Author Archives: WeimerMicroLab

Fast Transcript Quantification with Salmon

Contributed by Shawn Higdon Interpretation of Sequencing data from experiments targeting gene expression in any biological system requires a series of computational and analytical steps. After going through the motions of pre-processing sequencing reads into a state of high quality (trimming low-quality base calls and removing adapter sequences that slip through the cracks), the next […]

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Post ASM Conference reflections

Contributed by Darwin Bandoy, DVM I participated in the 2018 ASM Conference on Rapid Applied Microbial Next-Generation Sequencing and Bioinformatic Pipelines, September 23–26, 2018, in Tysons, Virginia and presented my work in the lab using next-generation sequencing of Campylobacter hyointestinalis. The most interesting talk for me, surprisingly, is the use of data analytics by the […]

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Pan-Genome Analysis with Roary

Contributed by Shawn Higdon Microbial Genomics involves the isolation of microbes from environmental samples, often times with the intent of generating a pure culture comprised by an organism of a single type of strain. While many isolation events lead to the generation of such cultures, large-scale isolation endeavors often lead to collections of banked isolates […]

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Diabetes and Gut Microbiome Study

Contributed by Carol Huang Metabolic disease diabetes and obesity have impacted quite some percentage of the population, over 600 million people in the world are obese, and over 400 million have diabetes. Type I diabetes often involves the loss of beta islet cells which produce insulin; Type II diabetes is a disorder of elevated blood […]

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Non-mammals and mammal gut defense

Contributed by Nguyet Kong Chitin is a fibrous substance containing polysaccharides and form the exoskeleton of arthropods such as insects and crustaceans and are commonly found on the cell walls of fungi. Non- mammals protect their gut walls with a layer of chitin and that layer will prevent bacterial infections. Whereas a mammal’s gut is […]

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Is there only one way to fix atmospheric nitrogen?

Contributed by Shawn Higdon Biological Nitrogen fixation energy-intensive process carried out by Bacteria and Archaebacteria that have been classified across many phyla. While there is an overwhelming amount of research that describes and characterizes the process of biological nitrogen fixation by microbes that have been proven to convert atmospheric dinitrogen into the organic form of […]

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Day Zero for Bacterial Comparative Genomics

Contributed by Darwin Bandoy DVM Learning microbiology is hard, learning genomics is hard and the learning curve is not simply exponential but factorial for learning bacterial genomics. I had the advantage of being a veterinarian with a training in microbiology and hence most of my struggle is with genomics. It is like learning a new […]

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NGS Library Construction for Microbiome Studies

Contributed by Carol Huang Studying the population composition of microbes within a particular environmental community has drawn more and more attention for understanding functions and interactions of microbial communities. Meta-RNA-Sequencing and Meta-Genomic-sequencing have been playing big roles in these studies. As a part of the study, I have been focusing on library construction. There have been […]

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