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As usual, our blog posts this summer spanned a wide range of topics relevant to the microbiology of the built environment, ranging from concrete to germophobia.





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Resource of the Month: Workshop Report    

This month we'd like to highlight the Workshop Report from "Building Science to Advance Research in the Microbiology of the Built Environment".   This report summarizes a small workshop held in May 2014 with the goal "to bring together a group of experts in building science and engineering with a smaller number of microbiologists and microbial ecologists to discuss existing gaps and future opportunities for research on the microbiology of the built environment."

The Workshop was aimed at prioritizing needs for the future in the field.   A summary of the report can be found in this microBEnet post by Brent Stephens.

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Recently, a bit of an uproar occurred when the CDC reported that workers there had been accidentally exposed to the bacterium that causes anthrax.  The lesson from this? Well, I think it is simple. Accidents happen.  And they can happen anywhere to anyone.  No matter how careful one is.


A few days ago a friend and colleague Marc Lipsitch wrote an Op-Ed in the New York Times that goes the next step from this incident: Anthrax? That's Not the Real Worry - NYTimes.com.  In the Op-Ed he points out that we / the CDC we actually lucky that this incident involved anthrax because anthrax does not get transmitted from person to person.  We should be much more concerned with potential accidental releases of infectious pathogens.  Most importantly - and I believe correctly - Lipsitch then assails some of the research that has involved creating in the lab extra-virulent pathogens such as varieties of flu. He writes:


There are dozens of safe research strategies to understand, prevent and treat pandemic flu. Only one strategy - creating virulent, contagious strains - risks inciting such a pandemic. The anthrax incident reminds us of the dangers in even the best labs. We should stop creating new potential pandemic flu strains and shift the research dollars to safer, more productive flu studies.  


I could not agree more.  Thank you Marc for writing this.  And here is hoping that researchers worldwide start to think more carefully about the real risks that their research might pose.



Termite mounds: another kind of built environment.
by Holly Ganz


Recently I was doing field work in southern Africa and marveling at the enormous termite mounds that dot the landscape. Composed of soil, saliva and poop, termite mounds are amongst the most spectacular of the structures built by animals. These fascinating structures maintain the ventilation of termite nests that are actually subterranean. This PBS blog post has a nice diagram of the structure of a termite mound.  


Termites have been tending fungal gardens for about 30 million years. In northern Namibia, all of the termite mounds tilt to the north (or towards the equator). Do the building scientists have any explanations to offer for this interesting natural history phenomenon?



Viruses - and why you should love them - really love them - really.  

by Jonathan Eisen

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 viral diversity, on viral functions and structure, and on the impact viruses have had and continue to have on various life forms.  And perhaps most importantly, the writing is geared towards a more general audience that in many big reports of this kind.  So I think most people who read it will learn something new.


Overall, I would say that viruses are generally poorly understood overall and it will be critical to include studies of viruses as part of any study of microbial diversity or microbial communities.  I note that when we started the GEBA "Genomic Encyclopedia of Bacteria and Archaea" project many of us wanted the project to be "A Genomic Encyclopedia of Microbomes - GEM" and wanted to include viruses (and microbial eukaryotes) as part of the project. Alas, we lost that argument - but I still think viral diversity is understudied and under appreciated.



Behind the scenes at the Earth Microbiome Project 

by Jack Gilbert


The Earth Microbiome Project started as a thought experiment. A 'what if' discussion to determine the potential scale of  the problem associated with characterizing the breadth and depth of our observable microbial world. A lot of ideas were discussed during that first meeting, but we were firmly in the middle of the heyday of the 'sequencing will solve it' paradigm, and as all we had were extrapolative estimates about the diversity of microbial life, we decided that further data was an imperative. So we started the EMP, by essentially crowd sourcing samples from colleagues around the world, and then processing these samples in a standard way. What started out as a data gathering exercise to see if we could perform the statistical power calculation to determine the number of samples required to capture the breadth of diversity, has turned into something bigger and potentially more important. Using the resources at the EMP, the microbial ecology community and beyond have gained through improved access to high quality sequence data to test their hypotheses, as well as access to appropriate data analysis software and infrastructure to enable interpretation of the results. The EMP is not an edifice, it is an organic collaboration between hundreds of people around the globe, and that family will continue to grow.


We have continually had to overcome hurdles and build novel solutions to cope with handling the acquisition of tens of thousands of different sample types; to process the resulting sequence data and make this public and accessible to original collaborators in an appropriate way; and to ensure that the standardized methods are up to date, and flexible enough to adapt to new information that is constantly being acquired about the data, biases in PCR primers, and technical issues with sequencing platforms. We are currently at the stage of trying to coalesce the first 20-30,000 samples into a single OTU matrix that can be used to start exploring how microbial communities assemble themselves across the globes myriad gradients of physicochemical parameters. The data are vast, and hence we are able to explore many nuanced differences within microbial ecosystems and between different biomes, but they are by no means perfect. Gaps in metadata, a lack of continuity in data fields between projects, and an imbalance between some environments compared to others, make these first analyses difficult to perform. While each project is in-of-itself an appropriate hypothesis driven study, we are still working to fill the gaps in our database that will enable the community of researchers that make up the EMP to test the broader hypotheses, which are manifold.


While we continue to explore new ways of processing and analyzing the data that has been generated, we are also continuing to acquire samples from new and exciting studies around the world. In fact, many research groups are working with us to plan studies that will specifically fill our research gaps, helping us to address primary scientific questions. We are continually keen to hear from any and all researchers, from all walks of life, and at any phase in their career, whether by email or in person, so that we can work as a community to refine and improve this project and the database of free, open-access information.

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