Tara N. Gaire
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View article: Enriched Long-Read Sequencing of Co-circulating Viruses in Complex Samples
Enriched Long-Read Sequencing of Co-circulating Viruses in Complex Samples Open
At present, no single workflow is available for quick and accurate identification and analysis of genomes of various viruses present together in a field or clinical sample, particularly when followed by long-read sequencing. Our work addre…
View article: Exploring the phylogenetic diversity and antimicrobial activity of non-aureus staphylococci and mammaliicocci isolated from teat apices of organic dairy cows
Exploring the phylogenetic diversity and antimicrobial activity of non-aureus staphylococci and mammaliicocci isolated from teat apices of organic dairy cows Open
Prior studies have suggested that non- aureus staphylococci and mammaliicocci (NASM) possess inhibitory activity against mastitis pathogens. However, their impact on udder health outcomes and the mechanisms underlying this potential protec…
View article: The impact of pooling on the observed microbiome profile of preweaned piglet feces
The impact of pooling on the observed microbiome profile of preweaned piglet feces Open
Pooling individual samples could be an efficient approach for large-scale population-based microbiome studies. However, it is unknown whether pooled samples accurately reflect the microbiome composition and diversity obtained from individu…
View article: Fresh pork microbiota is temporally dynamic and compositionally diverse across meat, contact surfaces, and processing lines in a pork processing facility
Fresh pork microbiota is temporally dynamic and compositionally diverse across meat, contact surfaces, and processing lines in a pork processing facility Open
The goal of this study was to analyze the microbial profiles of meat and contact surfaces from two different processing lines in a pork processing plant, using a 16S rRNA gene amplicon sequencing workflow specifically designed to investiga…
View article: Isolation of Bacteriophages Lytic to Fusobacterium necrophorum Subspecies necrophorum from Bovine Ruminal Fluid and City Sewage
Isolation of Bacteriophages Lytic to Fusobacterium necrophorum Subspecies necrophorum from Bovine Ruminal Fluid and City Sewage Open
Fusobacterium necrophorum subspecies necrophorum, a resident of the rumen, is the causative agent of bovine liver abscesses. Currently, tylosin, a macrolide, is used in the feed to reduce liver abscesses. Because macrolides are medically i…
View article: Microbiome characterization of two fresh pork cuts during production in a pork fabrication facility
Microbiome characterization of two fresh pork cuts during production in a pork fabrication facility Open
The goal of this study was to characterize the microbial profile of two different fresh pork cuts, bootjack (BJ) trim and tenderloin (TL), through a 16S rRNA sequencing workflow developed specifically for investigating low-biomass fresh me…
View article: Reducing skin microbiome exposure impacts through swine farm biosecurity
Reducing skin microbiome exposure impacts through swine farm biosecurity Open
Background Livestock work is unique due to worker exposure to animal-associated microbiomes within the workplace. Swine workers are a unique cohort within the US livestock labor force, as they have direct daily contact with pigs and undert…
View article: Analysis of the northern pitcher plant (Sarracenia purpurea L.) phytotelm bacteriome throughout a temperate region growing season
Analysis of the northern pitcher plant (Sarracenia purpurea L.) phytotelm bacteriome throughout a temperate region growing season Open
The insectivorous Northern Pitcher Plant, Sarracenia purpurea , recruits a dynamic biotic community in the rainwater collected by its pitcher-shaped leaves. Insect capture and degradation within the pitcher fluid (phytotelma) has been well…
View article: Temporal dynamics of the fecal microbiome in female pigs from early life through estrus, parturition, and weaning of the first litter of piglets
Temporal dynamics of the fecal microbiome in female pigs from early life through estrus, parturition, and weaning of the first litter of piglets Open
View article: Exploring the phylogenetic diversity and antimicrobial activity of non- <i>aureus staphylococci</i> and <i>mammaliicocci</i> isolated from teat apices of organic dairy cows
Exploring the phylogenetic diversity and antimicrobial activity of non- <i>aureus staphylococci</i> and <i>mammaliicocci</i> isolated from teat apices of organic dairy cows Open
Prior studies have suggested that non- aureus staphylococci and mammaliicoci ( NASM ) possess inhibitory activity against mastitis pathogens. However, their impact on udder health outcomes and the mechanisms underlying this potential prote…
View article: Influence of Rainfall on Size-Resolved Bioaerosols Around a Livestock Farm
Influence of Rainfall on Size-Resolved Bioaerosols Around a Livestock Farm Open
View article: Effect of castration timing and weaning strategy on the taxonomic and functional profile of ruminal bacteria and archaea of beef calves
Effect of castration timing and weaning strategy on the taxonomic and functional profile of ruminal bacteria and archaea of beef calves Open
Background Beef cattle experience several management challenges across their lifecycle. Castration and weaning, two major interventions in the early life of beef cattle, can have a substantial impact on animal performance. Despite the key …
View article: Evaluating variations in metabolic profiles during the dry period related to the time of hyperketonemia onset in dairy cows
Evaluating variations in metabolic profiles during the dry period related to the time of hyperketonemia onset in dairy cows Open
Hyperketonemia (HYK) in early lactation can have a different impact on health and productivity depending on the timing of HYK onset. While specific metabolites measured during the dry period may serve as biomarkers of HYK, the correlations…
View article: Temporal dynamics of the fecal microbiome in female pigs from early life through estrus, parturition, and weaning of the first litter of piglets
Temporal dynamics of the fecal microbiome in female pigs from early life through estrus, parturition, and weaning of the first litter of piglets Open
Background Age-associated changes in the gastrointestinal microbiome of young pigs have been robustly described; however, the temporal dynamics of the gut microbiome of the female pig from early life to first parity are not well understood…
View article: Age influences the temporal dynamics of microbiome and antimicrobial resistance genes among fecal bacteria in a cohort of production pigs
Age influences the temporal dynamics of microbiome and antimicrobial resistance genes among fecal bacteria in a cohort of production pigs Open
Background The pig gastrointestinal tract hosts a diverse microbiome, which can serve to select and maintain a reservoir of antimicrobial resistance genes (ARG). Studies suggest that the types and quantities of antimicrobial resistance (AM…
View article: The impacts of viral infection and subsequent antimicrobials on the microbiome-resistome of growing pigs
The impacts of viral infection and subsequent antimicrobials on the microbiome-resistome of growing pigs Open
View article: A longitudinal investigation of the effects of age, dietary fiber type and level, and injectable antimicrobials on the fecal microbiome and antimicrobial resistance of finisher pigs
A longitudinal investigation of the effects of age, dietary fiber type and level, and injectable antimicrobials on the fecal microbiome and antimicrobial resistance of finisher pigs Open
Age and diet are among the factors that influence the community composition of the fecal microbiome. Additionally, antimicrobial use can alter the composition of bacterial communities. An 86-d study with finisher pigs aimed to evaluate age…
View article: The microbiome of common bedding materials before and after use on commercial dairy farms
The microbiome of common bedding materials before and after use on commercial dairy farms Open
View article: Additional file 2 of The impacts of viral infection and subsequent antimicrobials on the microbiome-resistome of growing pigs
Additional file 2 of The impacts of viral infection and subsequent antimicrobials on the microbiome-resistome of growing pigs Open
Additional file 2: Dataset S1. Metadata for all samples presented in this study. Dataset S2. Results from microbiome (phylum and genus level) differential abundance testing of each treatment group, by sampling time point. Dataset S3. Resul…
View article: Additional file 1 of The microbiome of common bedding materials before and after use on commercial dairy farms
Additional file 1 of The microbiome of common bedding materials before and after use on commercial dairy farms Open
Additional file 1: Table S1. Metadata file for all samples included in this study. Table S2. ASVs assigned to each taxonomic level. Table S3. Read counts and mean abundance of assigned species stratified by sample ID. Table S4. Proportion …
View article: Modelling the antimicrobial pharmacodynamics for bacterial strains with versus without acquired resistance to fluoroquinolones or cephalosporins
Modelling the antimicrobial pharmacodynamics for bacterial strains with versus without acquired resistance to fluoroquinolones or cephalosporins Open
The results demonstrate predictable multiparameter changes in the PD of these first-line antimicrobials depending on the Salmonella strain's susceptibility phenotype and specific genes conferring reduced susceptibility. The generated PD pa…
View article: PSV-B-18 Characterization of the fecal microbiome of healthy adult beagle dogs supplemented with graded levels of bacillus coagulans GBI-30, 6086
PSV-B-18 Characterization of the fecal microbiome of healthy adult beagle dogs supplemented with graded levels of bacillus coagulans GBI-30, 6086 Open
This study aimed to evaluate the effect of Bacillus coagulans GBI-30, 6086 on the fecal microbiome of healthy adult dogs. Extruded diets containing graded levels of probiotic applied either to the base ration before extrusion or as a topic…
View article: Faecal concentrations of ceftiofur metabolites in finisher pigs administered intramuscularly with ceftiofur
Faecal concentrations of ceftiofur metabolites in finisher pigs administered intramuscularly with ceftiofur Open
The objective of this study was to determine the effects of dietary fibre level and source on faecal ceftiofur metabolites concentrations after intramuscular administration of therapeutic ceftiofur hydrochloride in finisher pigs. Pens of f…
View article: Author response for "Faecal concentrations of ceftiofur metabolites in finisher pigs administered intramuscularly with ceftiofur"
Author response for "Faecal concentrations of ceftiofur metabolites in finisher pigs administered intramuscularly with ceftiofur" Open
View article: Age Dependence of Antimicrobial Resistance Among Fecal Bacteria in Animals: A Scoping Review
Age Dependence of Antimicrobial Resistance Among Fecal Bacteria in Animals: A Scoping Review Open
Introduction: A phenomenon of decreasing antimicrobial resistance (AMR) among fecal bacteria as food animals age has been noted in multiple field studies. We conducted a scoping review to summarize the extent, range, and nature of research…
View article: Can the use of older-generation beta-lactam antibiotics in livestock production over-select for beta-lactamases of greatest consequence for human medicine? An in vitro experimental model
Can the use of older-generation beta-lactam antibiotics in livestock production over-select for beta-lactamases of greatest consequence for human medicine? An in vitro experimental model Open
Though carbapenems are not licensed for use in food animals in the U.S., carbapenem resistance among Enterobacteriaceae has been identified in farm animals and their environments. The objective of our study was to determine the extent to w…
View article: Variation in fluoroquinolone pharmacodynamic parameter values among isolates of two bacterial pathogens of bovine respiratory disease
Variation in fluoroquinolone pharmacodynamic parameter values among isolates of two bacterial pathogens of bovine respiratory disease Open
To design an antimicrobial treatment regimen for a bacterial disease, data on the drug pharmacodynamics (PD) against selected drug-susceptible strains of the pathogen are used. The regimen is applied across such strains in the field, assum…
View article: Prevalence of Bovine Viral Diarrhea Virus Infection in Dairy Herds of Nepal
Prevalence of Bovine Viral Diarrhea Virus Infection in Dairy Herds of Nepal Open
Background: The Bovine Viral Diarrhea Virus (BVDV) infection causes reproductive and respiratory disease in cattle and buffaloes and is an economically important livestock disease across the world.In Nepal, cattle and buffalo farming is an…
View article: Epidemiology, Impact and Control of Rabies in Nepal: A Systematic Review
Epidemiology, Impact and Control of Rabies in Nepal: A Systematic Review Open
Better data are needed to unravel the true burden of animal and human rabies. More collaboration, both within the country and within the region, is needed to control rabies. To achieve these goals, high level political commitment is essent…