The lab welcomes Mallika Iyer, a student in the Masters of Integrated Sciences Program. Mallika is studying the genomic and proteomic factors affecting the optimum growth temperature (OGT) of microorganisms. Her long term goal is to develop a predictor of OGT.
I had a productive whirlwind visit to THE Ohio State University last week, visiting the Wrighton Lab to discuss our collaborative project studying the microbial communities inhabiting freshwater wetlands, the Center for Applied Plant Sciences to give a talk to an inquisitive, sharp audience, and the OSU experimental wetlands, which – aside from hosting a lot of interesting research – are constructed in the shape of a pair of kidneys, adjacent to a cemetery.
The lab welcomes David Banks-Richardson, who is pursuing a MS in Integrative Biology. David comes to us with a background in environmental sciences and interesting work experience in water quality.
Congratulations to Adrienne, whose abstract has been selected for a student travel award to the 2015 General Meeting of the American Society for Microbiology in New Orleans. Adrienne will present a poster on our freshwater wetlands work with the Wrighton lab (OSU). Her abstract is titled, “Community level and genome level insights into methane cycling archaea in temperate freshwater wetlands.”
We have a new publication out in Microbiome describing the effects of low-level environmental triclosan exposure on the fathead minnow gut microbiome. Fathead minnows don’t appear to have particularly fat heads, but they are common model organisms in environmental toxicology, and our collaborator Alan Vajda and his lab know them well. Triclosan is the “antimicrobial” component in antimicrobial hand soaps and other consumer products, and an emerging environmental contaminant. This study integrates sequencing-based microbial ecology of host gut communities with the field of environmental toxicology, and asks the simple question of whether environmentally relevant levels of triclosan exposure might alter the gut community of fishes. Congratulations to Adrienne Narrowe (first author) and everyone else at CU Denver (3 labs, 2 PhD students, 1 staff, and 1 undergraduate student) who worked hard on this experiment.
We have received a MinION device as part of an early access program from Oxford Nanopore. This thing can sequence a single molecule of DNA by passing it through a nanopore and sensing changes in current, and the summary thus far is long reads, high error rate. It’s smaller than a stapler.
We’re exploring ways to use this data to aid metagenomic assembly.
Congratulations to Elmar, who will present a Keynote Talk at the 2014 Rocky Mountain Bioinformatics Conference. Elmar will present his PhD work developing the SILVA rRNA database and related tools. His talk is titled, “Tackling the rRNA big-data problem with ARB and SILVA.” Adrienne is also presenting her work at Rocky this year.