Category Archives: uncategorized

Where is the metadata?

Contributed by DJ Darwin Bandoy, PhD Candidate One distinguishing feature of this pandemic is the rapid release of whole genome sequencing data. These sequences are usually uploaded in public databases with minimal accompanying metadata. While dates and geographic origin are useful for creation of phylogenetic analysis, further sophisticated analysis requires more metadata, particularly associated with […]

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Quantify Structural Similarity Comparisons of Genome Assemblies

Contributed by Cory Schlesener, B.S. One important component of a genome’s overall composition is the larger structure of how conserved blocks of genetic sequence are arranged. As segments of DNA recombine, sequences are introduced into new locations and/or orientations in a genome. However, this composition of large genetic blocks can artificially be rearranged in a constructed genome […]

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More on the Equine Microbiome

Contributed by Ashleigh Flores, M.S. Within the GI Tract, horses can host up to 1015 bacterial cells, with the highest population residing within the caecum. Recent studies have revealed that distinct individual ecosystems for each compartment of the equine gut exist, with adjacent compartments having the most similarities in microbiome composition. The upper GI tract […]

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Pandemic Status as of July 12, 2020

Contributed by DJ Darwin Bandoy, Ph.D. Candidate California is in full lockdown again after a surge in cases. This is a consequence of opening too early when the cases are not fully suppressed. This requires people to wear masks, practice physical distancing, and a reduction of unnecessary travel. Heterogeneous properties of infection indicate super-spreading events […]

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Professor Bart C. Weimer, Ph.D.

Professor, School of Veterinary Medicine,       UC Davis        Director, 100K Pathogen Genome Project  Publication Summary: 22 book chapters 4 books 159 manuscripts 6 patents awarded 13 invention disclosures 540 presentations Google Scholar, ResearchGate, Orcid, ReseacherID (Publons)  UCDavis Microbiome Special Research Program Leadership Experience: Chair; Department of Population Health and Reproduction. 2019 – present Director, founder; Genomes4Health. 2019 […]

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Horses and “Pigeon Fever”

Contributed by Ashleigh Flores, M.S. Corynebacterium pseudotuberculosis biovar equi is responsible for the highly contagious disease in horses commonly known as “Pigeon Fever”. Although flies act as the primary vector, soil serves as a reservoir for this robust microorganism. Research has shown that C. pseudotuberculosis can persist in soil for months at a time, particularly […]

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Identifying horizontally acquired elements in bacterial genomes

Contributed by Cory Schlesener Bacterial genomes are composed of diverse genetic elements. Many of these elements are not exclusively passed down a parental lineage (vertically acquired), but can also be horizontally acquired from other bacteria of varying degrees of relatedness. As bacteria are asexual, mechanisms of horizontal transfer of genetic information provide ways to add diversity to a population. Novel genes […]

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The Equine Microbiome: A New Frontier in Veterinary Research

Contributed by Ashleigh Flores There has been growing interest in the link between the microbiota of the gut and disease mediated changes in both human and veterinary medicine. The horse gastrointestinal tract is one of the most unique displays of physiological engineering in any mammal. Horses are non-ruminant herbivores with the ability for microbial fermentation […]

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