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 …
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 …
The Marine Biological Laboratory in Woods Hole. MA will be offering their “STAMPS”: (Strategies & Techniques for Analyzing Microbial Population Structures) Course this August (8/3-8/13). Course Dates: August 3 — August 13, 2016 Deadline: April 8, 2016 | Apply here Course Website Course Schedule Directors: Mitchell L. Sogin, MBL and David B. Mark Welch, MBL …
This paper by John Chase and crew posted recently on PeerJ takes a deep look at the office microbiome composition and concludes that the biggest factors affecting differences in swabbed samples are the geography of the office and where the sample was taken inside it. Their experiment showed minimal impact from other factors that are …
I made a Storify summary of the Tweets from a workshop at the Pacific Symposium on Biocomputing that I attended on Tuesday on Computational Microbiology (with a big focus on microbiomes). [
Pat Schloss (pdschloss at gmail.com) offers excellent workshops on the Mothur software for analyzing 16S rRNA data for bacteria. He’s just announced the next one (February 8 to 10, 2016 near the Detroit airport). I had the pleasure of attending the December workshop. A diverse and international group attended the workshop, with many folks who are interested in the human microbiome. …