Browsing by Author "Johnson, Timothy"

Now showing 1 - 8 of 8
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    Changes in the Porcine Intestinal Microbiome in Response to Infection with Salmonella Enterica and Lawsonia Intracellularis
    (2015-05-13) Borewicz, Klaudyna; Kim, Hyeun; Singer, Randall; Gebhart, Connie; Sreevatsan, Srinand; Johnson, Timothy; Isaacson, Richard; isaac015@umn.edu; Isaacson, Richard
    Salmonella enterica is a leading cause of food borne illness. Recent studies have shown that S. enterica is a pathogen capable of causing alterations to the composition of the intestinal microbiome. A recent prospective cross-sectional study of French pork production farms found a statistically significant association between Lawsonia intracellularis and carriage of S. enterica. In the current study the composition of the gut microbiome was determined in pigs challenged with S. enterica serovar Typhimurium and or L. intracellularis and compared to non-challenged control pigs. Principal coordinate analysis demonstrated that there was a disruption in the composition of the gut microbiome in the colon and cecum of pigs challenged with either pathogen. The compositions of the microbiomes of challenged pigs were similar to each other but differed from the non-challenged controls. There also were statistically significant increases in Anaerobacter, Barnesiella, Pediococcus, Sporacetigenium, Turicibacter, Catenibacterium, Prevotella, Pseudobutyrivibrio, and Xylanibacter in the challenged pigs. To determine if these changes were specific to experimentally challenged pigs, we determined the compositions of the fecal microbiomes of naturally infected pigs that were carriers of S. enterica. Pigs that were frequent shedders of S. enterica were shown to have similar fecal microbiomes compared to non-shedders or pigs that shed S. enterica infrequently. In a comparison of the differentially abundant bacteria in the naturally infected pigs compared to experimentally challenged pigs, 9 genera were differentially abundant and each exhibited the same increase or decrease in abundance between the two groups. Thus, there were similar changes in the GI microbiome associated with carriage of S. enterica regardless of whether the pigs were experimentally challenged with S. enterica or acquired it naturally.
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    Data from "Diverse Bacterial Communities Exist on Canine Skin and are Impacted by Cohabitation and Time"
    (2016-11-17) Johnson, Timothy; Torres, Sheila; Danzeisen, Jessica; Clayton, Jonathan; Ward, Tonya; Knights, Dan; Huang, Hu; joh04207@umn.edu; Johnson, Timothy
    This related study sampled 40 dogs from 20 households over the course of three seasons. Three skin sites were examined. The goal of the study was to determine if a core skin microbiome exists in dogs across time and body site, and if cohabitation impacts sharing of the skin microbiome. This dataset is a part of the Torres_Johnson Canine Microbiome Study.
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    Design, Characterization, and Manufacturing of Ultra-sharp Metallic Probes for Near-field Optics
    (2014-05) Johnson, Timothy
    The ability to manipulate and nanofocus light has many potential applications such as surface-enhanced spectroscopy, optical trapping, heat-assisted magnetic recording, and near-field imaging. In this thesis a new method to fabricate devices for nanofocusing is introduced and then demonstrated for use in near-field imaging. This method uses a sharp, metallic tip to confine and focus the light. Current methods to produce these sharp tips suffer from low reliability and low-throughput processing methods. Here a fabrication method called template stripping is introduced. With this method, precise control over the fabrication of metal films with integrated bumps, grooves, and holes is shown. Next, the method is used to fabricate sharp, metallic tips. The tips are used for near-field imaging and show a resolution of < 20 nm and observed fluorescence enhancements of ~200x from single fluorescent molecules. The tips are also demonstrated for near-field Raman imaging of carbon nanotube bundles and show good results. These tips provide high-quality results, but one of the more important features is that the yield of the tips is around 95%, much higher than current methods for fabricating sharp, metallic tips. Also, different schemes to create nanofocusing are presented. One method makes use of an asymmetric metal deposition and another a C-shaped aperture around the tip to focus light illuminating the tip from inside itself. Both of these methods show significant nanofocusing and provide new structures for nanofocusing studies. The processes to fabricate these structures are developed with the hope that they will be widely disseminated to allow more researchers access to reliable tips and hopefully bringing more people into the field of near-field imaging.
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    E-supplement to: Efficacy of antibiotic and non-antibiotic interventions in preventing and treating necrotic enteritis in broiler chickens: a systematic review
    (2022) Bueno, Irene; Ricke, Isabel; Hwan, Haejin; Smith, Emily; Nault, Andre; Johnson, Timothy; Singer, Randall S.
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    FUTIs: An In-person or Online Graphing, Bioinformatics, and Scientific Literacy Exercise that Explores the Presence of Antibiotic Resistance in Foodborne Urinary Tract Infections
    (2023-03-01) Foster-Hartnett, Dawn; Dvorak, Cheryl; Johnson, Timothy; tjj@umn.edu; Johnson, Timothy
    This is the dataset for instructors to use when implementing coursework into their curriculum. These are assembled genomes from retail poultry meat.
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    Microbial Community Structure and its Relationship to Gut Health in Poultry
    (University of Minnesota. Minnesota Extension Service, 2013-09) Johnson, Timothy
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    More Than a "Washed-Up Has-Been:" Textual Aspects of the Holmes Icon
    (2013-10-25) Johnson, Timothy
    This paper focuses on textual exemplars from the Sherlock Holmes stories in support of an argument that these texts are just as important in understanding Holmes as a cultural icon as are the visual exemplars found in printed materials, theater, motion pictures, and television. Following a brief summary of the visual exemplars, the author presents six textual examples from the Holmesian canon to support the central argument of this paper—that the "textual logo" or "emblematic wording" is as much a part of the Holmesian iconography as the essential images. In the end, the author concludes that the idea of Holmes as a cultural icon has moved beyond the bounds of the English-speaking world, i.e. is understood in a global context, and that this understanding is rooted in a robust iconography that includes both textual phrases and visual images.
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    Relationships between cecum, ileum and litter bacterial microbiomes in a commercial turkey flock, and the impact of penicillin treatment on early bacterial community establishment
    (2015-10-19) Danzeisen, Jessica; Clayton, Jonathan; Huang, Hu; Knights, Dan; McComb, Brian; Hayer, Shivdeep; Johnson, Timothy; joh04207@umn.edu; Johnson, Timothy
    Gut health is paramount for commercial poultry production, and methods to assess gut health are critically needed to better understand how the avian gastrointestinal tract matures over time. One important aspect of gut health is the totality of bacterial populations inhabiting different sites of the avian gastrointestinal tract, and associations of these populations with the poultry farm environment, since these bacteria are thought to drive metabolism and prime the host immune system. In this study, a single flock of commercial turkeys was followed over the course of twelve weeks to examine bacterial microbiome inhabiting the ceca, ileum, and corresponding poultry litter. Furthermore, the effects of low-dose, growth-promoting penicillin treatment (50 g/ton) in feed on the ileum bacterial microbiome were also examined during the early brood period. The cecum and ileum bacterial communities of birds shifted independently but in parallel to one another over time, with distinct bacterial populations harboring each site. Corresponding poultry litter more closely represented the ileal bacterial populations than cecal bacterial populations, and also changed parallel to ileum bacterial populations over time. Penicillin applied at low doses in feed significantly enhanced early weight gain in commercial poults, and this correlated with predictable shifts in the ileum bacterial populations in control versus treatment groups. Overall, this study demonstrates the dynamic shifts in the turkey gastrointestinal microbiome during development, the correlations between bacterial populations in the gastrointestinal tract and the litter environment, and the impact of low-dose penicillin on the modulation of bacterial communities in the ileum. Alternatives to low-dose antibiotics would benefit by mimicking these effects in the gut, among others.