Some interesting things in this post from Kelly Rae Chi at the Scientist: Metagenomics Mash-Up. It includes a discussion of metagenomics generally and then some metagenomic tools including MEGAN5, Kraken, MG-RAST, Metavir, and HI-C. The section on HI-C discusses the work of Chris Beitel in my lab. If you are doing metagenomic analysis or considering it or …
Quick post here. The Robert Wood Johnson Foundation has a podcast on “Pioneering Ideas” and it covers microbiomes of the built environment this week:1 RWJF Pioneering Ideas Podcast: Episode 5 | Conspiracy Theories, Microbiomes & More – Robert Wood Johnson Foundation. They also give a nice plug for microBEnet. From their site: Microbiomes and Design (26:25) — …
Earlier this week I saw a fascinating talk by Rachel Dutton on the microbial communities in cheese rinds. Rachel is currently a Bauer Fellow at Harvard University and for the last few years she has been studying microbial communities in cheese rinds. She was at UC Davis on Monday to give a talk and it …
Many recent news stories have been discussing a case of an outbreak in a hospital in Greenville, SC that has apprently been traced to drinking water contamination. Thus this may be of interest to a variety of people. See some links below: 4th patient with GHS infection dies. Fourth bacterial infection death reported at South …
There is a paper that just was published that possibly will be of interest to those interested in studying microbial ecology of drinking water (or other water systems for that matter): Methodological approaches for studying the microbial ecology of drinking water distribution systems. Unfortunately the paper is not freely or openly available. The paper covers many topics …
Well, been having many discussions recently about PCR amplification happening from “negative” controls where no sample DNA was added. Such amplification is alas pretty common – due to contamination occurring in some other material added to the PCR reaction. Obviously it would be best to eliminate all DNA contamination of all reagents and all PCRs. …
Posted a request for help on Twitter but I thought it might be of interest to some other people so am also posting about it here. Basically what we (me and Lizzy Wilbanks in my lab) is to take some microbial genomes and to fully annotate all of the repeat elements and all of the …
There is a new report from the American Academy of Microbiology out that may be of interest: Viruses Throughout Life & Time: Friends, Foes, Change Agents. In a way this could be seen as a formal declaration of viral love by a collection of eminent scientists. Mostly I agree with what is in the report, through …
Got alerted to a very interesting paper because I have subscribed to Google Scholar automated updates for Brent Stephens (see a full list of Google Scholar pages for researchers working on microbiology of the built environment here). The paper is: Tools to improve built environment data collection for indoor microbial ecology investigations by Tiffanie Ramos and Brent Stephens …
For those interested in conducting “microbiome” type studies where DNA sequencing is used to characterize and compare microbial communities this could be uf use: Conducting a Microbiome Study by Julia K. Goodrich, Sara C. Di Rienzi, Angela C. Poole, Omry Koren, William A. Walters, J. Gregory Caporaso, Rob Knight, and Ruth E. Ley. It is a good overview …