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Welcome to microBEnet News
Resource of the Month 

Focusing on resources found on microBE.net


In this issue of microBEnet News, we are featuring two collections of microbiology resources:

The first is a collection of links that point to web sites containing information on microbiology. These websites encompass a large range of subjects including organizations, journals, news, social networking sites, conferences, and culture collections.


The second resource is the collection of RSS feeds from over 100 microbiology related blogs. These blogs focus on microbiology or have a reasonable number of posts about microbiology.  The web page may take a few moments to load, but the information is well worth the wait.


In a future edition of microBEnet News, we will feature these same collections for building science resources.  We are currently seeking information regarding web sites and blogs specifically related to building science and welcome suggestions you may have for this collection.

MicroBEnet Blogs

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


Posts highlighting new Sloan funded projects:

*        Amy Pruden

*        Greg Caporaso

*        Jack Gilbert

*        Jill Banfield

*        James Scott


Posts related to meetings:

*        Lake Arrowhead Microbial Genomics Meeting

*        QIIME/VAMPS Workshop

*        2012 ASM Beneficial Microbes Conference


There have also been other topics covered including ozone, hospitals, aquariums, leaf mold, and influenza.    


People Behind the Science
People Behind the Science


Excerpts from an interview with Jack Gilbert, Argonne National Laboratory, Chicago.




Complete video interview can be seen here.  


Question: How did you become interested in the microbiology of the built environment?


Jack: I am traditionally a marine microbiologist, so I am interested in bacteria that live in environments and how those bacteria respond to temporal changes or time changes with nutrients and pulses of the animals and the plants. It was very interesting to me to take the bacterial processes, and understanding the succession that we have been exploring in marine systems for so long, and how we could look at what happened in a building. Traditionally it has always been very hard to justify to the public why I am interested in bacteria in the sea. It's become very easy to justify our research, especially to my mum, on the kinds of processes that happen in built environments. Why did I want to study the sea when I could study bacteria that were directly interacting with us? That was actually our first foray, so we moved into the home micro biome project at homemicrobiome.com, which was a first investigation of how humans interacted with bacteria in a built environment inside a house, where you spend a large amount of your time. Most of it is sleep, but still.


Question: You just got a new Sloan project funded, can you tell us a little bit about that?


Jack: About a year ago it became evident that there was a new hospital being built at the University of Chicago and this new hospital was going to be an 850 million dollar institute completely isolated from the rest of the hospital and absolutely the most cutting edge architectural development designed to minimize infection processes in hospitals. Hospital acquired infections kill an awfully large number of people in the U.S. each year with these so-called multi-drug resistant bacteria. So there was a lot of interest in what was this new building going to do to actually prevent that and could we track that using molecular techniques to understand how those bacteria, or bacterial pools, these reservoirs of bad bacteria, how they developed in that system and recognize bad bacteria entering a hospital. So we had a workshop where we had everyone from microbial ecologists to statisticians to surgeons to medics to the infection control groups and lawyers, to architects, and building scientists, and we said to them, we have this unique opportunity. The hospital becomes active at the beginning of February 2013, and the first patient moves in on February 2, 2013. So we said, wouldn't it be fantastic if we could look at what happens to the microbial community in this building as this large infrastructure was populated by a lot of sick people and a lot of medical workers. So we proposed this hypothesis and worked with the community, massive multidisciplinary activity, to discuss what is the most appropriate strategy to capture the dynamics of the microbial community and also the facets of the succession? When I say that I mean; how does the microbial community develop in a building. What do you leave behind when go to the hospital and what do you pick up?   Is there a pattern to that in terms of the disease? That was very important to us and it captured the imagination of a lot of people in the medical sphere who had not really considered the use of these technologies, and also captured our imagination as microbial ecologists. This was a unique environment, something we could have never studied in a natural environment. It's a unique opportunity to study a really dramatic shift in the use of a system.


Question: There are pictures of you sampling floors. Have you analyzed any of the results?


Jack:  We took a bunch of researchers and program officers around the hospital infrastructure that currently exists, and as we went around we took our q-tips and we swabbed different surfaces. We even swabbed the shoes of the people walking around, before they entered the hospital, and after they entered the hospital. We were really interested to determine, in this study, what was the base like? This isn't an investigation of a publish, but it is something which gives us some kind of perception of the variability between a toilet and a shower head, between the water system at the top of the building, between the ice spigots in the ice making machine, and the operating room floor to the bed area where the patients were to be living.   So we did some investigation of this and we have some analysis coming out on the hospitalmicrobiome.com website very soon.


Question: What's your favorite aspect of studying the built environment or approach to studying the built environment?


Jack: It's a unique system that enables us to investigate how humans interact with that system. We are constantly exposed to it so I find it very interesting that I can take the micro biome of your nose, your hand and your feet and I can see specifically how you influence the bacteria that survive on the surfaces of a building.


I have a real desire to generate predictive models as I think this is fundamental to science. I generate predictive models all the time in my day-to-day life like: Do I have enough petrol to get to work? I'm very interested in how we can use this information to enable medics, architects and building scientists to better plan architectural development of buildings. Being within a group such as the Microbiology of the Built Environment Network has been fundamental to our capacity to actually perform these operations. It enables us to actually reach out to groups such as the Biology and the Built Environment Center in Oregon. They are very interested in these topics. We hope our research initiatives, designed to understand microbial successions in ecology, will enable them to develop better and more appropriately designed buildings.


Question: What is one big scientific question for the microBEnet community?


Jack:  I am currently very interested in the development of appropriate tools to analyze quantification of microbial populations in certain areas. Let's say maybe a big question for the whole of microbial ecology? For the last seven to eight years we have been playing around with our new toys, our new sequencing machines, our new kits that enable us to really get in depth at what the ecology of the microbial community means. Now we have to really take a step back and say: we have found out an awful lot, but what's the next step? Can we quantify those processes? Everything we have learned we have put it in some kind of quantifiable measure that enables us to say, this number of bacterial cells occurs at time point one, this number at time point two, and this number at time point three. Those changes will influence how we perceive the successional development and the ecology of that system. So I would say understanding quantifiably the microbial processes in the built environment is fundamental to generating predictive analysis and fundamental to driving forward a better design of those buildings to reduce and minimize the impact to humans.


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Featured Articles

Going for a walk or drive in the country and viewing the fall colors when the leaves turn in the Boston area is a favorite pastime of residents of and visitors to the area. Leaf mold associated with autumn leaves in Massachusetts may have gotten into the indoor environment of the New England Compounding Center of Framingham, Mass., the source of a steroid used to treat back pain.

The F.D.A. warned that some vials of steroids used to treat back pain had become contaminated with leaf mold. These injections have been associated with meningitis. according to the Associated Press report published October 3rd.


According to the AP story, it "...became apparent Thursday that hundreds, and perhaps thousands, of people who got the shots between July and September could be at risk. Officials disclosed that a steroid suspected in the fungal meningitis outbreak in the South had made its way to 75 clinics in 23 states."

So the connection between the indoor environment where drugs are prepared and the microbes commonly found outdoors can be important and more attention is likely to be paid to it in the future.


(they go far)

Heard about an interesting paper today (sadly not open access) describing airflow simulations in an aerosol chamber.  Basically they showed that if you release bugs from a mannequin, they spread all over the room... up to 3.5 meters away.   A worthwhile study, but not something that wasn't known already.    What made this get so much press is that the authors used Staphyloccus aureus, the same bug that when resistant to certain antibiotics we know as MRSA.


Enter the headlines  Fears of risk of air transmission of superbug and  Airborne superbugs elude hospital cleaning regimes.   A bit over the top in my opinion.


by Hal Levin


The Virginia Tech group has published another paper looking at the impacts of indoor environmental conditions on microbes. In this case, it's potentially a key clue to the on-going search for an explanation to the seasonality of influenza puzzle. It's not just airborne humidity but also the droplet. composition that matter. Past efforts to find an explanation in relative or absolute humidity, temperature, or season have never resolved the questions. This paper sheds a lot of light on some of the key factors, and they turn out to be the interactions between the indoor environmental conditions, especially relative humidity, and the droplet's composition. Mucus, salinity, and proteins were all found to make a difference in this study intended to discover the effect of respiratory fluids in combination with various relative humidity levels. You can see the paper  here on PLoS One.

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