Biology subjects

Mrofchak, R.

Publications and source records attributed to Mrofchak, R..

5 recordsLinked to original sources

bioRxiv2023

All about urine: Longitudinal examination of urine pH, specific gravity, proteins, culture, and resistance profiles in healthy dogs

BackgroundUrine is routinely evaluated in dogs to assess health. Reference ranges for many urine properties are well established, but the scope of variation in these properties over time within heathy dogs is not well characterized. ObjectivesLongitudinally characterize urine properties in healthy dogs over 3 months. AnimalsFourteen healthy client-owned dogs. MethodsDogs were evaluated for health; then, mid-stream free catch urine was collected from each dog at 12 timepoints: Mornings / afternoons of Days 1, 2, 3; end of Weeks 4, 5, 6, 7 and Months 2 and 3. Urine pH, urine specific gravity (USG), protein, cultures, and antimicrobial resistance profiles were evaluated at each timepoint. ResultsUrine pH varied significantly within and between dogs over time (Friedmans test: within p = 0.031; between p < 0.005). However, USG, protein, and bacterial richness of urine were consistent within dogs over time, and only varied significantly between dogs (Kruskal-Wallis: between all p < 0.005). Antimicrobial resistant isolates were identified in 13 out of 14 dogs with 71% (34 of 48) of the isolates demonstrating resistance to amoxicillin. Conclusions and clinical importance1) Urine pH should be assessed at multiple timepoints via pH meter prior to making clinical decisions. 2) Mid-stream free catch urine from multiple healthy dogs yielded high concentrations of bacteria in culture (>105 CFU/mL) and should not be considered the only indicator of urinary tract infection. 3) Bacterial isolates demonstrated widespread resistance to amoxicillin / oxacillin underscoring the need for antimicrobial stewardship.

zoology↗

bioRxiv2022

Zinc and laboratory emerge date impact honey bee gut microbiota and survival

Honey bees (Apis mellifera) may be exposed to a wide variety of chemicals in the environment, including pesticides, antibiotics, and metals. Zinc, for example, is commonly included in fertilizers, pesticides, and feed additives, and is found in agricultural runoff. Honey bees can be exposed to zinc directly or indirectly by consuming zinc-contaminated nectar and pollen. However, there is a paucity of studies addressing the putative effects of zinc on honey bees health. In this study, we tested the effects of zinc on honey bee survivorship and gut microbiota. To evaluate survivorship, we exposed bees to six concentrations of zinc (0, 50, 100, 250, 500, or 1000 mg/L) and assessed survival daily for 10 days. To evaluate effects of zinc on gut microbiota, we exposed bees to 5 or 100 mg/L zinc. Bees were sampled before (day 0) and after zinc exposure (days 3, 6, and 9). Abdominal contents underwent DNA extraction and 16S rRNA sequencing (V3-V4) on an Illumina MiSeq. Sequences were filtered and processed through QIIME2 and DADA2. Zinc treatment had minimal effects on bacterial DNA concentrations and absolute cell counts while emerge date (the date a bee emerged from the brood comb) had a significant effect with decreased bacterial concentrations and cell counts observed at later emerge dates. Survival was only minimally impacted (>89% survival) at zinc concentrations up to 100 mg/L. Zinc had limited effects on overall gut microbial composition, diversity, and taxonomic abundances, with the greatest differences noted in the bee group exposed to the higher concentration of zinc (100 mg/L). In this group, several beneficial taxa (Lactobacillus, Rhizobiaceae, Gilliamella) were found at reduced abundances, while Paenibacillus, a potentially pathogenic taxa, was found at increased abundances. This suggests that zinc exposure, even at relatively low levels, may negatively impact honey bee health, even if survivorship is not dramatically impacted. Notably, emerge date effects were also observed in microbial composition. These results demonstrate the need to include assessments of honey bee gut microbiota in addition to other metrics of honey bee health and survivorship when evaluating the potential effects of agrochemicals on honey bees

ecology↗

bioRxiv2021

Urine and Fecal Microbiota in a Canine Model of Bladder Cancer

IntroductionUrothelial carcinoma (UC) is the tenth most diagnosed cancer in humans worldwide. Dogs are a robust model for invasive UC as tumor development and progression is similar in humans and dogs. Recent studies on urine microbiota in humans revealed alterations in microbial diversity and composition in individuals with UC; however, the potential role of microbiota in UC has yet to be elucidated. Dogs could be valuable models for this research, but microbial alterations in dogs with UC have not been evaluated. ObjectiveThe objective of this this pilot study was to compare the urine and fecal microbiota of dogs with UC (n = 7) and age-, sex-, and breed-matched healthy controls (n = 7). MethodsDNA was extracted from mid-stream free-catch urine and fecal samples using Qiagen Bacteremia and PowerFecal kits, respectively. 16S rRNA gene sequencing was performed followed by sequence processing and analyses (QIIME 2 and R). ResultsCanine urine and fecal samples were dominated by taxa similar to those found in humans. Significantly decreased microbial diversity (Kruskal-Wallis: Shannon, p = 0.048) and altered bacterial composition were observed in the urine but not feces of dogs with UC (PERMANOVA: Unweighted UniFrac, p = 0.011). The relative abundances of Fusobacterium was also increased, although not significantly, in the urine and feces of dogs with UC. ConclusionThis study characterizes urine and fecal microbiota in dogs with UC, and it provides a foundation for future work exploring host-microbe dynamics in UC carcinogenesis, prognosis, and treatment.

cancer biology↗

bioRxiv2021

Gut microbiota and age shape susceptibility to clostridial enteritis in lorikeets under human care

BackgroundEnteritis is a common cause of morbidity and mortality in lorikeets that can be challenging to diagnose and treat. In this study, we examine gut microbiota in two lorikeet flocks with enteritis (Columbus Zoo and Aquarium - CZA; Denver Zoo - DZ). Since 2012, the CZA flock has experienced repeated outbreaks of enteritis despite extensive diet, husbandry, and clinical modifications. In 2018, both CZA and DZ observed a spike in enteritis. Recent research has revealed that the gut microbiota can influence susceptibility to enteropathogens. We hypothesized that a dysbiosis, or alteration in the gut microbial community, was making some lorikeets more susceptible to enteritis, and our goal was to characterize this dysbiosis and determine the features that predicted susceptibility. ResultsWe employed 16S rRNA sequencing to characterize the cloacal microbiota in lorikeets (CZA n = 67, DZ n = 24) over time. We compared the microbiota of healthy lorikeets, to lorikeets with enteritis, and lorikeets susceptible to enteritis, with "susceptible" being defined as healthy birds that subsequently developed enteritis. Based on sequencing data, culture, and toxin gene detection in intestinal contents, we identified Clostridium perfringens type A (CZA and DZ) and C. colinum (CZA only) at increased relative abundances in birds with enteritis. Histopathology and immunohistochemistry further identified the presence of gram-positive bacilli and C. perfringens, respectively, in the necrotizing intestinal lesions. Finally, using Random Forests and LASSO models, we identified several features (young age and the presence of Rhodococcus fascians and Pseudomonas umsongensis) associated with susceptibility to clostridial enteritis. ConclusionsWe identified C. perfringens type A and C. colinum associated with lorikeet necrohemorrhagic enteritis at CZA and DZ. Susceptibility testing of isolates lead to an updated clinical treatment plan which ultimately resolved the outbreaks at both institutions. This work provides a foundation for understanding gut microbiota features that are permissive to clostridial colonization and host factors (e.g. age, prior infection) that shape responses to infection.

microbiology↗

bioRxiv2021

Evaluating Extraction Methods to Study Canine Urine Microbiota

The urinary microbiota is the collection of microbes present in urine that play a role in host health. Studies of urine microbiota have traditionally relied upon culturing methods aimed at identifying pathogens. However, recent culture-free sequencing studies of the urine microbiota have determined that a diverse array of microbes are present in health and disease. To study these microbes and their potential role in diseases like bladder cancer or interstitial cystitis, consistent extraction and detection of microbial DNA from urine is critical. However, urine is a low biomass substrate, requiring sensitive methods to capture DNA and making the risk of contamination high. To address this challenge, we collected urine samples from ten healthy dogs and extracted DNA from each sample using five different commercially available extraction methods. Extraction methods were compared based on total and bacterial DNA concentrations and microbial community composition and diversity assessed through 16S rRNA gene sequencing. Significant differences in the urinary microbiota were observed by dog and sex but not extraction method. The Bacteremia kit yielded the highest total DNA concentrations (Kruskal-Wallis, p = 0.165, not significant) and the highest bacterial DNA concentrations (Kruskal-Wallis, p = 0.044). Bacteremia also extracted bacterial DNA from the greatest number of samples. Taken together, these results suggest that the Bacteremia kit is an effective option for studying the urine microbiota. This work lays the foundation to study the urine microbiome in a wide range of urogenital diseases in dogs and other species. HighlightsO_LICanine urine microbiota differed by sex and dog but not extraction method. C_LIO_LIQiagen Bacteremia kit yielded the highest bacterial DNA concentrations from urine. C_LIO_LIThe Bacteremia kit extracted bacterial DNA from the greatest number of samples. C_LIO_LIAbsolute abundance of Sphingomonas species increased in female dog urine. C_LIO_LIPasteurellaceae bacterium canine oral taxon 272 increased in male dog urine. C_LI

microbiology↗