis from different genomic clades. Avian Diseases. 64(1):7-15. https://doi.org/10.1637/0005-2086-64.1.7.The future of monitoring poultry processing microbiology: A requirement for the future, best practices and avenues for success

- (Peer Reviewed Journal)Gastrointestinal Microbiomes Of Broilers And Layer Hens In Alternative Production Systems.

- (Peer Reviewed Journal)Ricke, S.C., Rothrock Jr, M.J. 2020. Gastrointestinal Microbiomes Of Broilers And Layer Hens In Alternative Production Systems. Poultry Science. 99(2):660-669.Adapterama II: Universal amplicon sequencing on Illumina platforms(TaggiMatrix).

- (Peer Reviewed Journal)Glenn, T.C., Pierson, T.W., Bayona-Vasquez, N.J., Kieran, T.J., Hoffberg, S.L., Thomas, J., Lefever, D.E., Finger, J.W., Gao, B., Bian, X., Louha, S., Kolli, R., Bentley, K., Rushmore, J., Wong, K., Haw, T.L., Rothrock Jr, M.J., Mckee, A.M., Guo, T.L., Mauricio, R., Molina, M., Cummings, B., Lash, L.H., Lu, K., Gilbert, G.S., Hubbell, S.P., Faircloth, B.C. 2019. Adapterama II: Universal amplicon sequencing on Illumina platforms(TaggiMatrix). PeerJ. e7786.Pastured Poultry Production in the United States: Strategies to Balance System Sustainability and Environmental Impact

- (Peer Reviewed Journal)Rothrock Jr, M.J., Gibson, K.E., Micciche, A.C., Ricke, S. 2019. Pastured Poultry Production in the United States: Strategies to Balance System Sustainability and Environmental Impact. Frontiers in Sustainable Food Systems. 3:74.Relationships Between Broiler Feed and Feed Efficiency and Their Gut Microbiomes.

- (Abstract Only)Rothrock Jr, M.J. 2019. Relationships Between Broiler Feed and Feed Efficiency and Their Gut Microbiomes. Poultry Science Association Meeting Abstract. 2A.A newly developed Escherichia coli isolate panel from a cross section of U.S. animal production systems reveals geographic and commodity-based differences in antibiotic resistance gene carriage
                                                        

- (Peer Reviewed Journal)Ducey, T.F., Durso, L.M., Ibekwe, A.M., Dungan, R.S., Jackson, C.R., Frye, J.G., Castleberry, B., Rashash, D.M., Rothrock Jr, M.J., Boykin, D.L., Whitehead, T.R., Ramos, Z.D., McManus, M.N., Cook, K.L. 2020. A newly developed Escherichia coli isolate panel from a cross section of U.S. animal production systems reveals geographic and commodity-based differences in antibiotic resistance gene carriage. Journal of Hazardous Materials. 382. https://doi.org/10.1016/j.jhazmat.2019.120991.Optimization of in-package cold plasma treatment conditions for raw chicken breast meat with response surface methodology
                                                        

- (Peer Reviewed Journal)Zhuang, H., Rothrock Jr, M.J., Line, J.E., Lawrence, K.C., Gamble, G.R., Bowker, B.C., Keener, K. 2020. Optimization of in-package cold plasma treatment conditions for raw chicken breast meat with response surface methodology. Innovative Food Science and Emerging Technologies. 66:e102477. https://doi.org/10.1016/j.ifset.2020.102477.A microbiomic analysis of a pasture-raised broiler flock elucidates foodborne pathogen ecology along the farm-to-fork continuum

- (Peer Reviewed Journal)Rothrock Jr, M.J., Locatelli, A., Feye, K.M., Caudill, A.J., Guard, J.Y., Hiett, K., Ricke, S.C. 2019. A microbiomic analysis of a pasture-raised broiler flock elucidates foodborne pathogen ecology along the farm-to-fork continuum. Frontiers in Veterinary Science. 6:260.Importance of farm environment to shape poultry-related microbiomes throughout the farm-to-fork continuum of pasture-raised broiler flocks.
                                                        

- (Peer Reviewed Journal)Rothrock Jr, M.J., Locatelli, A. 2019. Importance of farm environment to shape poultry-related microbiomes throughout the farm-to-fork continuum of pasture-raised broiler flocks. Frontiers in Sustainable Food Systems. 3:48. https://doi.org/10.3389/fsufs.2019.00048.Current trends of rice milling byproducts for agricultural applications and alternative food production systems
                                                        

- (Peer Reviewed Journal)Bodie, A.R., Micciche, A.C., Atungulu, G.G., Rothrock Jr, M.J., Ricke, S.C. 2019. Current trends of rice milling byproducts for agricultural applications and alternative food production systems. Frontiers in Sustainable Food Systems. 3:47. https://doi.org/10.3389/fsufs.2019.00047Applications of microbiome analyses in alternative poultry broiler production systems
                                                        

- (Peer Reviewed Journal)Shi, Z., Rothrock Jr, M.J., Ricke, S.C. 2019. Applications of microbiome analyses in alternative poultry broiler production systems. Frontiers in Veterinary Science. 6:157. https://doi.org/10.3389/fvets.2019.00157.Intestinal microbial ecology associated with metabolic efficiency in commercial broilers

- (Abstract Only)Rothrock Jr, M.J., Ellestad, L.E., Guard, J.Y. 2019. Intestinal microbial ecology associated with metabolic efficiency in commercial broilers. Poultry Science Association Meeting Abstract. 234.Efficacy of a novel, all-natural bioproduct to reduce microbial populations within poultry litter

- (Abstract Only)Rothrock Jr, M.J., Cook, K., Wagner, A.L., Girard, I.D. 2019. Efficacy of a novel, all-natural bioproduct to reduce microbial populations within poultry litter. Poultry Science Association Meeting Abstract. 683 p.Physiological mechanisms regulating metabolic efficiency in commercial broilers.

- (Abstract Only)Ellestad, L., Latzsch, S., Rothrock Jr, M.J., Guard, J.Y. 2019. Physiological mechanisms regulating metabolic efficiency in commercial broilers. Poultry Science Association Meeting Abstract. 233.Essential oils as an intervention strategy to reduce Campylobacter in poultry production: A review
                                                        

- (Peer Reviewed Journal)Micciche, A., Rothrock Jr, M.J., Yang, Y., Ricke, S.C. 2019. Essential oils as an intervention strategy to reduce Campylobacter in poultry production: A review. Frontiers in Microbiology. 10:1058. https://doi.org/10.3389/fmicb.2019.01058.Listeria occurrence and potential control strategies in alternative and conventional poultry processing and retail.
                                                        

- (Peer Reviewed Journal)Rothrock Jr, M.J., Micciche, A.C., Bodie, A.R., Ricke, S.C. 2019. Listeria occurrence and potential control strategies in alternative and conventional poultry processing and retail.  Frontiers in Sustainable Food Systems. 3:(33). https://doi.org/10.3389/fsufs.2019.00033.The effects of feeding a soybean-based or a soy-free diet on the gut microbiome of pasture-raised chickens throughout their lifecycle.
                                                        

- (Peer Reviewed Journal)Lourenco, J.M., Rothrock Jr, M.J., Sanad, Y.M., Callaway, T.R. 2019. The effects of feeding a soybean-based or a soy-free diet on the gut microbiome of pasture-raised chickens throughout their lifecycle. Frontiers in Sustainable Food Systems. 3:36. https://doi.org/10.3389/fsufs.2019.00036.The successional changes in the gut microbiome of pasture-raised chickens fed soy-containing and soy-free diets
                                                        

- (Peer Reviewed Journal)Lourenco, J.M., Rothrock Jr, M.J., Fluharty, F.L., Callaway, T.R. 2019. The successional changes in the gut microbiome of pasture-raised chickens fed soy-containing and soy-free diets. Frontiers in Sustainable Food Systems. 3:35. https://doi.org/10.3389/fsufs.2019.00035.Gut Microbiome and Incidence of Foodborne Pathogens are affected by diet in pasture-raised Chickens.

- (Abstract Only)Dynamic changes of Gut Microbiome and Immune Response during the actue state of stroke in a Pig Model.

- (Abstract Only)Jeon, J., Lourenco, J., Kaiser, E., Waters, E.S., Scheulin, K.M., Fagan, M.M., Fang, X., Kinder, H.A., Platt, S.R., Duberstein, K.J., Rothrock Jr, M.J., Callaway, T.R., West, F.D., Park, H. 2019. Dynamic changes of Gut Microbiome and Immune Response during the actue state of stroke in a Pig Model. Current Developments in Nutrition. 13:3(1).Comparison between random forest and gradient boosting machine methods for predicting Listeria spp. prevalence in the environment of pastured poultry farms.
                                                        

- (Peer Reviewed Journal)Golden, C.E., Rothrock Jr, M.J., Misra, A. 2019. Comparison between random forest and gradient boosting machine methods for predicting Listeria spp. prevalence in the environment of pastured poultry farms. Food Research International. 122:47-55. https://doi.org/10.1016/j.foodres.2019.03.062.In-package antimicrobial treatment of chicken breast meat with high voltage dielectric barrier discharge – Electric voltage effect

- (Peer Reviewed Journal)Zhuang, H., Rothrock Jr, M.J., Hiett, K.L., Lawrence, K.C., Gamble, G.R., Bowker, B.C., Keener, K.M. 2019. In-package antimicrobial treatment of chicken breast meat with high voltage dielectric barrier discharge – Electric voltage effect. Journal of Applied Poultry Research. 28(4):801-807.Using farm practice variables as predictors of Listeria spp. prevalence in pastured poultry farms
                                                        

- (Peer Reviewed Journal)Golden, C.E., Rothrock Jr, M.J., Misra, A. 2019. Using farm practice variables as predictors of Listeria spp. prevalence in pastured poultry farms. Frontiers in Sustainable Food Systems. 3(15). https://doi.org/10.3389/fsufs.2019.00015In-package air cold plasma treatment of chicken-breast meat- treatment time effect
                                                        

- (Peer Reviewed Journal)Zhuang, H., Rothrock, M.J., Hiett, K.L., Lawrence, K.C., Gamble, G.R., Bowker, B.C., Keener, K. 2019. In-package air cold plasma treatment of chicken-breast meat- treatment time effect. Journal of Food Quality. https://doi.org/10.1155/2019/1837351.Supplementation of protected sodium butyrate alone or in combination with essential oils modulated the cecal microbiota of broiler chickens challenged with coccidia and Clostridium perfringens.
                                                        

- (Peer Reviewed Journal)Bortoluzzi, C., Rothrock Jr, M.J., Vieira, B.S., Mallo, J.J., Puyalto, M., Hofacre, C., Applegate, T.J. 2019. Supplementation of protected sodium butyrate alone or in combination with essential oils modulated the cecal microbiota of broiler chickens challenged with coccidia and Clostridium perfringens.. Frontiers in Sustainable Food Systems. 2:72.  https://doi.org/10.3389/fsufs.2018.00072.Semi-quantification of total Campylobacter and Salmonella during egg incubations using a combination of 16S rDNA and specific pathogen primers for qPCR

- (Peer Reviewed Journal)Rothrock Jr, M.J., Feye, K.M., Kin, S., Park, S., Locatelli, A., Hiett, K., Gamble, J., Sellers, H., Ricke, S.C. 2018. Quantification of total Campylobacter and Salmonella during egg incubations using a combination of 16S rDNA and specific pathogen primers for qPCR. Frontiers in Microbiology. 9:2454.Doi: 10.3389/fmicb.2018.02454Antibiotic profiles of bacteria isolated on selective campylobacter media

- (Abstract Only)Hinton Jr, A., Rothrock Jr, M.J., Cosby, D.E., Ingram, K.D., Cox Jr, N.A. 2018. Antibiotic profiles of bacteria isolated on selective campylobacter media [abstract]. Poultry Science Association Meeting Abstract. 97(E-Suppl.1):207.Foodborne Pathogen Ecology Throughout the Pastured Poultry Farm-to-Fork Continuum

- (Abstract Only)Comparisons of microbiomes in conventional and alternative poultry production systems

- (Abstract Only)American Pastured Poultry Producers Association (APPPA) Perspective of Alternative Poultry Production Practices

- (Abstract Only)Investigation of Foodborne Pathogen Ecology throughout the Pastured Poultry Farm-to-Fork Continuum using a Microbiome Approach

- (Abstract Only)Complete genome sequence of Listeria monocytogenes strain MR310, isolated from a pastured-flock poultry farm system

- (Peer Reviewed Journal)Rothrock Jr, M.J., Fan, P., Jeong, K.C., Kim, S.A., Ricke, S.C., Park, S. 2018. Complete genome sequence of Listeria monocytogenes strain MR310, isolated from a pastured-flock poultry farm system. Genome Announcements. 6:e00171-18.Antimicrobial Resistance Gene Transfer in Drug Resistant Acinetobacter Species

- (Abstract Only)Urea hydrolysis and calcium carbonate precipitation in gypsum-amended
broiler litter.
                                                        

- (Peer Reviewed Journal)Burt, C., Cabrera, M., Rothrock Jr, M.J., Kissel, D.E. 2018. Urea hydrolysis and calcium carbonate precipitation in gypsum-amended broiler litter. Journal of Environmental Quality. 47(1):162.169. 10.2134/jeq2017.08.0337.Assessing Commercial and Alternative Poultry Processing Methods using Microbiome Analyses

- (Abstract Only)Rothrock Jr, M.J. 2018. Assessing Commercial and Alternative Poultry Processing Methods using Microbiome Analyses. International Poultry Scientific Forum. p. M121.The distribution of Listeria in pasture-raised broiler farm soils is potentially related to University of Vermont medium enrichment bias toward Listeria innocua over Listeria monocytogenes.
                                                        

- (Peer Reviewed Journal)Locatelli, A., Lewis, M.A., Rothrock Jr, M.J. 2017. The distribution of Listeria in pasture-raised broiler farm soils is potentially related to University of Vermont medium enrichment bias toward Listeria innocua over Listeria monocytogenes. Frontiers in Veterinary Science. 4:227. 10.3389/fvets.2017.00227.Listeria Occurrence in Poultry Flocks: Detection and Potential Implications

- (Review Article)Rothrock Jr, M.J., Davis, M.L., Locatelli, A., Bodie, A., Mcintosh, T., Donaldson, J.R., Ricke, S.C. 2017. Listeria Occurrence in Poultry Flocks: Detection and Potential Implications. Frontiers in Veterinary Science. 4:125. doi:10.3389/fvets.2017.00125.Investigation of environmental drivers of antimicrobial resistance in foodborne bacterial pathogens in antibiotic-free, all natural, pastured poultry flocks.

- (Abstract Only)Rothrock Jr, M.J., Miller, D., Roquemore, A., Hiett, K.L., Guard, J.Y. 2017. Investigation of environmental drivers of antimicrobial resistance in foodborne bacterial pathogens in antibiotic-free, all natural, pastured poultry flocks. Meeting Abstract. p. 23.A Combined 16S Microbiome and Culture-Based Analysis of Foodborne Pathogens Throughout the Entire Lifecycle of A Single Pastured-Raised Broiler Flock

- (Abstract Only)Rothrock Jr, M.J., Locatelli, A., Hiett, K., Caudill, A. 2017. A Combined 16S Microbiome and Culture-Based Analysis of Foodborne Pathogens Throughout the Entire Lifecycle of A Single Pastured-Raised Broiler Flock. Poultry Science Association Meeting Abstract. p. 536.Does differential growth affect the distribution and recovery of Listeria spp. in pasture-raised broiler farm soils?

- (Abstract Only)Locatelli, A., Rothrock Jr, M.J. 2017. Does differential growth affect the distribution and recovery of Listeria spp. in pasture-raised broiler farm soils?. Poultry Science Association Meeting Abstract. p 542.POULTRY-RELATED MICROBIOME CHANGES FROM EMBRYONIC DEVELOPMENT TO FINAL PRODUCT:  A SINGLE PASTURED-RAISED FLOCK FARM-TO-FORK ANALYSIS

- (Abstract Only)Rothrock Jr, M.J., Locatelli, A., Hiett, K.L., Caudill, A.J. 2017. POULTRY-RELATED MICROBIOME CHANGES FROM EMBRYONIC DEVELOPMENT TO FINAL PRODUCT:  A SINGLE PASTURED-RAISED FLOCK FARM-TO-FORK ANALYSIS (abstrect). FEMS 2017 Congress. FEMS7-0636.IS THE DISTRIBUTION OF LISTERIA SPP. ISOLATED FROM ALL-NATURAL, MIXED SPECIES, PASTURED-RAISED BROILER FARMS RELATED TO DIFFERENTIAL GROWTH?

- (Abstract Only)Locatelli, A., Rothrock Jr, M.J. 2017. IS THE DISTRIBUTION OF LISTERIA SPP. ISOLATED FROM ALL-NATURAL, MIXED SPECIES, PASTURED-RAISED BROILER FARMS RELATED TO DIFFERENTIAL GROWTH?. Federation of European Microbiological Societies Microbiology Letters. FEMS7-1359.Flue-gas desulfurization gypsum effects on urea-degrading bacteria and ammonia volatilization from broiler litter.

- (Peer Reviewed Journal)Burt, C.D., Cabrera, M.L., Rothrock Jr, M.J. 2017. Flue-gas desulfurization gypsum effects on urea-degrading bacteria and ammonia volatilization from broiler litter. Poultry Science. doi:10.3382/ps/pex044.Do fecal and litter microbiomes vary within the major areas of a commercial poultry house, and does this effect sampling strategies for whole house microbiomic studies?

- (Peer Reviewed Journal)Locatelli, A., Hiett, K.L., Caudill, A., Rothrock Jr, M.J. 2017. Do fecal and litter microbiomes vary within the major areas of a commercial poultry house, and does this effect sampling strategies for whole house microbiomic studies?Applied Poultry Research. 26(3):325-336.In-package cold plasma inactivation of pathogenic and spoilage bacteria commonly found on raw chicken carcasses

- (Peer Reviewed Journal)Rothrock Jr, M.J., Zhuang, H., Lawrence, K.C., Bowker, B.C., Gamble, G.R., Hiett, K.L. 2016. In-package cold plasma inactivation of pathogenic and spoilage bacteria commonly found on raw chicken carcasses. Current Microbiology. 74(2):149-158.Microbial population analysis of broilers in different flock and embryonic ages from GI, yolk and egg wash via Illumina MiSeq and QIIME pipeline (abstract)

- (Abstract Only)Lee, S., Park, S., Hiett, K.L., Sellers, H., Rothrock Jr, M.J., Ricke, S. 2017. Microbial population analysis of broilers in different flock and embryonic ages from GI, yolk and egg wash via Illumina MiSeq and QIIME pipeline (abstract). International Poultry Scientific Forum, January 30-31, 2017, Atlanta, Georgia.Use of NGS in Commercial Broiler Production

- (Abstract Only)Rothrock Jr, M.J. 2016. Use of NGS in Commercial Broiler Production (abstract). Arkansas Association of Food Protection Meeting,September 13-15, 2016, Fayeteville, Arkansas.Metabolic parameters linked by phenotype microarray to acid resistance profiles of poultry-associated Salmonella enterica.

- (Peer Reviewed Journal)Guard, J.Y., Rothrock Jr, M.J., Shah, D., Jones, D.R., Gast, R.K., Sanchez-Ingunza, R., Madsen, M., El-Attrache, J., Lungu, B. 2016. Metabolic parameters linked by phenotype microArray to acid resistance profiles of poultry-associated Salmonella enterica. Research in Microbiology. 167(9-10):745-756.Assessing the Microbiomes of Scalder and Chiller Tank Waters throughout a typical commercial poultry processing day.

- (Peer Reviewed Journal)Rothrock Jr, M.J., Locatelli, A., Glenn, T.C., Thomas, J.C., Caudill, A.C., Kiepper, B.H., Hiett, K.L. 2016. Assessing the Microbiomes of Scalder and Chiller Tank Waters throughout a typical commercial poultry processing day. Poultry Science. 95(10):2372-2382.ANTIMICROBIAL SENSITIVITY PATTERNS OF MAJOR ZOONOTIC PATHOGENS FROM A SEASON-LONG “FARM-TO-FORK” STUDY OF ALL NATURAL, ANTIBIOTIC-FREE, PASTURE-RAISED BROILER FLOCKS IN THE SOUTHEASTERN UNITED STATES

- (Abstract Only)Rothrock Jr, M.J., Hiett, K.L., Guard, J.Y., Jackson, C.R. 2016. ANTIMICROBIAL SENSITIVITY PATTERNS OF MAJOR ZOONOTIC PATHOGENS FROM A SEASON-LONG “FARM-TO-FORK” STUDY OF ALL NATURAL, ANTIBIOTIC-FREE, PASTURE-RAISED BROILER FLOCKS IN THE SOUTHEASTERN UNITED STATES. International Association for Food Protection. St. Louis, Mo, July 31-Aug 3, 2016. p. 3-168.Effect of processing method on bacterial community recovered from scalder and chiller water tanks in a commercial broiler processing facility.

- (Abstract Only)Locatelli, A., Rothrock Jr, M.J., Hiett, K.L. 2016. Effect of processing method on bacterial community recovered from scalder and chiller water tanks in a commercial broiler processing facility. Poultry Science Association Meeting Abstract. New Orleans, Louisiana, July 11-14, 2016. P. 516.Subtyping of Salmonella enterica Subspecies I using Single-Nucleotide Polymorphisms in Adenylate Cyclase (cyaA).

- (Peer Reviewed Journal)Guard, J.Y., Abdo, Z., Byers, S.O., Kriebel, P., Rothrock Jr, M.J. 2016. Subtyping of Salmonella enterica subspecies I using single nucleotide polymorphisms in adenylate cyclase (cyaA). Foodborne Pathogens and Disease. 13(7)350-362.Antibiotics in agroecosystems: Introduction to the special section
                                                        

- (Peer Reviewed Journal)Franklin, A.M., Aga, D.S., Cytryn, E., Durso, L.M., Mclain, J.E., Pruden, A., Roberts, M.C., Rothrock Jr, M.J., Snow, D.D., Watson, J.E., Dungan, R.S. 2016. Antibiotics in agroecosystems: Introduction to the special section. Journal of Environmental Quality. 43:377-393.Background antibiotic resistance patterns in antibiotic-free pastured poultry production

- (Popular Publication)Rothrock Jr, M.J., Hiett, K.L., Guard, J.Y., Jackson, C.R. 2016. Background antibiotic resistance patterns in antibiotic-free pastured poultry production. CSA News. 61(2):13.How should we be determining background and baseline antibiotic resistance levels in agroecosystem research?

- (Peer Reviewed Journal)Rothrock Jr, M.J., Keen, P., Cook, K.L., Durso, L.M., Franklin, A.M., Dungan, R.S. 2016. How should we be determining background and baseline antibiotic resistance levels in agroecosystem research? Journal of Environmental Quality. 45:420-431.Antibiotic resistance patterns of major zoonotic pathogens from all-natural, antibiotic-free, pasture-raised broiler flocks in the southeastern United States

- (Peer Reviewed Journal)Rothrock Jr, M.J., Hiett, K.L., Guard, J.Y., Jackson, C.R. 2016. Antibiotic resistance patterns of major zoonotic pathogens from all-natural, antibiotic-free, pasture-raised broiler flocks in the southeastern United States. Journal of Environmental Quality. 45(2):593-603.ANTIMICROBIAL SENSITIVITY PATTERNS OF MAJOR ZOONOTIC PATHOGENS FROM A SEASON-LONG “FARM-TO-FORK” STUDY OF ALL NATURAL, ANTIBIOTIC-FREE, PASTURE-RAISED BROILER FLOCKS IN THE SOUTHEASTERN UNITED STATES

- (Abstract Only)Rothrock Jr, M.J., Hiett, K.L., Guard, J.Y., Jackson, C.R. 2015. ANTIMICROBIAL SENSITIVITY PATTERNS OF MAJOR ZOONOTIC PATHOGENS FROM A SEASON-LONG “FARM-TO-FORK” STUDY OF ALL NATURAL, ANTIBIOTIC-FREE, PASTURE-RAISED BROILER FLOCKS IN THE SOUTHEASTERN UNITED STATES. Campylobacter Helicobacter and Related Organisms International Workshop. November 1-5, 2015. Rotorua, New Zealand.THE EFFECT OF EMBRYONIC AGE AND BREEDER FLOCK AGE ON THE GASTROINTESTINAL MICROBIOME OF DEVELOPING BROILER CHICKEN: POTENTIAL IMPLICATIONS FOR FOOD SAFETY

- (Abstract Only)Rothrock Jr, M.J., Hiett, K.L., Caudill, A., Sellers, H. 2015. THE EFFECT OF EMBRYONIC AGE AND BREEDER FLOCK AGE ON THE GASTROINTESTINAL MICROBIOME OF DEVELOPING BROILER CHICKEN: POTENTIAL IMPLICATIONS FOR FOOD SAFETY (abstract). Campylobacter Helicobacter and Related Organisms International Workshop. Rotorua, New Zealand, Nov 1-5, 2015, p.81.Campylobacter spp. from a season-long “farm-to-fork” study of all natural, antibiotic-free, pasture-raised broiler flocks in the southeastern united states

- (Abstract Only)Hiett, K.L., Rothrock Jr, M.J., Plumblee, J. 2015. Campylobacter spp. from a season-long “farm-to-fork” study of all natural, antibiotic-free, pasture-raised broiler flocks in the southeastern united states[abstract]. Campylobacter Helicobacter and Related Organisms International Workshop.Molecular approaches for the characterization of foodborne pathogens in poultry

- (Abstract Only)Hiett, K.L., Rothrock Jr, M.J., Plumblee, J. 2015. Molecular approaches for the characterization of foodborne pathogens in poultry[abstract]. Campylobacter Helicobacter and Related Organisms International Workshop.Addressing the Natural Antibiotic Resistome in Studies of Soil Resistance

- (Abstract Only)Mclain, J.E., Rothrock Jr, M.J. 2015. Addressing the Natural Antibiotic Resistome in Studies of Soil Resistance. ASA-CSSA-SSSA Annual Meeting Abstracts. Minneapolis, MN, November 15-18, 2016. p. 257.Recovery of Salmonella enterica serovar Enteritidis from hens initially infected with serovar Kentucky

- (Peer Reviewed Journal)Guard, J.Y., Sanchez-Ingunza, R., Shah, D.H., Rothrock Jr, M.J., Gast, R.K., Jones, D.R. 2015. Recovery of Salmonella enterica serovar Enteritidis from hens initially infected with serovar Kentucky. Journal of Food Chemistry, 189:86-92. 2015.Nonthermal plasma system for extending shelf life of raw broiler breast fillets

- (Peer Reviewed Journal)Kronn, T.G., Lawrence, K.C., Zhuang, H., Hiett, K.L., Rothrock Jr, M.J., Huang, Y., Keener, K.M., Abdo, Z. 2015. Nonthermal plasma system for extending shelf life of raw broiler breast fillets. Transactions of the ASABE (American Society of Agricultural and Biological Engineers). 58(2):493-500. DOI 10.13031/trans.58.10887.The characterization of Salmonella enterica serovars isolated from the scalder tank water of a commercial poultry processing plant: Recovery of a multi-drug resistant S. Heidelberg

- (Peer Reviewed Journal)Rothrock Jr, M.J., Ingram, K.D., Gamble, J., Guard, J.Y., Cicconi-Hogan, K.M., Hinton Jr, A., Hiett, K.L. 2015. The characterization of Salmonella enterica serovars isolated from the scalder tank water of a commercial poultry processing plant: Recovery of a multi-drug resistant S. Heidelberg. Poultry Science. 94(3):467-472.A hybrid DNA extraction method for the qualitative and quantitative assessment of bacterial communities from poultry production samples

- (Peer Reviewed Journal)Rothrock Jr, M.J., Hiett, K.L., Gamble, J., Caudill, A., Cicconi-Hogan, K., Caproaso, G.J. 2014. A hybrid DNA extraction method for the qualitative and quantitative assessment of bacterial communities from poultry production samples. Journal of Visualized Experiments.94:e52161, doi: 10.3791/52161.Development and application of novel SNP-based serotyping assays in targeting Salmonella enterica within the poultry production and processing continuum.

- (Abstract Only)Development of a rapid serotyping method for Salmonella enterica using serotype-specific single-nucleotide polymorphisms

- (Abstract Only)The prevalence of Salmonella enterica serovars Heidelberg and Kentucky in the scalder water of a commercial poultry processing plant in the southeastern United States.

- (Abstract Only)Ciconi-Hogan, K.M., Hiett, K.L., Ingram, K.D., Hinton Jr, A., Guard, J.Y., Gamble, J., Rothrock Jr, M.J. 2014. The prevalence of Salmonella enterica serovars Heidelberg and Kentucky in the scalder water of a commercial poultry processing plant in the southeastern United States.  International Poultry Scientific Forum. Meeting Abstract.Quantification of zoonotic bacterial pathogens within commercial poultry processing water samples using droplet digital PCR.

- (Peer Reviewed Journal)Rothrock Jr, M.J., Hiett, K.L., Kiepper, B., Ingram, K.D., Hinton Jr, A. 2013. Quantification of zoonotic bacterial pathogens within commercial poultry processing water samples using droplet digital PCR. Advances in Microbiology. 3:403-411.Effect of in-package ozonation on quality of raw broiler breast meat during storage

- (Abstract Only)Zhuang, H., Kronn, T.G., Lawrence, K.C., Yao-Wen, H., Bowker, B.C., Rothrock Jr, M.J., Hiett, K.L., Kenner, K.M. 2013. Effect of in-package ozonation on quality of raw broiler breast meat during storage. Poultry Science Meeting. 92:50-51.Characterization of the Campylobacter jejuni cryptic plasmid pTIW94 recovered from wild birds in the southeastern United States

- (Peer Reviewed Journal)Hiett, K.L., Rothrock Jr, M.J., Seal, B.S. 2013. Characterization of the Campylobacter jejuni cryptic plasmid pTIW94 recovered from wild birds in the southeastern United States . Plasmid Journal. 70:268-271.Recovery of ammonia from poultry litter using flat gas permeable membranes

- (Peer Reviewed Journal)Rothrock Jr, M.J., Szogi, A.A., Vanotti, M.B. 2013. Recovery of ammonia from poultry litter using flat gas permeable membranes. Journal of Waste Management. 33(6):1531-1538.Polymerase chain reaction detection of naturally occurring Campylobacter in commercial broiler chicken embryos

- (Peer Reviewed Journal)Hiett, K.L., Cox Jr, N.A., Rothrock Jr, M.J. 2013. Polymerase chain reaction detection of naturally occurring Campylobacter in commercial broiler chicken embryos. Poultry Science. 92(4):1134-1137.Microbiomic investigation of the poultry production chain: Using next generation sequencing to study general microbial and foodborne pathogen dynamics

- (Abstract Only)Recovery of ammonia from poultry litter using gas-permeable membranes

- (Abstract Only)Effect of volumetric water content and clover (Trifolium incarnatum) on the survival of Escherichia coli O157:H7 in a soil matrix

- (Peer Reviewed Journal)Rothrock Jr, M.J., Frantz, J., Burnett, S.E. 2012. Effect of volumetric water content and clover (Trifolium incarnatum) on the survival of Escherichia coli O157:H7 in a soil matrix. Current Microbiology. 65(3):272-283.Rapid molecular pathotyping of major salmonella enterica serotypes based on single-nucleotide polymorphisms (SNPs) in the adenylate cyclase (cyaA) gene

- (Abstract Only)Rothrock Jr, M.J., Guard, J.Y. 2012. Rapid molecular pathotyping of major salmonella enterica serotypes based on single-nucleotide polymorphisms (SNPs) in the adenylate cyclase (cyaA) gene. International Association for Food Protection Proceedings. p. 3-160.A microbial approach to understanding the production of ammonia in poultry litter

- (Research Technical Update)Cook, K.L., Rothrock Jr, M.J., Lovanh, N.C., Sistani, K.R. 2012. A microbial approach to understanding the production of ammonia in poultry litter. Natural Resources Research Update (NRRU). NRRU only.Amending poultry litter to reduce ammonia producing bacteria

- (Research Technical Update)Cook, K.L., Rothrock Jr, M.J., Lovanh, N.C., Sistani, K.R. 2012. Amending poultry litter to reduce ammonia producing bacteria. Natural Resources Research Update (NRRU). Technical update.Utilization of poultry litter for pesticide bioremediation

- (Book / Chapter)Lovanh, N.C., Ruiz-Aguilar, G., Rothrock Jr, M.J., Cook, K.L. 2012. Utilization of poultry litter for pesticide bioremediation. Applied Research in Animal Manure Management: Challenges and Opportunities beyond the Adverse Environmental Impacts. 11:285-296.Effect of volumetric water content and crimson clover (Trifolium incarnatum) growth on the survival of Escherichia Coli O157:H7 in a soil matrix

- (Abstract Only)Cook, K.L., Rothrock Jr, M.J., Frantz, J., Burnett, S. 2012. Effect of volumetric water content and crimson clover (Trifolium incarnatum) growth on the survival of Escherichia Coli O157:H7 in a soil matrix. ASA-CSSA-SSSA Annual Meeting Abstracts. Abstract.Effect of volumetric water content and crimson clover (Trifolium incarnatum) growthon the survival of Escherichia coli O157:H7 in a soil matrix

- (Abstract Only)Rothrock Jr, M.J., Frantz, J., Burnett, S., Cook, K.L. 2011. Effect of volumetric water content and crimson clover (Trifolium incarnatum) growthon the survival of Escherichia coli O157:H7 in a soil matrix. ASA-CSSA-SSSA Annual Meeting Abstracts. p. 1.Impact of amendments on microbial communities associated with nitrogen mineralization in poultry litter

- (Abstract Only)Cook, K.L., Rothrock Jr, M.J., Warren, J.G., Gilfillen, R., Netthisinghe, A., Sistani, K.R. 2011. Impact of amendments on microbial communities associated with nitrogen mineralization in poultry litter. ASA-CSSA-SSSA Annual Meeting Abstracts. Abstract.Effect of volumetric water content and crimson clover (trifolium incarnatum)growth on the survival of escherichia coli o157:h7 in a soil matrix

- (Abstract Only)Rothrock Jr, M.J., Frantz, J., Bumett, S., Cook, K.L. 2011. Effect of volumetric water content and crimson clover (trifolium incarnatum)growth on the survival of escherichia coli o157:h7 in a soil matrix [abstract]. ASA-CSSA-SSSA Annual Meeting Abstracts.Comparison of microvolume DNA quantification methods for use with volume-sensitive environmental DNA extracts

- (Peer Reviewed Journal)Rothrock Jr, M.J. 2011. Comparison of microvolume DNA quantification methods for use with volume-sensitive environmental DNA extracts. Journal of Natural and Environmental Science. 2(1):34-38.Experiences with anammox in the USA: Isolation, preservation and treatment performance of Brocadia caroliniensis

- (Proceedings)Vanotti, M.B., Fujii, T., Szogi, A.A., Rothrock Jr, M.J., Garcia, M., Kunz, A., Magri, A., Furukawa, K. 2011. Experiences with anammox in the USA: Isolation, preservation and treatment performance of Brocadia caroliniensis. In: Proceedings of 1st International Anammox Symposium (IANAS), May 19-21, 2011, Kumamoto, Japan. p. 99-106.Long-term preservation of Anammox bacteria

- (Peer Reviewed Journal)Rothrock Jr, M.J., Vanotti, M.B., Szogi, A.A. 2011. Long-term preservation of Anammox bacteria. Applied Microbiology and Biotechnology. DOI: 10.1016/j.jplph.2011.04.002.Long-term preservation of Anammox bacteria

- (Peer Reviewed Journal)Rothrock Jr, M.J., Vanotti, M.B., Szogi, A.A., Gonzalez, M.G., Fujii, T. 2011. Long-term preservation of Anammox bacteria. Applied Microbiology and Biotechnology. 92:147-157.Recovery of ammonia nitrogen in livestock and industrial wastes using gas permeable membranes

- (Proceedings)Vanotti, M.B., Szogi, A.A., Rothrock Jr, M.J. 2011. Recovery of ammonia nitrogen in livestock and industrial wastes using gas permeable membranes. In: Proceedings II International Symposium on Agricultural and Agroindustrial Waste Management (SIGERA), March 13-15, 2011, Foz de Iguacu, Brazil. 4p.Submission to GenBank of full 16S rRNA gene sequence of novel anammox bacterium Candidatus "Brocadia caroliniensis" NRRL B-50286

- (Popular Publication)Vanotti, M.B., Szogi, A.A., Rothrock Jr, M.J. 2011. Submission to GenBank of full 16S rRNA gene sequence of novel anammox bacterium Candidatus "Brocadia caroliniensis" NRRL B-50286. National Center for Biotechnology Information (NCBI). Available: http://www.ncbi.nlm.nih.gov/nuccore/328550468.Skatole biodegradation via isolates from swine manure

- (Proceedings)Lovanh, N.C., Cook, K.L., Rothrock Jr, M.J. 2011. Skatole biodegradation via isolates from swine manure. Bioremediation and Sustainable Environmental Technologies. Abstract.Evaluation of amendments to manage nitrogen loss and microbiological quality in poultry litter.

- (Peer Reviewed Journal)Cook, K.L., Rothrock Jr, M.J., Eiteman, M.A., Lovanh, N.C., Sistani, K.R. 2011. Evaluation of amendments to manage nitrogen loss and microbiological quality in poultry litter. Journal of Environmental Management. 92:1760-1766.Effect of Litter Amendments on Microbial and Nitrogen Dynamics in  Poultry Houses

- (Abstract Only)Cook, K.L., Rothrock Jr, M.J., Parekh, R.R., Warren, J.G., Lovanh, N.C., Sistani, K.R. 2011. Effect of Litter Amendments on Microbial and Nitrogen Dynamics in  Poultry Houses. Poultry International Exposition. Meeting - No page numbers.Removal and recovery of ammonia from liquid swine manure and poultry litter using gas permeable membranes

- (Proceedings)Vanotti, M.B., Szogi, A.A., Rothrock Jr, M.J. 2010. Removal and recovery of ammonia from liquid swine manure and poultry litter using gas permeable membranes. In: Proceedings of the 14th Ramiran International Conference, September 12-15, 2010, Lisboa, Portugal. 4 p.Acidification delays the microbial mineralization of organic N forms in poultry litter

- (Popular Publication)Rothrock Jr, M.J., Cook, K.L., Warren, J.G., Eiteman, M.A., Sistani, K.R. 2010. Acidification delays the microbial mineralization of organic N forms in poultry litter. CSA News. 55(10):11-13.Recovery of ammonia from poultry litter using gas-permeable membranes

- (Peer Reviewed Journal)Rothrock Jr, M.J., Szogi, A.A., Vanotti, M.B. 2010. Recovery of ammonia from poultry litter using gas-permeable membranes. Transactions of the American Society of Agricultural and Biological Engineers. 53(4):1267-1275.Microbial mineralization of organic nitrogen forms in poultry litters

- (Peer Reviewed Journal)Rothrock Jr, M.J., Cook, K.L., Warren, J.G., Eiteman, M.A., Sistani, K.R. 2010. Microbial mineralization of organic nitrogen forms in poultry litters. Journal of Environmental Quality. 39:1848-1857.Uses and management of poultry litter

- (Peer Reviewed Journal)Bolan, N.S., Szogi, A.A., Chuasavathi, T., Seshadri, B., Rothrock Jr, M.J., Panneerselvam, P. 2010. Uses and management of poultry litter. World's Poultry Science Journal. 66:673-698.Utilization of Poultry Litter to Enhance Fungal Activity and Microbial Dynamics in the Presence of Pesticide Mixture: Implication on Pesticide Bioremediation

- (Proceedings)Lovanh, N.C., Ruiz-Aguilar, G., Rothrock Jr, M.J., Cook, K.L. 2010. Utilization of Poultry Litter to Enhance Fungal Activity and Microbial Dynamics in the Presence of Pesticide Mixture: Implication on Pesticide Bioremediation. Residuals and Biosolids Conference. Abstract presented at proceeding.Effect of Watering Trough Chlorination on Persistence of Mycobacterium avium subsp. Paratuberculosi

- (Peer Reviewed Journal)Cook, K.L., Bolster, C.H., Britt, J., Rothrock Jr, M.J. 2010. Effect of Watering Trough Chlorination on Persistence of Mycobacterium avium subsp. Paratuberculosi. Bovine Practitioner Journal. 44(1):69-76.New technology for ammonia recovery from poultry litter

- (Abstract Only)Rothrock Jr, M.J., Szogi, A.A., Vanotti, M.B. 2009. New technology for ammonia recovery from poultry litter [abstract]. American Society of Agronomy-Crop Science Society of America-Soil Science Society of America International Meeting Abstracts.Development of long-term preservation and re-activation techniques for ANAMMOX bacteria

- (Abstract Only)Rothrock Jr, M.J., Vanotti, M.B., Szogi, A.A. 2009. Development of long-term preservation and re-activation techniques for ANAMMOX bacteria [abstract]. American Society of Agronomy-Crop Science Society of America-Soil Science Society of America International Annual Meeting Abstracts.Influence of seasonal changes on the microbial community in an anaerobic swine waste treatment lagoon

- (Abstract Only)Cook, K.L., Rothrock Jr, M.J., Lovanh, N.C., Sorrell, J. 2009. Influence of seasonal changes on the microbial community in an anaerobic swine waste treatment lagoon. ASA-CSSA-SSSA Annual Meeting Abstracts.Spatial and Temporal Changes in the Microbial Community in an Anaerobic Swine Waste Treatment Lagoon

- (Peer Reviewed Journal)Cook, K.L., Rothrock Jr, M.J., Sorrell, J., Lovanh, N.C., Loughrin, J.H. 2010. Spatial and Temporal Changes in the Microbial Community in an Anaerobic Swine Waste Treatment Lagoon. Anaerobe. 16:74-82.Spatial and Temporal Changes in the Microbial Community in an Anaerobic Swine Waste Treatment Lagoon

- (Abstract Only)Cook, K.L., Rothrock Jr, M.J., Lovanh, N.C., Sorrell, J., Loughrin, J.H. 2009. Spatial and Temporal Changes in the Microbial Community in an Anaerobic Swine Waste Treatment Lagoon. Conference on Gastrointestinal Function.Comparative quantification of Campylobacter jejuni from environmental samples using traditional and molecular biological techniques

- (Peer Reviewed Journal)Rothrock Jr, M.J., Cook, K.L., Bolster, C.H. 2009. Comparative quantification of Campylobacter jejuni from environmental samples using traditional and molecular biological techniques. Canadian Journal of Microbiology. 55: 633–641Alum affects ammonia-producing microorganisms in poultry litter

- (Popular Publication)Cook, K.L., Rothrock Jr, M.J., Warren, J.G., Sistani, K.R. 2009. Alum affects ammonia-producing microorganisms in poultry litter. CSA News. 54(1):5.The Effect of Stratification and Seasonal Variability on the Profile of an Anaerobic Swine Waste Treatment Lagoon.

- (Peer Reviewed Journal)Lovanh, N.C., Loughrin, J.H., Cook, K.L., Rothrock Jr, M.J., Sistani, K.R. 2009. The Effect of Stratification and Seasonal Variability on the Profile of an Anaerobic Swine Waste Treatment Lagoon. Bioresource Technology.  100:3706-3712Survival of Mycobacterium avium subsp. paratuberculosis in Biofilms on Livestock Watering Trough Materials

- (Proceedings)Britt, J., Cook, K.L., Rothrock Jr, M.J., Sorrell, J. 2008. Survival of Mycobacterium avium subsp. paratuberculosis in Biofilms on Livestock Watering Trough Materials. American Association of Bovine Practitioners Proceedings.Effect of Litter Amendments on Poultry Litter Microbial Communities and the Subsequent Effect on Nitrogen Dynamics

- (Abstract Only)Rothrock Jr, M.J., Cook, K.L., Warren, J.G., Lovanh, N.C., Sistani, K.R. 2008. Effect of Litter Amendments on Poultry Litter Microbial Communities and the Subsequent Effect on Nitrogen Dynamics. ASA-CSSA-SSSA Annual Meeting Abstracts.Effect of Alum Treatment on the Concentration of Total and Ureolytic Microorganisms in Poultry Litter

- (Peer Reviewed Journal)Cook,K.L., Rothrock Jr,M.J., Warren,J.G., Sistani,K.R., Moore Jr,P.A. 2008. Effect of Alum Treatment on the Concentration of Total and Ureolytic Microorganisms in Poultry Litter. Journal of Environmental Quality. 37:2360-2367The effect of alum addition on microbial communities in poultry litter

- (Peer Reviewed Journal)Rothrock Jr, M.J., Cook, K.L., Warren, J.G., Sistani, K.R. 2008. The effect of alum addition on microbial communities in poultry litter. Poultry Science. 87(8) 1493-1503Comparison of Molecular Methods and Traditional Plate Counting for Detecting Campylobacter Jejuni and Escherichia Coli from Environmental Samples

- (Abstract Only)Rothrock Jr, M.J., Cook, K.L., Bolster, C.H., Sorrell, J. 2008. Comparison of Molecular Methods and Traditional Plate Counting for Detecting Campylobacter Jejuni and Escherichia Coli from Environmental Samples. American Society for Microbiology Annual Meeting.Survival of Mycobacterium avium subsp. paratuberculosis in Biofilms on Livestock Watering Trough Materials

- (Abstract Only)Cook, K.L., Britt, J., Rothrock Jr, M.J., Sorrell, J. 2008. Survival of Mycobacterium avium subsp. paratuberculosis in Biofilms on Livestock Watering Trough Materials. American Society for Microbiology Annual Meeting.Development of a Quantitative Real-Time Polymerase Chain Reaction Assay to Target a Novel Group of Ammonia-Producing Bacteria Found in Poultry Litter

- (Peer Reviewed Journal)Rothrock Jr, M.J., Cook, K.L., Lovanh, N.C., Warren, J.G., Sistani, K.R. 2008. Development of a Quantitative Real-Time Polymerase Chain Reaction Assay to Target a Novel Group of Ammonia-Producing Bacteria Found in Poultry Litter . Poultry Science. 87(6):1058-1067Spatial Shifts in Microbial Population Structure Within Poultry Litter Associated with Physicochemical Properties

- (Peer Reviewed Journal)Lovanh, N.C., Cook, K.L., Rothrock Jr, M.J., Miles, D.M., Sistani, K.R. 2007. Spatial Shifts in Microbial Population Structure Within Poultry Litter Associated with Physicochemical Properties. Poultry Science. Vol 86 pages 1840-1849Spatial Variability of Ammonia Production in Poultry House: Biological, Chemical, and Physical Effects at Microscale.

- (Proceedings)Lovanh, N.C., Cook, K.L., Rothrock Jr, M.J., Miles, D.M., Sistani, K.R. 2007. Spatial Variability of Ammonia Production in Poultry House: Biological, Chemical, and Physical Effects at Microscale.. International Ammonia Conference in Agriculture.Effect of Stratification on the Profile of an Anaerobic Swine Waste Treatment Lagoon in Kentucky: A Case Study for Designing Alternative Remediation Options.

- (Proceedings)Lovanh, N.C., Loughrin, J.H., Cook, K.L., Rothrock Jr, M.J., Sistani, K.R. 2007. Effect of Stratification on the Profile of an Anaerobic Swine Waste Treatment Lagoon in Kentucky: A Case Study for Designing Alternative Remediation Options.. ASABE Annual International Meeting.Characterization of acetogenic bacteria associated with skatole production in swine lagoon slurry.

- (Abstract Only)Cook, K.L., Loughrin, J.H., Rothrock Jr, M.J. 2007. Characterization of acetogenic bacteria associated with skatole production in swine lagoon slurry.. Conference on Gastrointestinal Function. Microbial Ecology in Health and Disease (2007) V19 pp42Characterization of skatole-producing microbial populations in enriched swine lagoon slurry.

- (Peer Reviewed Journal)Cook, K.L., Rothrock Jr, M.J., Loughrin, J.H., Doerner, K. Characterization of skatole-producing microbial populations in enriched swine lagoon slurry.Federation of European Microbiological Societies Microbiology Letters. 60:329-340Effect of Alum Amendment on the Bacterial and Fungal Populations in Poultry Litter

- (Abstract Only)Rothrock Jr, M.J., Warren, J.G., Cook, K.L., Sistani, K.R. 2006. Effect of Alum Amendment on the Bacterial and Fungal Populations in Poultry Litter . ASA-CSSA-SSSA Annual Meeting Abstracts.Quantification of a Novel Group of Ammonia Producing Bacteria Found in Poultry Litter by Quantitative Real-Time PCR

- (Abstract Only)Rothrock Jr, M.J., Cook, K.L., Lovanh, N.C., Warren, J.G., Sistani, K.R. 2006. Quantification of a Novel Group of Ammonia Producing Bacteria Found in Poultry Litter by Quantitative Real-Time PCR	 . ASA-CSSA-SSSA Annual Meeting Abstracts.Survival and Transport of Campylobacter Jejuni from Poultry Litter

- (Abstract Only)Cook, K.L., Bolster, C.H., Rothrock Jr, M.J., Warren, J.G., Sistani, K.R. 2006. Survival and Transport of Campylobacter Jejuni from Poultry Litter. ASA-CSSA-SSSA Annual Meeting Abstracts.EFFECT OF BROILER LITTER PHYSICAL, CHEMICAL, AND SPATIAL CHARACTERISTICS ON THE MICROBIAL POPULATION EVALUATED USING MOLECULAR TECHNIQUES

- (Abstract Only)Cook, K.L., Lovanh, N.C., Rothrock Jr, M.J., Miles, D.M., Sistani, K.R. 2006. Effect of broiler litter physical, chemical, and spatial characteristics on the microbial population evaluated using molecular techniques. ASA-CSSA-SSSA Annual Meeting Abstracts.Characterization of skatole-producing microbial populations in enriched swine lagoon slurry.

- (Abstract Only)Rothrock Jr, M.J., Cook, K.L., Loughrin, J.H., Doerner, K. 2006. Characterization of skatole-producing microbial populations in enriched swine lagoon slurry.. American Society for Microbiology Branch Meeting.CHARACTERIZATION OF MICROBIAL POPULATIONS IN SWINE LAGOON SLURRIES ENRICHED FOR SKATOLE PRODUCTION

- (Abstract Only)Cook, K.L., Loughrin, J.H., Rothrock Jr, M.J. 2006. Characterization of microbial populations in swine lagoon slurries enriched for skatole production. American Society for Microbiology Annual Meeting. ISBN 1-55581-389-5 Pg A127CHARACTERIZATION OF SKATOLE-PRODUCING MICROBIAL POPULATIONS IN ENRICHED SWINE LAGOON SLURRY

- (Proceedings)Cook, K.L., Loughrin, J.H. 2006. Characterization of Skatole-Producing Microbial Populations in Enriched Swine Lagoon Slurry. Proceedings of the Workshop on Agricultural Air Quality: State of the Science. pp 547-551
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