Full Text Journal Articles by
Author Michael J Rothrock

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The relationship between the rumen microbiome and carcass merit in Angus steers.

Taylor R Krause, Jeferson M Lourenco, Christina B Welch, Michael J Rothrock, Todd R Callaway, T Dean Pringle,

The objective of this study was to explore the relationships between ruminal microbial populations from Angus steers that were divergent in carcass traits related to adipose accumulation. Twenty-four feedlot-finished Angus steers (age: 538 ± 21 d; body weight following lairage: 593.9 ± 43.7 kg) were slaughtered, and ruminal contents and ... Read more >>

J Anim Sci (Journal of animal science)
[2020, 98(9):]

Cited: 0 times

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The impact of feed efficiency selection on the ruminal, cecal, and fecal microbiomes of Angus steers from a commercial feedlot.

Christina B Welch, Jeferson M Lourenco, Dylan B Davis, Taylor R Krause, Mia N Carmichael, Michael J Rothrock, T Dean Pringle, Todd R Callaway,

Feed is the greatest cost of animal production, so reducing it is critical to increase producer profits. In ruminants, the microbial population within the gastrointestinal tract (GIT) is critical to nutrient digestion and absorption in both the rumen and the hindgut. The objective of this study was to determine the ... Read more >>

J. Anim. Sci. (Journal of animal science)
[2020, 98(7):]

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Assessment of a Potential Role of Dickeya dadantii DSM 18020 as a Pectinase Producer for Utilization in Poultry Diets Based on in silico Analyses.

Dana K Dittoe, Ravi D Barabote, Michael J Rothrock, Steven C Ricke,

Currently, the poultry industry has been faced with consumer pressure to utilize only vegetable feedstuffs in poultry diets, eliminate antibiotics from poultry production, and rear poultry in free range systems. To maintain current production standards, the industry must determine ways to enhance nutrient uptake and utilization further. One possible solution ... Read more >>

Front Microbiol (Frontiers in microbiology)
[2020, 11:751]

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Farm management practices that affect the prevalence of Salmonella in pastured poultry farms

Daizy Hwang, Michael J Jr, Michael J Rothrock, Hao Pang, Govindaraj Dev Kumar, Abhinav Mishra,

Farm practices can affect the prevalence of Salmonella in the final product when poultry are exposed to the outside environment. Pastured poultry farms in the Southeastern United States were investigated in this study. Farm practice and processing variables that may affect the presence of Salmonella were determined by developing predictive ... Read more >>

(Lebensmittel-Wissenschaft + [i.e. und] Technologie. Food science + technology. Science + technologie alimentaire)
[2020, 127:Not Available]

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Predicting Salmonella prevalence associated with meteorological factors in pastured poultry farms in southeastern United States.

Daizy Hwang, Michael J Rothrock, Hao Pang, Miao Guo, Abhinav Mishra,

Consumer demand has increased for pastured poultry products as the drive for sustainable farming practices and ethical treatments of livestock have become popular in the press. It is necessary to identify the important meteorological factors associated with the prevalence of Salmonella in the pastured poultry settings since the presence of ... Read more >>

Sci. Total Environ. (The Science of the total environment)
[2020, 713:136359]

Cited: 1 time

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Gastrointestinal microbiomes of broilers and layer hens in alternative production systems.

Steven C Ricke, Michael J Rothrock,

Alternative poultry production systems consisting of free-range or pasture flock raised poultry continues to increase in popularity. Based on the perceived benefits of poultry products generated from these alternative poultry production systems, they have commercial appeal to consumers. Several factors impact the health and well being of birds raised and ... Read more >>

Poult. Sci. (Poultry science)
[2020, 99(2):660-669]

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Adapterama II: universal amplicon sequencing on Illumina platforms (TaggiMatrix).

Travis C Glenn, Todd W Pierson, Natalia J Bayona-Vásquez, Troy J Kieran, Sandra L Hoffberg, Jesse C Thomas Iv, Daniel E Lefever, John W Finger, Bei Gao, Xiaoming Bian, Swarnali Louha, Ramya T Kolli, Kerin E Bentley, Julie Rushmore, Kelvin Wong, Timothy I Shaw, Michael J Rothrock, Anna M McKee, Tai L Guo, Rodney Mauricio, Marirosa Molina, Brian S Cummings, Lawrence H Lash, Kun Lu, Gregory S Gilbert, Stephen P Hubbell, Brant C Faircloth,

Next-generation sequencing (NGS) of amplicons is used in a wide variety of contexts. In many cases, NGS amplicon sequencing remains overly expensive and inflexible, with library preparation strategies relying upon the fusion of locus-specific primers to full-length adapter sequences with a single identifying sequence or ligating adapters onto PCR products. ... Read more >>

(PeerJ)
[2019, 7:e7786]

Cited: 3 times

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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.

Thomas F Ducey, Lisa M Durso, Abasiofiok M Ibekwe, Robert S Dungan, Charlene R Jackson, Jonathan G Frye, B Lana Castleberry, Diana M C Rashash, Michael J Rothrock, Debbie Boykin, Terence R Whitehead, Zeanmarj Ramos, Morgan McManus, Kimberly L Cook,

There are limited numbers of Escherichia coli isolate panels that represent United States food animal production. The majority of existing Escherichia coli isolate panels are typically designed: (i) to optimize genetic and/or phenotypic diversity; or (ii) focus on human isolates. To address this shortfall in agriculturally-related resources, we have assembled ... Read more >>

J Hazard Mater (Journal of hazardous materials)
[2020, 382:120991]

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A Microbiomic Analysis of a Pasture-Raised Broiler Flock Elucidates Foodborne Pathogen Ecology Along the Farm-To-Fork Continuum.

Michael J Rothrock, Aude Locatelli, Kristina M Feye, Andrew J Caudill, Jean Guard, Kelli Hiett, Steven C Ricke,

While conventionally grown poultry continues to dominate the U. S. poultry industry, there is an increasing demand for locally-grown, "all natural" alternatives. The use of next generation sequencing allows for not only the gross (e.g., community structure) but also fine-scale (e.g., taxa abundances) examination of these complex microbial communities. This ... Read more >>

(Frontiers in veterinary science)
[2019, 6:260]

Cited: 2 times

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Comparison between random forest and gradient boosting machine methods for predicting Listeria spp. prevalence in the environment of pastured poultry farms

Chase E Golden, Michael J Rothrock, Abhinav Mishra,

Foodborne pathogens such as Listeria spp. contain the ability to survive and multiply in poultry farming environments, which provides a route of contamination for poultry processing environments and final poultry products. An understanding of the effect of meteorological variables on the prevalence of Listeria spp. in the farming environment is ... Read more >>

Food Res Int (Food research international (Ottawa, Ont.))
[2019, 122:47-55]

Cited: 0 times

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Applications of Microbiome Analyses in Alternative Poultry Broiler Production Systems.

Zhaohao Shi, Michael J Rothrock, Steven C Ricke,

While most of the focus on poultry microbiome research has been directed toward conventional poultry production, there is increasing interest in characterizing microbial populations originating from alternative or non-conventional poultry production. This is in part due to the growing general popularity in locally produced foods and more specifically the attractiveness ... Read more >>

(Frontiers in veterinary science)
[2019, 6:157]

Cited: 2 times

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Comparison between random forest and gradient boosting machine methods for predicting Listeria spp. prevalence in the environment of pastured poultry farms.

Chase E Golden, Michael J Rothrock, Abhinav Mishra,

Foodborne pathogens such as Listeria spp. contain the ability to survive and multiply in poultry farming environments, which provides a route of contamination for poultry processing environments and final poultry products. An understanding of the effect of meteorological variables on the prevalence of Listeria spp. in the farming environment is ... Read more >>

Food Res Int (Food research international (Ottawa, Ont.))
[2019, 122:47-55]

Cited: 0 times

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Semi-Quantification of Total Campylobacter and Salmonella During Egg Incubations Using a Combination of 16S rDNA and Specific Pathogen Primers for qPCR.

Michael J Rothrock, Kristina M Feye, Sun Ae Kim, Si Hong Park, Aude Locatelli, Kelli L Hiett, John Gamble, Holly Sellers, Steven C Ricke,

Rapid molecular techniques that evaluate eggs for the presence of foodborne pathogens is an essential component to poultry food safety monitoring. Interestingly, it is not just table eggs that contribute to outbreaks of foodborne disease. Broiler layer production actively contributes to sustaining of foodborne pathogens within a flock. The surface ... Read more >>

(Frontiers in microbiology)
[2018, 9:2454]

Cited: 0 times

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Complete Genome Sequence of Listeria monocytogenes Strain MR310, Isolated from a Pastured-Flock Poultry Farm System.

Michael J Rothrock, Peixin Fan, Kwangcheol C Jeong, Sun Ae Kim, Steven C Ricke, Si Hong Park,

Investigation of Listeria monocytogenes transmission from environmental sources associated with pasture-raised chickens to poultry products is needed to determine ways to prevent potential foodborne illness. Here, we report the complete genome sequence of Listeria monocytogenes MR310, one of the isolates from a pastured-flock poultry management system. ... Read more >>

(Genome announcements)
[2018, 6(10):]

Cited: 0 times

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Urea Hydrolysis and Calcium Carbonate Precipitation in Gypsum-Amended Broiler Litter.

Christopher D Burt, Miguel L Cabrera, Michael J Rothrock, D E Kissel,

Broiler () litter is subject to ammonia (NH) volatilization losses. Previous work has shown that the addition of gypsum to broiler litter can increase nitrogen mineralization and decrease NH losses due to a decrease in pH, but the mechanisms responsible for these effects are not well understood. Therefore, three laboratory ... Read more >>

J. Environ. Qual. (Journal of environmental quality)
[2018, 47(1):162-169]

Cited: 0 times

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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.

Aude Locatelli, Micah A Lewis, Michael J Rothrock,

The occurrence of Listeria monocytogenes has been widely investigated in the poultry production chain from the processing plant to the final product. However, limited data are available on Listeria species, including Listeria monocytogenes, in the poultry farm environment. Therefore, fecal and soil samples from 37 pastured poultry flocks from 10 ... Read more >>

(Frontiers in veterinary science)
[2017, 4:227]

Cited: 2 times

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Listeria Occurrence in Poultry Flocks: Detection and Potential Implications.

Michael J Rothrock, Morgan L Davis, Aude Locatelli, Aaron Bodie, Tori G McIntosh, Janet R Donaldson, Steven C Ricke,

Foodborne pathogens such as Salmonella, Campylobacter, Escherichia coli, and Listeria are a major concern within the food industry due to their pathogenic potential to cause infection. Of these, Listeria monocytogenes, possesses a high mortality rate (approximately 20%) and is considered one of the most dangerous foodborne pathogens. Although the usual ... Read more >>

(Frontiers in veterinary science)
[2017, 4:125]

Cited: 7 times

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Flue-gas desulfurization gypsum effects on urea-degrading bacteria and ammonia volatilization from broiler litter.

Christopher D Burt, Miguel L Cabrera, Michael J Rothrock, D E Kissel,

A major concern of the broiler industry is the volatilization of ammonia (NH3) from the mixture of bedding material and broiler excretion that covers the floor of broiler houses. Gypsum has been proposed as a litter amendment to reduce NH3 volatilization, but reports of NH3 abatement vary among studies and ... Read more >>

Poult. Sci. (Poultry science)
[2017, 96(8):2676-2683]

Cited: 0 times

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In-Package Inactivation of Pathogenic and Spoilage Bacteria Associated with Poultry Using Dielectric Barrier Discharge-Cold Plasma Treatments.

Michael J Rothrock, Hong Zhuang, Kurt C Lawrence, Brian C Bowker, Gary R Gamble, Kelli L Hiett,

The goal of this study was to test the efficacy of in-package dielectric barrier discharge-cold plasma (DBD-CP) treatment to inactivate poultry-associated spoilage (Pseudomonas fluorescens) and pathogenic (Salmonella enterica Typhimurium, Campylobacter jejuni) bacteria. Liquid cultures of the bacterial isolates were sealed within packages containing ambient air (Trial 1) or modified air ... Read more >>

Curr. Microbiol. (Current microbiology)
[2017, 74(2):149-158]

Cited: 1 time

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Metabolic parameters linked by phenotype microarray to acid resistance profiles of poultry-associated Salmonella enterica.

Jean Guard, Michael J Rothrock, Devendra H Shah, Deana R Jones, Richard K Gast, Roxana Sanchez-Ingunza, Melissa Madsen, John El-Attrache, Bwalya Lungu,

Phenotype microarrays were analyzed for 51 datasets derived from Salmonella enterica. The top 4 serotypes associated with poultry products and one associated with turkey, respectively Typhimurium, Enteritidis, Heidelberg, Infantis and Senftenberg, were represented. Datasets were partitioned initially into two clusters based on ranking by values at pH 4.5 (PM10 A03). ... Read more >>

Res. Microbiol. (Research in microbiology)
[2016, 167(9-10):745-756]

Cited: 2 times

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How Should We Be Determining Background and Baseline Antibiotic Resistance Levels in Agroecosystem Research?

Michael J Rothrock, Patricia L Keen, Kimberly L Cook, Lisa M Durso, Alison M Franklin, Robert S Dungan,

Although historically, antibiotic resistance has occurred naturally in environmental bacteria, many questions remain regarding the specifics of how humans and animals contribute to the development and spread of antibiotic resistance in agroecosystems. Additional research is necessary to completely understand the potential risks to human, animal, and ecological health in systems ... Read more >>

J. Environ. Qual. (Journal of environmental quality)
[2016, 45(2):420-431]

Cited: 4 times

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Antibiotics in Agroecosystems: Introduction to the Special Section.

Alison M Franklin, Diana S Aga, Eddie Cytryn, Lisa M Durso, Jean E McLain, Amy Pruden, Marilyn C Roberts, Michael J Rothrock, Daniel D Snow, John E Watson, Robert S Dungan,

The presence of antibiotic drug residues, antibiotic resistant bacteria, and antibiotic resistance genes in agroecosystems has become a significant area of research in recent years and is a growing public health concern. While antibiotics are used in both human medicine and agricultural practices, the majority of their use occurs in ... Read more >>

J. Environ. Qual. (Journal of environmental quality)
[2016, 45(2):377-393]

Cited: 12 times

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Antibiotic Resistance Patterns of Major Zoonotic Pathogens from All-Natural, Antibiotic-Free, Pasture-Raised Broiler Flocks in the Southeastern United States.

Michael J Rothrock, Kelli L Hiett, Jean Y Guard, Charlene R Jackson,

The use of antibiotics in agroecosystems has been implicated in the rise in antibiotic resistance (AR), which can affect environmental, animal, and human health. To determine the environmental impact of antibiotic use in agroecosystems, appropriate background levels of AR in agricultural environments in the absence of antibiotic application must be ... Read more >>

J. Environ. Qual. (Journal of environmental quality)
[2016, 45(2):593-603]

Cited: 11 times

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Recovery of Salmonella enterica serovar Enteritidis from hens initially infected with serovar Kentucky.

Jean Guard, Roxana Sanchez-Ingunza, Devendra H Shah, Michael J Rothrock, Richard K Gast, Deana R Jones,

Salmonella enterica serovars Enteritidis and Kentucky differ greatly in epidemiology. We wanted to know if the non-pathogenic serotype Kentucky impacted the recovery of the pathogen Enteritidis from chickens. To explore this issue, 4 groups of hens were treated as follows: (i) hens were inoculated orally with Kentucky and injected intramuscularly ... Read more >>

Food Chem (Food chemistry)
[2015, 189:86-92]

Cited: 3 times

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A hybrid DNA extraction method for the qualitative and quantitative assessment of bacterial communities from poultry production samples.

Michael J Rothrock, Kelli L Hiett, John Gamble, Andrew C Caudill, Kellie M Cicconi-Hogan, J Gregory Caporaso,

The efficacy of DNA extraction protocols can be highly dependent upon both the type of sample being investigated and the types of downstream analyses performed. Considering that the use of new bacterial community analysis techniques (e.g., microbiomics, metagenomics) is becoming more prevalent in the agricultural and environmental sciences and many ... Read more >>

J Vis Exp (Journal of visualized experiments : JoVE)
[2014, (94):]

Cited: 3 times

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