Category Archives: uncategorized

Next Generation Antimicrobial Resistance Profiling Using Whole Genome Sequences

Contributed by Darwin Bandoy, DVM Antimicrobial resistance is a key issue as pathogens develop resistance due to the misuse of antimicrobials in food animals. While some countries have already banned the use of antibiotics as growth promotants, emerging economies find it difficult to implement due to numerous factors. From a monitoring point of view, large […]

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Preprint is Out!

Contributed by Darwin Bandoy, DVM We are proud to announce the preprint publication of our paper wherein we identified a misclassified species of Hungatella from the Human Microbiome Project. This project demonstrates the power of pangenome analysis to resolve species identity by clustering. The impact of the misclassification is amplified because of numerous microbiome papers using […]

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Comprehensive Carbohydrate Active Enzyme Analysis with meta-dbCAN

Contributed by Shawn Higdon The focus of my graduate research involves the investigation of nitrogen-fixing bacteria inhabiting a terrestrial environment that is rich in complex carbohydrate – the aerial root exudate (mucilage) of an isolated maize landrace. Within this arc, I have embarked on a quest to characterize the genomes of cultured bacteria derived from […]

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Post Conference Reflections: Bay Area Microbial Pathogenesis Symposium

Contributed by Darwin Bandoy DVM I presented a poster at BAMPS (Bay Area Microbial Pathogenesis Symposium) with my work on using machine learning bacterial genome-wide association study. First of all, it was radically different as most posters focus on defining a mechanism for a single gene, while my work is about extracting insights from population-scale […]

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