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. …
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 …
Another really interesting microbial diversity paper in mBio. This one is from Josh Neufeld and colleagues: Multisubstrate Isotope Labeling and Metagenomic Analysis of Active Soil Bacterial Communities. The key thing they did is summarized in their abstract: We incubated samples from three disparate Canadian soils (tundra, temperate rainforest, and agricultural) with five native carbon (12C) or …
Got pointed to this paper by automated Google Scholar searches that I have for many of the authors of the paper: Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity in mBio by Ashley Shade, Stuart E. Jones, J. Gregory Caporaso, Jo Handelsman, Rob Knight, Noah Fierer, and Jack A. Gilbert. In the paper (which is, …
Definitely worth checking out this paper from Kyle Bibby’s lab: PLOS ONE: Shift in the Microbial Ecology of a Hospital Hot Water System following the Introduction of an On-Site Monochloramine Disinfection System. A key figure in the paper is Figure 2 which I post here. The figure shows a PCA based clustering of samples based on …
Paper of potential interest to the microBEnet crowd: Phylogenetics and the human microbiome. It is a preprint in ArXiv by Erick Matsen. It focuses on the human microbiome but discusses the history of methods for phylogenetic analysis of microbial communities and it is quite good. Thanks to Erick for posting this to arXiv so that people …
There is an article by Carrie Arnold in the new issue of EHP (Environmental Health Perspectives) should be of interest to some people out there: EHP — Rethinking Sterile: The Hospital Microbiome. In the article, Carrie Arnold discusses Jack Gilbert’s hospital microbiome project, hospital acquired infections, DNA based surveys of microbes, and work from the …