The Department of Statistics at Oregon State University is hosting a summer REU (Research Experiences for Undergraduates) program that focuses on microbiome data analysis. This is a unique, paid research and training opportunity for STEM undergraduate students who want an interdisciplinary research experience in both biology and statistics. During a ten week training period, students will be …
I was at a meeting a few weeks ago where the topic of fungal diversity surveys was discussed and many people there commented on how ITS based surveys (one of the main approaches for culture independent studies of fungi) had some limitations. ITS stands for the “internal transcribed sequence” and it is a region in …
A few weeks ago we wrapped up Spring Quarter here at UC Davis and the end of our experimental “Swabs to Genomes” class, taught as a freshman seminar. As we introduced here, the idea was to take a set of students from colonies on a plate (from a swab) through a collection of ready to …
Ok I saw this Tweet and I thought it sounded cool: Autonomous Sewer Robots Live-Stream Neighborhood Microbiome Data – Nickolaus Hines https://t.co/fr8Xfs8XxQ pic.twitter.com/e5mDTGU44Y – Elisabeth Bik (@MicrobiomDigest) May 5, 2016 And definitely worth looking into in more detail. And, well, after looking I still think it is cool but not quite what the headline suggests. …
On April 11 there was a meeting in Washington DC that was part of an effort from a new study being conducted by the National Academies of Science, Medicine, and Engineering on “Microbiomes of the Built Environment”. Videos and slides from the meeting have now been posted. I have compiled them below. In addition, I …
These will almost certainly be of interest to the MoBE community. There is a new paper in mSystems “Geography and Location Are the Primary Drivers of Office Microbiome Composition” by John Chase, Jennifer Fouquier, Mahnaz Zare, Derek L. Sonderegger, Rob Knight, Scott T. Kelley, Jeffrey Siegel, J. Gregory Caporaso. I found out about the paper via …
Sloan has just renewed our funding to build on our foundational research at Virginia Tech that has established general factors broadly shaping the composition of the premise plumbing microbiome! In this next phase we will focus on shifts in water chemistry and temperature, using brain-eating amoebae as a key exemplar (need to protect those brains!). …
I was casually browsing Twitter yesterday when something caught my eye DNA from dead #bacteria (and extruded DNA) may inflate species counts (depending on protocol). Early DNAse step? https://t.co/YQvUJq10Df – Michael J Wise (@some_wise) March 22, 2016 This Tweet embedded one from Carl Zimmer. Here is the original: The Earth is filled with relic DNA. https://t.co/eJ0lmggmAw …
So I had two thoughts when I read the article title “Indexed PCR Primers Induce Template-Specific Bias in Large-Scale DNA Sequencing Studies“… #1: Ack! Yet another thing to worry about in the insanely complicated craziness that is 16S amplicon sequencing. #2: I probably shouldn’t be the person to blog about this because I’ve honestly never …
In this new paper in MycoKeys we present a set of automatically updated lists of the most abundant fungal species hypotheses known from sequence data, but for which little to no taxonomic information is available. If anyone can shed light on the taxonomic affiliation of these species hypotheses, we’d be all ears. Through a “built environment” switch, …