Methodological approaches for studying the microbial ecology of drinking water distribution systems

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 of interest including both culture based and culture independent and a diversity of methods within these categories. It has a focus on methods as they would be applied to studies of microbes in drinking water distribution systems but much of the information would be of … Continue reading

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Who are the contaminants in your sequencing project?

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.  But if that does not happen, it is possible to try to detect contamination after it has happened.  Below I post some papers related to post-sequencing detection of contamination: Common Contaminants in Next-Generation Sequencing That Hinder Discovery of Low-Abundance Microbes. Abundant Human DNA Contamination Identified … Continue reading

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New Joint Initiative from the Knight and Sogin Labs as a Follow-up to the MoBEDAC Initiative

If you’ve been reading our posts, you are quite familiar with our efforts at characterizing the bacterial and fungal communities of the built environment. We’ve described our study design, experimental protocols, and results. One thing we may have left you wondering about, however, is the nuts and bolts behind the analyses we and other MoBe researchers are doing. The analysis of built environment microbial communities is not as straightforward as it may seem at first glance.  The way nearly every step of a project is carried out-from sample collection to the specific tools utilized in analysis-can affect the final results, … Continue reading

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Help wanted: Repeat annotation in microbial genomes

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 possible mobile genetic elements in the genome. There are many reasons we want to do this but what we are struggling with right now is good informatics tools for doing it. So if anyone has any suggestions for good computational methods for doing this it … Continue reading

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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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