Biology subjects

Cooper, K. K.

Publications and source records attributed to Cooper, K. K..

5 recordsLinked to original sources

bioRxiv2026

Characterization of household microbiomes from three unique cities around the world

Characterizing the household bacterial microbiome allows for a stronger understanding of the various microbes that a person is exposed to everyday in their home. Exploring household microbiomes in different countries around the world increases - our understanding of the impact cultural differences might have on niche microbial communities in the house. The goal of this study was to use shotgun metagenomics to characterize the microbiome for ten locations around the home in ten different houses from three different countries (Mysuru, India; Dubai, United Arab Emirates (UAE); and Tucson, United States of America (USA)). There was a significant difference in alpha diversity between the three countries (ANOVA, p<0.05) with homes in Mysuru, India showing significantly higher bacterial diversity compared to Dubai, UAE and Tucson, AZ, USA. Beta diversity analysis of the homes found that bacterial communities significantly differed between cities (PERMANOVA, p<0.01) and within cities by household locations (PERMANOVA, p<0.001). Locations such as underneath the toilet rim, bathroom and kitchen sinks had the highest levels of bacterial diversity across the three cities compared to other sampling areas. A core microbiome of Actinomycetes and Gammaproteobacteria was found in all homes in all three cities. Within each city, a core microbiome was identified at the species level within specific household locations in each city. Over 90% of bacterial taxa found in the homes were a part of the human-associated phyla Actinomycetes (eg. genera Brevibacterium, Corynebacterium, and Microbacterium), Pseudomonadota (eg. genera Acinetobacter, Moraxella, Pantoea, Paracoccus, and Psuedomonas), and Bacillota (genus Streptococcus), which was comparable to previous studies. The household microbiome is variable in different locations in the house and on a global scale. Factors such as human activity, cultural practices, climate, and surface type and use may drive this diversity. Characterizing the household microbiome on a global scale allows for a better understanding of what drives microbial diversity, increasing our understanding of how microbial communities are shaped by the environment and how humans influence their dynamics, as well as any risks to human health that the built microbiome may potentially pose. Impact StatementThis research contributes to the understanding of the built microbiome, specifically how it varies within the house, within cities, and across the globe. This can aid in our understanding of microbial dynamics in environments with heavy human influence and help develop and improve hygiene habits and products which are mindful of the existing microbiome. Data SummaryDNA sequence data from this research is publicly available on the NCBIs Sequence Read Archive under BioProject PRJNA1416920. Data was analyzed using python and R code. Analysis protocols and information on software versions, packages, and more can be found within the text and in the following github repository: https://github.com/carolinescranton01/Global_Household_Microbiome. The authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.

microbiology↗

bioRxiv2025

Optimization and Comparative Evaluation of SimpliAmp and Bio-Rad Thermal Cyclers for PCR-Based Detection of Vibrio cholerae

Cholera continues to pose a significant public health risk in low- and middle-income countries (LMICs), necessitating quick, cost-effective, and dependable diagnostics for effective outbreak surveillance and management. In this study, we optimized and tested two PCR-based assays targeting a uniplex assay with the ompW gene, and a multiplex assay with ctxA, O1-rfb, and O139-rfb genes of Vibrio cholerae (V. cholerae) on two thermal cycler platforms with different cost: the Bio-Rad C1000 Touch, which is more expensive, and the SimpliAmp, which is cheaper. Cycling conditions, annealing temperatures, and primer concentrations were systematically optimized to improve efficiency and reagent use. We tested our assay sensitivity by serially diluting gBlock DNA from 2000 to 50 copies. Quo data software was used to estimate the limit of detection and Fishers exact tests with Holm-Bonferroni correction to assess any differences (p<0.05) across all dilution levels on both platforms. The ompW assay achieved identical performance on both platforms, with 100% detection down to 250 copies and an LOD of 523 copies (95% CI: 347- 786; p = 1.000). For the multiplex assay, O1-rfb showed slightly higher sensitivity on SimpliAmp (LOD= 509 copies, 95% CI: 339-766) than on Bio-Rad (LOD = 333 copies, 95% CI: 255-688; p = 0.217). The ctxA assay had an LOD of 684 copies (95% CI: 501-1323) on SimpliAmp and 974 copies (95% CI: 714-1784) on Bio-Rad (p = 0.089). For O139-rfb, SimpliAmp and Bio-Rad achieved LOD values of 639 (95% CI: 490-1251) and 1060 copies (95% CI: 719-1562), respectively (p = 0.179). In general, the differences in performance between platforms were not statistically significant. These results highlight the potential of SimpliAmp as a reliable, low-cost alternative for cholera diagnostics in LMICs and low-resource settings, supporting broader access to molecular tools for outbreak investigation and public health surveillance.

molecular biology↗

bioRxiv2025

Growth rates and Metabolic Traits Differentiate Campylobacter jejuni Strains by Diarrheal Manifestation

IntroductionCampylobacter jejuni is the leading cause of bacterial gastroenteritis worldwide. Infections with C. jejuni can result in two different diarrheal manifestations in humans: watery diarrhea or bloody/inflammatory diarrhea. Hypothesis/Gap StatementCurrently, little is known about C. jejuni and/or host factors associated with elicitation of these two distinct diarrheal manifestations. We hypothesize that these factors may include growth and metabolic trait differences between C. jejuni strains associated with watery diarrhea and bloody/inflammatory diarrhea. AimUsing C. jejuni strains with a defined diarrheal manifestation in the neonatal piglet model, we aimed to assess differences in temperature dependent growth rates, motility, biofilm production, and carbon utilization between diarrheal manifestation groups. MethodologyStrains were initially assessed for 192 different carbon sources using phenotypic microarrays followed by specific carbon utilization, growth, motility, and biofilm assays at 37{degrees}C and/or 42{degrees}C. ResultsWe found that at 37{degrees}C, watery diarrhea associated C. jejuni strains grew significantly faster compared to bloody/inflammatory diarrhea associated C. jejuni strains. However, there was no significant growth difference at 42{degrees}C between the groups, due to bloody/inflammatory diarrhea associated strains growing faster at 42{degrees}C compared to 37{degrees}C. Additionally at 37{degrees}C, we found that L-fucose utilization was significantly higher among watery diarrhea associated strains, while L-glutamine utilization was significantly higher among bloody/inflammatory diarrhea associated strains. ConclusionThe results indicate there are distinct metabolic adaptations between watery and/or bloody/inflammatory diarrhea associated C. jejuni strains particularly at 37{degrees}C, which may be one of the factors associated with differing diarrheal manifestations.

microbiology↗

bioRxiv2025

STRAIN-SPECIFIC VIRULENCE SIGNATURES OF CAMPYLOBACTER JEJUNI ASSOCIATED WITH WATERY VERSUS BLOODY DIARRHEA IN NEONATAL PIGLET MODEL

Campylobacter jejuni is the leading cause of bacterial gastroenteritis globally, presenting with either watery or bloody/inflammatory diarrhea. Despite this clinical variability, the underlying mechanisms driving these distinct diarrheal manifestations remain unclear. The neonatal piglet model provides a unique opportunity to investigate these differences using strains with defined disease manifestations. We evaluated ten C. jejuni strains previously shown to cause consistent diarrheal manifestations in neonatal piglets: five strains associated with watery diarrhea and five associated with bloody/inflammatory diarrhea. The study found significant strain to strain variation among most assays, but overall strains associated with bloody/inflammatory diarrhea exhibited significantly higher levels of epithelial cell invasion, intracellular survival, macrophage survivability, and disruption of intestinal barrier integrity compared to watery diarrhea strains. Notably, both groups had similar levels of adherence, produced similar levels of cytolethal distending toxin (CDT) and elicited comparable IL-8 responses. While both groups facilitated translocation of commensal E. coli, only bloody/inflammatory strains caused increased paracellular permeability, as shown by TEER and FITC-dextran assays. This study reveals that there is significant variation in the virulence phenotype of C. jejuni strains and identifies several characteristics consistently associated with a specific diarrheal manifestation group. These findings provide new insights into the strain-specific pathogenic mechanisms of C. jejuni, with implications for understanding host-pathogen interactions and informing targeted diagnostic and therapeutic strategies. Author SummaryCampylobacter jejuni is one of the most common bacterial causes of diarrhea worldwide, affecting millions each year. Infected individuals may experience either watery or bloody/inflammatory diarrhea, but the reasons why different strains cause different types of illness have remained a mystery. In this study, we used a neonatal piglet model, which accurately mimics human diarrheal disease, to investigate why certain C. jejuni strains cause more severe symptoms than others. We compared strains known to cause either watery or bloody diarrhea and found key differences in their ability to invade intestinal cells, survive inside immune cells, and damage the intestinal barrier. While both groups of strains could trigger inflammation and translocate E. coli through the intestinal lining, only the strains linked to bloody diarrhea caused significant barrier disruption and had increased intracellular survival. These findings reveal that different C. jejuni strains follow distinct paths during infection, which helps explain why they produce different symptoms. Unraveling these differences improves our overall understanding of Campylobacter pathogenesis that could lead to improved diagnostics and/or treatments to reduce the burden of campylobacteriosis around the world.

microbiology↗

bioRxiv2023

Urbanization spreads antimicrobial resistant enteric pathogens in wild bird microbiomes

Human behaviour is dramatically changing global ecology. Nowhere is this more apparent than in urbanization, where novel high human density habitats are disrupting long established ecotones. Resultant changes to the transitional areas between organisms, especially enhanced contact between humans and wild animals, provides new opportunities for the spread of zoonotic pathogens, posing a serious threat to global public health. Here, by studying the multi-host enteric pathogen Campylobacter jejuni isolated from the gut of 30 bird species in 8 countries, we investigated how proximity to urbanization influenced the spread of antimicrobial resistant (AMR) strains. Generalized linear models compared multiple behavioural and ecological traits and confirmed a positive correlation between proximity to urbanization and the number of C. jejuni genotypes and AMR genes in wild bird hosts. Wild birds from highly urban areas harboured up to four times more C. jejuni genotypes and six times more AMR genes. This is consistent with increased frequency of transition events. Quantifying zoonotic transmission and gene pool spread is essential for quantitative one health surveillance and control measures against future zoonosis emergences.

genomics↗