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Welcome to microBEnet News
May 2013 
MicroBEnet Blogs

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


A few guest posts this month which is great!  We started off with Walking in the footsteps of van Leeuwenhoek by Keith Seifert.   Other guest posts included a software carpentry workshop summary by Jenna Lang and a post on Size Matters by Rachel Adams.


A couple posts on reference genome papers coming out of the microBEnet project (here and here)


Meeting reports from ASM (here and here, here, and here ) as well as the Sloan MBE conference.


Article on microbes on pacifiers, the hygiene hypothesis, social media, antibiotic resistance, a post-doc funding opportunity in the field, an NTP factsheet on mold, hospital microbiome project, NYT article describing the field, subway microbes, Project MERCCURI and the shoe fairy, microeukaryotes in tap water, and an interview with Scott Kelley.

People Behind the Science
People Behind the Science
Interview with Scott Kelley from San Diego State University.




Interview with Scott Kelley from San Diego State University.


Question:  Tell us about the research you do in the Built Environment.


Scott:  I have been doing research in the built environment for a long time.  I started out with shower curtains, hospital drapery pulls, and airplanes and I was doing microbial diversity in these environments.    Lately I have moved in to biodiversity in these environments.  There is very little known about environmental biodiversity in any environment much less in the indoor setting where it is almost completely unknown.  People have cultured a lot of things and you can get influenza, rhinovirus and norovirus.  But there is clearly loads more viruses in these environments and we really don't have any idea about how they spread, how they build, where they come from, what's the association with the bacteria that are there, what is the association with fungi, what's the association with gender or airflow.  So, that is what I am working on. 


Question:  So you are doing some pretty cool stuff and just presented a talk where you were taking bleach and you were trying to wipe the viruses away.  They are pretty persistent, right?  And they wouldn't go away?


Scott:  That's right.  It is part of a larger study.  We are looking at microbial diversity succession and changes over time.  We chose the restroom as our model because it already had a brilliant study done at the University of Colorado.  We could follow up that study because we knew that they had very distinct communities in different parts of a restroom setting.  For example the floor in front of the toilet seat was really different from the soap dispenser and it was very consistent.  So we could go in repeating that model with the same kind of bacterial primers, 16s.  We saw the exact same patterns.  So now we are looking at how fast does that kind of thing develop? 


So what we did was sterilize it in the morning and see what happened 8 hours later.  We did that repeatedly over time but each time was like a new starting point.  It turned out to be quite interesting.  First of all, it took a lot longer to kill everything off than we thought.  So we didn't do culturing, but what we did was look under the microscope to see if we saw any trace of any cells, either bacterial or viral.  We found that if we placed 10% bleach on an area, at time 0 there was lots of stuff.  After two minutes there was still lots of stuff. Ten minutes later there were still a few things.  Twenty minutes later it was all gone.  It took twenty minutes to eradicate everything.  Then we sampled eight hours later. 


Question:  Another thing you are dealing with is that bacteria are tiny enough, but viruses are even smaller.  So, we are talking about really small amounts of DNA so that is a huge issue you have been dealing with, right?


Scott:  Exactly.  When you do the bacteria you have a massive advantage for diversity studies because you can target a single gene that they have, then you can use PCR to get enough of it to do something with.  So that's one advantage that we already have to look at the diversity.  Viruses don't have that so you rally have to do what is called metagenomics.   You really have to purify them because you want to separate out the massive amounts of bacterial DNA, which is like a 100:1 ratio genome size.  There are all sorts of problems.  There are also viral cells in the bacteria that you won't want to confuse with the free-living viruses.  So, purification of course looses that.


We found out, first of all, that the ration of viruses to bacteria was .7:1 where it is normally 10:1 so you are starting with really low bio mass and you purify it and it loses things.  We checked it and double checked it and got rid of all the free DNA.  Then we had to amplify it randomly to get enough to sequence. 


Question:  What is one overarching big question in the study of the built environment that really excites you right now?


Scott:  We are looking at how quickly and rapidly and repeatedly things progress.  How long does it take, who is really doing it because I am starting to suspect that humans are doing 90% of what is going on there.  It is really them and their behavior that is generating all of this.  I am getting the sense that a lot of these dry surfaces that we are talking about, that things aren't really happening there they are just waiting for their opportunity.  So, I would like to know how long they can wait around, who can survive these environments long enough to find their opportunity to grow again and become a problem. 


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Featured Article

by   Hal Levin


In their just published paper in Environmental Science & Technology, "Tetracycline Resistance and Class 1 Integron Genes Associated with Indoor and Outdoor Aerosols," Alison L. Ling, Norman R. Pace, Mark T. Hernandez, and Timothy M. LaPara have found that genes escape the indoor environment and can be found 2 km away. The abstract can be read and the article can be accessed here. (ES&T is not open access, but it is the most widely-read and respected journal in the environmental engineering community.


"...[Q]uantitative polymerase chain reaction (qPCR) was used to determine the abundance of tetracycline resistance and Class 1 integrase genes in aerosol samples collected from livestock farms, human-occupied indoor spaces, and outdoor air along the Rocky Mountain Front Range in Colorado, USA. [They] hypothesized that CAFOs and clinics may contribute significant concentrations of aerosolized resistance genes which can potentially spread via aerosol transfer." They found that antibiotic genes escaping from two confined animal feeding operations (CAFO), one swine and one dairy, could be found in outdoor air 2 km distant from the CAFO.


"The widespread subtherapeutic use of antibiotics in animal feed has been controversial in the United States, since it has been considered a major source of antibiotic resistance to nearby soil and water, and is often considered to be unnecessary or avoidable.4,5 In general, hospitals and confined animal feeding operations (CAFOs) are assumed to be the most significant sources of antibiotic resistance because of their extremely high utilization
of antibiotics."


While much of the Sloan Foundation's Microbiology of the Built Environment Program focuses on characterizing microbes indoors (air, surfaces, dust, and water), this paper reports research, partially funded by the Sloan Foundation, that looked at genes escaping from the indoor environment and traveling as aerosols. The study found that CAFOs are a source of the relatively high abundance of airborne bacterial genes, "...a substantial fraction of which carry antibiotic resistance genes."


The authors concluded that "...our recovery of antibiotic resistance genes from aerosols across different indoor environments has implications for public health, hospital quarantine measures, and indoor air quality."

This study of airborne bacterial transport from indoors to outdoors reminds me of studies of SARS spread in the Amoy Gardens apartment complex in Hong Kong where the index case was in a building across a very large open area from a downwind building where many cases occurred. (See Ignatius et al, 2004, "Evidence of Airborne Transmission of the Severe Acute Respiratory Syndrome Virus," NEJM:350:1731-1739.),


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