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Summer 2013 
MicroBEnet Blogs

A brief summary of the recent topics posted on microBE.net  


Each issue we give a brief summary of the topics discussed in our blog over the last month (3 months this time!).  Be sure to check it out here.


We started off the month with a couple of posts on Social Media for STEM (here and here).


We posted about several new Sloan Program projects, namely those by Jordan Peccia, Kyle Bibby (see also our People Behind the Science interview with him), Roberto Kolter, and Susan Lynch (followed later by an "Intro to the Lynch Lab" post).


Space was a popular theme this summer including microbes on the ISS, effects of spaceflight on Pseudomonas growth, and a satellite to monitor slime mold growth in space.  Also more Project MERCCURI sampling photos here


A few posts about funding and training including; open science training, funding from the DoD, and a reminder for the MoBE postdoc.


As always we report on conferences, past and future;

Sloan Symposium at Indoor Air 2014, talks uploaded from the 2013 Sloan Conference, and another summary of ASM2013 


Some of our posts were to point out various online an informational resources; the FHiTING software tool for fungal ID, summary of our Undergraduate Genome Sequencing Project, and a post about Pathomap.


We had a number of guest posts over the summer; a three part series by Russell Neches on our troubles with culture plates for the space station (part 1, part 2, part 3).  Part two of a pair of posts by Keith Seifert on following in the footsteps of van Leeuwenhoek (part 1, part 2).  Rachel Adams posted about biomass bias in NGS surveys (and we posted about the paper itself here)


And then there's the usual list of posts that don't fit together; yet another article about Jessica Green, NYT article about Norm Pace's work on water systems, a paper on asthma and fungal spores, a couple papers on uncultured genomes from sink biofilms (here and here), germs on planes, MRSA in a sport facility, bacteria growing on nuclear waste, EPA report on natural and built environments, winery microbiota, yoga mat microbiota, hospital microbiome project, economics of copper for infection control, masking Salmonella infections on foods with chemical treatments, legionella outbreaks, life in the "plastisphere", a post on microbial mold art, and the microbiome on NPR.

People Behind the Science
People Behind the Science
Excerpts from an interview with Kyle Bibby, from the University of Pittsburgh.





Question: You are a new Sloan grantee. Tell us a bit about your project.


Response: Myself and my co-grantee, Dr. Janet Stout, are investigating the change in microbial ecology within a hospital hot water plumbing system, before and after the hospital introduced an on-site disinfection system. They introduced a monochloramine disinfection system which we know isn't going to kill everything, it's just going to change the ecology and we don't know how yet. We have about forty sites within the hospital that are sampled for two months before and about four months after. We have all these samples stored and we're just gearing up to sequence them.


Question: So you are looking at disinfection practices in hospitals. Do you have any preliminary data, and how far along are you in the project?


Response: This project is actually being rolled into another concurrent project, which was focused specifically on the Legionella disinfection. So from that project, there is some data that shows that it looks like the disinfection was successful at knocking down total bacterial counts and a little bit of other data. But as far as the ecology portion, which is this study, we just got started.


Question: We have been hearing from a lot of different people that we really don't know what the ecology of these species are. We know we can find species, but we have no idea how that relates to human health or cleanliness.


Response: We are really just on the tip of the iceberg. I am really interested in investigating the ecology of premise plumbing systems; plumbing systems that are within our homes and buildings, as opposed to the water distribution systems that bring water to us. It is really important and really interesting from a health perspective and an ecology perspective.


Question: Are you collaborating with any other hospital projects like the Hospital Microbiome Project?


Response: Yes. I am a member of the Hospital Microbiome Consortium. I just started a faculty position so was a little bit late, but I am really looking forward to the results and hopeful that I will be a part of that conversation.


Question: What is one major challenge or big research question in the research area related to the built environment?


Response: When we are sampling in the built environment, there are so many variables that are changing in every single environment we sample. So, if we're sampling a floor, there are all sorts of different dust on the floor and different flooring. Some people have pets, some people don't. Some people keep the house warmer. If we're talking about premise plumbing systems, there are different materials, different temperatures, and different water quality coming in to these. How do we generalize these conclusions we have from these specific cases to more broadly be able to apply them with all of these confounding variables and how do we tease out the fundamentals, as opposed to just observational changes in these specific instances?



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What's living on your yoga mat?

by   Holly Bik  


As a yoga devotee and general fitness fanatic, I often use communal exercise

equipment when I'm traveling or unexpectedly drop into a class after work. I've been wondering lately about scientific studies specifically looking at surfaces such as yoga mats, but after a quick literature search it seems that knowledge is thin in this area. If you know of any papers, please do let me know, but in the meantime I found two interesting articles:

In this Philadelphia Magazine article, "Penn dermatology professor Elizabeth Grice, whose research focuses on skin-bacteria microbes, says that while there are no specific studies involving yoga mats, it's likely that bacteria from your skin could get on your mat, colonize (ew), and cause infection. Since bacteria thrive in warm, dark, moist environments, rolling up your yoga mat while it's still wet, from sweat or cleaning, is the worst thing you can do." Grice advises us to never share our yoga mat, and says you should always try to bring your own equipment to


And according to another article in Yoga Journal, "Unlike restaurants (overseen by health departments) and gyms (following guidelines set by the International Health, Racquet and Sportsclub Association), yoga studios aren't subject to strict sanitary standards." The article goes on to describe some good tips and best practices for reducing your risk of infections when going to yoga class, since not all studios have high cleanliness standards.


And then there's the new trend of "Naked Yoga"  

- which just seems like a bad idea in general, given the fabric barrier and microbe protection that clothes usually offer...

NPR Discussion of 'Full Upright And Locked Position' includes discussion of germy parts of planes

by Jonathan Eisen

On Fresh Air w/ Terry Gross yesterday (June 10, 2013) there was a discussion of a book about air travel: Flying High And Low In ˜Full Upright And Locked Position‚€™ | KQED Public Media for Northern CA.  And one of the topics that came up was the germ/microbe content of different parts of a plane.

  Not sure what the evidence behind this is/was but the author of the book implied the part of the plane with the most microbes was the seat back pocket.  Of course, the number of microbes in any place does not tell us that much about whether the microbes are bad for us.  But it might tell us something about how much those areas are cleaned.  Too bad they did not discuss general issues with how little we know about microbial diversity on planes.  Maybe next time ..


Health economics assessment of antimicrobial copper for infection control  

by David Coil

I've posted a couple of times in the past about the potential for using copper in the built environment to limit bacterial growth and/or pathogenicity (e.g. here and here).  I've heard and read things about copper which cover the whole spectrum from "it's a magic bullet" to "snake oil".   I'm guessing it's somewher e in between, though I have seen some convincing lab data about the effect of copper on microbes.   The bigger question comes when that copper is in a real building, exposed to air, chemicals, repeated touch etc.


Enter this very interesting  study from the UK looking at the "Health economics assessment of antimicrobial copper for infection control" in ICUs.  Since I can't find the actual paper, I can't dig into whatever assumptions they used about the efficacy of copper.  But I like the fact that they're looking at the economics of the whole thing which is what a lot of infection control really boils down to in the end.

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