Many Legionnaires Disease cases are attributed to water distribution systems, especially cooling towers that form a critical part of air-conditioning systems. Tamara McNealy (Clemson U.) studied the effect of gold nano particles on Legionella p. biofilms, Since she was looking at metal interactions, I asked her about other metals, ones that might be used for cooling tower water circulation, e.g., stainless steel, copper, and galvanized. It turns out her lab has looked at these metals although that was not what she reported on at ASM in Denver. But the copper industry has been pushing its product as a “natural” biocide with useeful antimicrobial properties. If I understood McNealy correctly, their work has not supported that claim, at least not with respect to Legionella p.. Of course contact time in a piping system would be expected to be a critical factor in piping, so only a small part of the water flowing through a pipe might actually have significant contact time. But McNealy’s focus was not on piping but on biofilms, and many investigations of cooling tower water have focused on the biofilms on the surfaces of the water tanks, typically open to the air. Cleaning these tanks to remove the biofilms is an oft-recommended preventive or remedial measure. Can metal nano-particles added to cooling tower water assist in preventing Legionella p. growth in air-conditioning water systems? McNealy plans to look at other metals now that they have shown an effect of their gold nano-particles.

So I would ask questions related to the built environment application or relevance, like, ‘At what temperature did you try to grow those things?’ Or ‘what was the substrate or the duration of the experiment?’

Of course this works better at the poster sessions than in the large symposium where most of the attendees would probably be asking themselves, “who let this guy in here?” (We won’t tell them it’s all due to the Sloan Foundation’s dramatic efforts to make microbial ecology something that is useful in the sciences applied to the built environment. My own interests are primarily the indoor environment.)

So when I asked Kenneth Flynn (U of New Hampshire) about his poster, “Population genomics of experimentally evolved pseudomonas biofilms provides insight into the molecular mechanisms of ecological specificity,” what were the temperatures at which he did his experiments, I learned that there are people doing lung cultures of Pseudomonas. This will be worth following up on in terms of what they know about the temp and RH of inhaled air.

I have been very interested in linking the indoor environmental conditions (e.g., temperature, relative humidity, pH of moisture on surfaces, ventilation, surface material composition, topography, and chemistry) with the abundance, evolution, and pathogenicity or toxicity of indoor microbial communities. The human skin microbiome is most likely (my hypothesis) affected by some or many of these indoor environmental characteristics. But what about the respiratory tract? (The second of the three most environmentally-exposed surfaces, the gut being the third, of course)? The peer-reviewed literature indicates that the upper respiratory tract is a perfect air conditioner. But the experiments I have read about are fairly short in duration, a matter of minutes. What if someone works or plays or walks outdoors in hot humid or cold dry climate conditions for several hours? How long can the air we inhale be conditioned to reasonably constant temps and RHs? Well, obviously, not for many hours on end, not at least without a significant toll on the individual’s ability to sustain this. So the “climate” in the lung may not be some idealized (37 C) body core temperature all the time.

Robert Parker (Michigan State University) “Role of the rgf Operon in biofilm formation in Group B Streptococcus” — I asked about his substrates and he told me that the biofilm grew better on glass than on PVC. I found that surprising but discussed with him the fact that nearly all surfaces in human-occupied indoor environments are coated with a thin film of human skin oils (squalene compounds), and water and, a large range of volatile and semi-volatile organic chemicals. So surfaces are not always so simple to understand, and our assumptions about them may mislead us. I also mentioned that PVC contains phthalate plasticizers that are known endocrine disruptors. There will typically be a layer of such chemicals at the surface of a plastic token.

If this stuff interests you, come back soon for more of the building science jewels I mined from ASM presenters at discussions of their posters: in the lineup, Legionella, bacteria counts in “natural” air on a university campus, and the development of pseudomonas-biofilm resistant surfaces through manipulation of the surface topography.

Started off the day with the “Microbes in Action! Dynamics of Single Cells to Communities” which included some great talks by Greg Caporaso, Sarah Cobey, Mary Lidstrom, Trina McMahon, and Jeff Gore.

The afternoon was a tough call between “Microbiology’s Next Top Model: Predicting the Future with Math and Microbes” organized by Jack Gilbert and the “Role of Microbes in Environmental Sustainability” session at the same time.  After a talk by Saeed Tavozoie in the modeling session I switched over to hear more built environment talks.  Tucker Burch gave an interesting talk on the fate of antibiotic resistance genes in waste-water treated soils… basically showing that existing treatment doesn’t appear to be super-effective.  Paula Mouser talked about the role of microbes in shale energy development which is something I haven’t heard much about.  James Meadow gave his usual interesting talking on the microbiology of the built environment (James is at the BioBE Center) and showed some new data from experiments where they put people into sterile boxes and measure their “microbial cloud”.  This was followed by talks on metagenomics of oiled beaches, the NEON project, and the Mississippi River.

Day 3:

Started off the day with a session of relevance to the built environment, but something that I think isn’t talked about enough, this was the session on food microbiology called “The Good, the Bad, and the Ugly:  Food Microbiology in the Omics Age”.   Say a nice series of talks by Thaddeus Stanton, Lee-ann Jaykus, Bart Weimer, Martin Weidmann, and James Steele.   I would say the major take home messages were the following:

Huge volumes of livestock antibiotics are probably a bad idea

Norovirus is an awesome pathogen (conceptually, not if you actually have it, in which case it’s no fun at all)

Omics approaches can really help regulators and scientists better control food safety issues.

I went from there straight to the Late Breaking Session on “Pandemic Threats from Emerging Avian Influenza Viruses (H7N9 and H5N1): Challenges for Public Health, Research, Surveillance and Countermeasures”.  I would classify this just like the Soviet Bioweapons session from the first day… both fascinating and scary.  The speakers all seemed to be big names in the field (Robert Webster, Albert Osterhaus, Carol Heilman, Stephen Redd).  I felt like I was in a Richard Preston novel when Stephen Redd (CDC/ICU) stood up there in full military uniform describing the current outbreak of H7N9 that’s going on in Eastern China.

Had to watch a citizen science collaborator of ours drawing his poster by hand at the poster session.  Here’s a little video that Jonathan put together.

Last up was the session organized by Holly Bik in the lab called “Phylogenomics and Microbial Species Concepts”.  Sadly I could only attend the first three talks but was happy to be able to make that.  Kosta Konstantinidis presented evidence for the species concept in bacteria, Carlonia Gonzalez talked about psychrotolerant acidophiles, and Cameron Thrash talked about a SAR11 Bathytype.

Great meeting, great people.  Would do again.   Now off to the Sloan Microbiology of the Build Environment Conference!

Went to a special interest session before lunch called “Accomplishments and Legacy of the Soviet Bioweapons Program, 1928-1992″ by Raymond Zilinskas from the Center for Non-Proliferation Studies.  His talk was both fascinating and quite scary.

In the afternoon was our microBEnet-sponsored session called “Citizen Microbiology:  Enhancing Microbiology Education and Research with the Help of the Public”.   The goal of this session was to have a series of talks by the few folks who are actually doing citizen microbiology, with a particular focus on problems and issues they’ve encountered.   A good description of the rationale for this session can be found on Jonathan’s blog here.

First Graham Hatfull talked about his awesome phage discovery project which has now involved thousands of students and a number of institutions as well as characterized many many new phages and produced several publications.

Then Georgia Colares talked about the cell phone and shoe sampling citizen science project undertaken in Jack Gilbert’s lab.

Jack Gilbert and Dan Smith then gave a tag-team talk about the home microbiome project they’ve been working on.

Then Darlene Cavlier (founder of Science Cheerleader and SciStarter.com) gave an inspiring talk on those two organizations and on citizen science in general.  I got the feeling a lot of people were surprised at the scope of many of the (non-micro) citizen science projects out there.

This was followed by Jessica Richmond who talked about the uBiome project.

In a very similar vein was the next talk by Antonio Pena who talked about the American Gut Project.

Rounding out the session (in his trademark hysterical and informative style) was Rob Dunn who talked about the Wildlife of Our Homes project and the various “turns” in his life that lead him there.

All in all a great day.

From the paper:

Curtobacterium flaccumfaciens strain UCD-AKU was isolated from a residential carpet in Davis, California, as part of a project to produce reference genomes for microorganisms living in the built environment. Carpet fibers were placed in Luria broth (LB), incubated overnight at 37°C, and plated on LB agar ….

And then the genome was sequenced …

We are doing this project for many reasons not just to generate reference genomes for microbes from the built environment.  Another reason is to get students interest in microbes from the built environment and what better way than to have them isolate such microbes and work on them.  Also – we figured if we are going to write about studies of microbes in the built environment, well, it would be good to do some work on such microbes.  And for many other reasons.

Anyway – just a quick post here.  Congratulations to UC Davis undergraduate Jennifer Flanagan for this work and to the rest of the team. For more on the project see here.

On Day 1, Tracy Teal gave a great introduction to the shell. I would describe the pace as quick baby steps, which was perfect for most of the room. Even those who use the shell all day every day, like myself, were able to pick up a few new tricks. And, Tracy has such a quick wit, that if you didn’t pay constant attention, you were going to miss something really funny. Then, Azalee introduced git, which I had heard about before, but I’d always felt was something that “real” programmers used. It never occurred to me that I could use it for version control, or even that version control was something that I should be doing. And, holy cow, I should DEFINITELY have been using git or something like it for at least the last 7 years. She made many compelling arguments for using it, but the two that stuck with me were 1) avoiding the existence of files named Dissertation_final_last_MostRecentVersion_7.doc and 2) avoiding the scenario in which you’re feeling pretty good about yourself because your new script actually does what you want it to do, so you decide that you’re going to add one minor tweak to make it even more awesome, and then it stops working, and you don’t understand how you broke it, and so you try to fix it, but you end up getting so far away from a functional script that you decide to delete it and start from scratch because, well, when you started from scratch the first time, that’s when it worked.

I made python cookies for Day 2!

On Day 2, Matt introduced us to Python using the iPython Notebook. As someone with a decent amount of self-taught experience with Perl, I originally did not understand why we were playing with colored blocks. I admittedly spent too much time trying to figure out how I was going to be incorporating colored blocks into my research. But, when we switched from manipulating colored blocks to manipulating text files, it was like the clouds parted and I was already programming in Python! It took me a while to figure out how I would use the notebook for my research (well, I’m still not 100% sure, but I’ll give it a try) but there are some things that I loved about it right away. For example, help is easily accessed while you’re writing the code, so if you can’t remember the syntax, you don’t have to do yet another Google search for: perl split syntax. The other thing I really, really like is being able to test little chunks of code without saving and running the entire script.

Chloe gave a nice introduction to making pretty figures with matplotlib. She tied in the basics that we’d learned from Matt to convince us that “Yes, we can!” plot our data! I love that there’s a gallery of plots to choose from, and I hope that the reviewers don’t mind (or notice?) when my next publication includes a figure that’s been XKCDified!

Overall, it was a great boot camp! These folks have clearly invested a lot of time into thinking about how to teach scientists to be smarter computer users, and it shows in the quality of the instruction. I would love to host a boot camp at UC Davis on a regular basis, so if you are interested in attending one in the future, please send me an email, and I will notify you when the next one is coming!

Jenna Lang

jennomics@gmail.com

The Foundation seeks to further the development of talented early stage Ph.D. scientists and engineers by establishing the Microbiology of the Built Environment (MoBE) Postdoctoral Fellowship program. The program will provide support for postdoctoral researchers in laboratories engaged in research on the microbiology of the built environment in the U.S. or Canada. Eight awards of $120,000 each will be awarded over the 24 months of the program. Successful fellows will have developed an innovative project in consultation with an established advisor in the research area.

Deadline for applications: September 1, 2013

Announcement: October 2013

Research Area of Interest: Applications most likely to be of interest should describe innovative fundamental research in the microbiology of the built environment. Cross-disciplinary studies in microbial biology and engineering are encouraged.

Eligibility: Applications will be accepted from graduate students for their first postdoctoral fellowship, and the fellowship must begin within one year of completion of the Ph.D. degree. Awards are open to applicants in academic and other not-for-profit organizations, the states, districts, and territories of the United States of America and Canada. Graduate students will initiate the applications for the fellowships but these applications must include a letter of commitment from the potential postdoctoral advisor. Successful applicants must be committed to conducting research on the Microbiology of the Built Environment during their postdoctoral fellowship.

Selection Awards will be based on several factors: assessment of the proposed research, the arrangements for the interdisciplinary educational broadening of the fellow, and the previous research records of the potential fellow and advisor. Distinguished scientists and engineers who are knowledgeable in the field will review the applications. The Sloan Foundation is committed to enhancing diversity in the science and engineering communities and applications from graduate students from underrepresented groups are especially encouraged.

Budget The MoBE Postdoctoral Fellowship program provides a $120,000 award, payable in two $60,000 installments. Funds are normally expended over a period of two years after the appointment of the fellow. Charges associated with indirect costs or institutional overhead are not allowed. The stipend support for the fellow should be at least $48,000 of the total annual award amount (stipends may be supplemented from institutional or other sources). $2,000 is provided as a stipend to the fellow for travel or research expenses. Fringe benefits from this award may not exceed $10,000 per year. In the event that institutions/laboratories receiving the MoBE Postdoctoral Fellowship award have higher rates for fringe benefits, the institution must provide the difference

Application Procedure All application materials must be received electronically by the deadline of September 1, 2013. Winners will be announced in October 2013.

Application package: The application and application details can be requested from Wolf@sloan.org

If you have specific questions, please contact Paula Olsiewski at olsiewski@sloan.org.

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.),