Viruses – and why you should love them – really love them – really

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 I do have a few issues here and there. Overall, the report provides a wealth of useful information about new findings relating to how viruses can be viewed as beneficial to a variety of organisms and ecosystems. There is information here on viral evolution, on … Continue reading

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Must read paper of the week: Tools to improve built environment data collection for indoor microbial ecology investigations

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 and it is in the journal Building and Environment under a Creative Commons license. Abstract: Recent studies have greatly increased our knowledge of microbial ecology of the indoor environments in which we live and work. However, the number of studies collecting robust, long-term data using … Continue reading

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Nice Primer on “Conducting a Microbiome Study”

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 and has some nice figures that could be useful for teaching or talks.

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American Society for Microbiology Letter on CDC/NIH lapses in biosafety

Just got this email letter from the American Society for Microbiology and I thought it would be useful and important to share.  Please – everyone out there doing work involving potential harmful microbes – redouble your efforts to do that work as safely as possible.  And also consider careful the risk – benefit balance for the work. Dear Colleague: The recent events at the Centers for Disease Control and Prevention (CDC) and the National Institutes of Health (NIH), which are documented in the report below, reveal significant lapses in biosafety, biosecurity, oversight and compliance with the Select Agents and Toxins regulations.  … Continue reading

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A really important technique for metagenomic studies: stable isotope probing

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 stable-isotope-labeled (13C) carbohydrates (glucose, cellobiose, xylose, arabinose, and cellulose). Indicator species analysis revealed high specificity and fidelity for many uncultured and unclassified bacterial taxa in the heavy DNA for all soils and substrates. And then they sequence metagenomes from the samples and use the labelled … Continue reading

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PhD Opportunity “Fungal Growth on porous materials: the roles of the water supply” (Netherlands)

Quick posting here for a PhD-track job opening in Eindhoven, Netherlands; “Fungal Growth on porous materials: the roles of the water supply”.  The job description is below and contact information can be found on the website. Job description Introduction Fungi form a unique group of organisms. As holds for every organism, water is a key factor for growth.  In the real world this water is not always abundantly present and its availability fluctuates in time. As many natural substrates are porous in nature, they can act as a buffer when a period of drought sets in, but can also cause … Continue reading

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Human Microbiome Coursera this Fall with Rob Knight and others

I have to admit I don’t know much about MOOCs (Massive Open Online Courses) or about Coursera, but the idea does sound pretty intriguing. A new one is starting this fall called “Gut Check: Exploring your Microbiome” that sounds particularly awesome.  It’s hosted by Rob Knight and others in his lab, with “visiting” lectures from experts around the world.   Seems like a really good way to dive into a deeper understanding of the human microbiome.

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A very important paper for any interested in microbial ecology: importance of rare taxa

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, thankfully, fully Open Access) the authors use new informatics methods to look at what they call (conditionally rare taxa [CRT]).  They report: We discovered that CRT made up 1.5 to 28% of the community membership, represented a broad diversity of bacterial and archaeal lineages, and explained large … Continue reading

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Nice resource: BRIK – Building Research Information Knowledgebase

Recently I participated in the Society for Building Science Educators (SBSE) annual retreat (more about this soon).  And at the retreat I saw a fascinating presentation rom Richard L. Hayes who runs helps facilitate something called the Building Research Information Knowledgebase (aka BRIK). BRIK is a “collaborative effort of the American Institute of Architects and the National Institute of Building Sciences, the Building Research Information Knowledgebase (BRIK) is an interactive portal offering online access to peer-reviewed research projects and case studies in all facets of building, from predesign, design, and construction through occupancy and reuse.” Browsing around BRIK shows a variety of resources … Continue reading

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The American Institute of Architects are looking for “Educational Proposals” for their 2015 Convention #microBEnet

The American Institute of Architects are looking for “Educational Proposals” for their 2015 Convention: See Abstract Scorecard.  I just put in a simple proposal to have a 60 minute panel discussion on “Architecture and Microbiology”.  But maybe someone else out there would want to put together a more comprehensive proposal on Microbiomes and Architecture and Design and, well, lots of other things?  Just a little push to people out there to think about this

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