AAAS Microbiomes of the Built Environment Symposium videos available on-line

AAAS symposium March 27 2014

Registrants for the March AAAS Symposium are recipients today of the following message from Anette Olsen at AAAS.

“I’d like to let you know that the videos of each panel is now online, but they currently remain unedited. We anticipate another two weeks before the edited versions are placed online. In the meantime, here is the link with the current videos: You can also see some of the comments during the sessions.”

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Where do biological particles found indoors come from?

Most of us spend most of our time indoors amidst suspended biological particles – spores, pollen, bits of dead skin, bacteria, viruses, and so on. We care about these particles because they may have human health impacts (positive or negative), effects on building materials, and possible forensic uses.

Two sources known to be important for biological particles in indoor air are: outdoor air, blown in through ventilation systems and leaked in through windows and doors; and the living occupants of a room – potentially humans, mold, dust mites, insects, rodents, plants, etc.

Our recent study in Indoor Air adds to the understanding of indoor bioaerosols through high-resolution (every 5 min) sampling that offers a glimpse into the influence of short-duration human dynamics (such as students walking into and out of a class) over the course of many days, in a way that has not been done in earlier studies, which used either short-term or time-averaged (e.g. collecting particles over a period of hours or days) approaches.

A key novelty of the bioaerosol sensor we utilized – an ultraviolet aerodynamic particle sizer (UV-APS) – is that it sizes particles as it counts them. Since size is a key parameter influencing particle behavior indoors (as was recently summarized by Brent Stephens), these data were important input parameters for the material balance model we used to quantify occupant emission rates based on observed concentrations.

In our study classroom – which, importantly, was ‘healthy’ with no history of water damage, and was located in the interior of a building with a good ventilation filtration system – we found that baseline (i.e., outdoor origin) bioaerosol concentrations were low. Levels spiked during the high-activity transitions between classes, and remained higher than the baseline even during the quiet occupancy conditions of lecture classes. During occupied periods – which are the most relevant for health impacts – people were by far the dominant source of indoor bioaerosols, across all seasons.

Here’s some more detail on our methods and areas of uncertainty.

We measured fluorescent particles in the 1-15 micron size range in a university classroom continuously during four separate weeks over the course of a year. Autofluorescence at characteristic wavelengths was treated as an indicator of biological origin, so the targeted particles were called fluorescent biological aerosol particles, or FBAPs. Emissions of numbers of FBAPs by students (via the processes of shedding and resuspension) – both in absolute terms and normalized by the mass of carbon dioxide emitted by the students – peaked in the 3-4 micron size range.


Photo courtesy of TSI Incorporated. We treated particles exhibiting fluorescence at characteristic wavelengths as proxies for biological particles (including non-microbial components such as skin flakes), and quantified them with a UV-APS (TSI, Inc.;

A caveat: Our results are based on autofluorescence. Various bioaerosol metrics are known to be influenced by room occupancy in different ways – e.g., bacteria have been more strongly linked to humans, whereas indoor fungi have been tied more strongly to outdoor sources. Moreover, our findings rely on numbers of particles; outcomes based on composition may tell a different story.

Looking forward, a host of questions remain open: We saw that classroom air particulate matter had a distinct fluorescent signal compared to urban ambient air. Occupants were the dominant proximate cause of the observed FBAPs. But what was the ultimate source of the occupant-emitted fluorescent coarse particles: the human body, building materials, consumer products, or bioaerosols that originated outdoors and were tracked in by humans or the ventilation system? What part of the fluorescent signal represents non-biological interferents, and can signatures based on size/fluorescence-intensity differentiate them from true biological particles? How useful is fluorescence as a tool for understanding the activity of indoor airborne microbes?

Overall, there remains much to learn about indoor bioaerosols. Better characterization of sources and dynamic behaviors can contribute.

[Credit to Rachel Adams for her helpful feedback]

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Microbes from the built environment finally head to space, #spacemicrobes

3a431a6c-a2e0-4df8-9e28-62442b097a9fAfter 1.5 years of collection events, culturing, identification, and selection of candidates our space microbes experiment finally is in orbit.  Our 48 microbes, collected from a variety of built environments on earth, are now whipping around the planet.  The rocket took off from Kennedy Space Center at Cape Canaveral at 3:25pm EST yesterday.  In a couple of days they’ll dock with the International Space Station (ISS) and start growing.

Equally exciting is the fact that in our “cube” are 15 swab kits for the astronauts to take samples from around the ISS.  In collaboration with Jack Gilbert and the Earth Microbiome Project, we will analyze these swabs for 16S, 18S, and ITS… hopefully giving us a complete picture of the (non-viral, sorry Scott Kelly) microbes present on the ISS.

Really excited to get both the growth data from the “microbial playoffs in space” as well as start working on the swabs.

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Microbes Can Light Up the World

Researchers at the Japan Science and Technology Agency found in this 2012 study that microbes like Geobacter sulfurreducens and Thiobacillus denitrificans can form small electric grids. These species cooperatively create electric currents through conductive minerals in soil, and can probably do so over a (relatively to microbes) large distance. These microbes and others like them are being studied in an attempt to create a source of electricity for humans. Although this idea has a long way to go in terms of development, I think it’s worthwhile to explore the uses of such microbes. Perhaps one day, microbes will be lighting up our world, in addition to all the other useful jobs they already do for us.

Alex Alexiev is an undergraduate in Jonathan Eisen’s lab, working on aquariums as part of the microbiology of the built environment

Light up the world

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Citizen Irony

I’m working on a manuscript describing the different and particular challenges scientists in various disciplines face when incorporating citizen science into their research. So, I thought I would go looking for other articles about it, and found one with the promising title A new dawn for citizen science by Jonathan Silvertown.

I’m holed up in a hotel in Florida waiting for SpaceX to launch our experiment to the ISS (I just can’t resist dropping that into conversation). When I try to read the Silvertown’s article, I see this :


Huh. $37.95. Let it not escape your notice that Dr. Silvertown, who I don’t know and is probably a nice fellow, teaches at the Open University.

The. Open. University.

tl;dr : Let’s not involve the public in our discussions about their utility in our research.

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The microbial aura of our pets

In Dirty Dog: Do Pets Track Bacteria in Your Home? on the Popular Science blog, science journalist Brooke Borel describes her recent experience contributing to the citizen science experiment called The Wild Life of Our Homes run by Rob Dunn and Holly Menninger at North Carolina State University. Here she presents a beautiful graphic depicting how the samples that she collected from her house, herself and her dog compared with some of the other participants in the study. This graphic was published as a sidebar to a longer article on the Wild Life of Our Homes project by Joel Warner in the April issue of Popular Science. One of the interesting things Brooke learned from participating in the study is that apparently she has dog microbes on her tongue and other parts of her body. She wants to know what we all think about sharing our houses, beds, couches and microbes with our pets.

Yuki picking up some soil microbes to bring back home

Yuki picking up some soil microbes to bring back home. Photo by Holly Ganz.

Personally I’m all for microbial sharing with our pets. I even think that we should allow dogs in restaurants, trains, buses and other public places like they do in Europe. I was going to posit that maybe Europeans are better at picking up after their dogs than we are but then I remembered that when I stepped in dog poop last year while visiting Marseille, my friend Marie said “Welcome to France!”

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Manipulating the Unseen Microbial Ecosystem—The Future of Hospitals? (NOVA Online)

Great article from Brooke Borel writing for NOVA Online, “Manipulating the Unseen Microbial Ecosystem—The Future of Hospitals?”.

This covers some of the background of microbiology in hospitals, discusses work by both the BioBE Center and microBEnet… and of course the Hospital Microbiome Project as well as the NICU study from Jill Banfield’s lab.  The article doesn’t explicitly go into the topic of building probiotics (a favorite of ours) but does discuss possible implications of these kinds of studies for building design.

A very good introduction to the topic…

US Navy 030415-N-1056B-001 A Navy Hospital Corpsman prepares the operating room at Fleet Hospital Eight (FH-8), located at Naval Station Rota, in preparation for the arrival of 39 wounded Marines and Soldiers from Operation Ir

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Potentially useful tool for culture collection: LIIS

Quick post here.  This seems like a potentially useful tools for labs to keep track of their culture collections.  We definitely need something like this in my lab.

LIIS: A web-based system for culture collections and sample annotation | Forster | Journal of Open Research Software.


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Microbes and the design of animal shelters

Animal shelters provide an essential and beneficial social service, caring for an estimated 9 million pets each year in the United States. Many animals entering a shelter are highly stressed and lack the benefits of standard veterinary care, including vaccinations. Moreover animal shelters are an intensive housing situation that amplifies the transmission of infectious diseases (Pesavento and Murphy 2014). Consequently shelter staff devote a lot of time and resources to cleaning and disinfection, in addition to providing animal care.

Architect George Miers of Swatt Miers Architects has designed and built many animal shelters on the West Coast. In this video, he discusses some of the considerations that go into designing a new animal shelter. If you are like me, you will be amazed by the amount of attention paid to drain design and power washing.

Is there a better way to disinfect animal housing areas? Would UV be a better alternative to chemical disinfectants? Animal shelters are built environments with an important and under-appreciated microbiology and there are many unanswered questions. As part of a very preliminary study, we sampled the air in a walkway adjacent to the dog kennels in a local shelter using a Petri dish air sampler to provide a pretty picture of the diverse and abundant bacteria and fungi found inside animal shelters.

Sample from kennel walkway, 100 L air sampled, 44 hour incubation.

Sample from kennel walkway, 100 L air sampled, 44 hour incubation.


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‘Frozen’ Microbial Ecology

This past Saturday, my wife picked ‘Frozen’ for movie night (no, we don’t have kids). In the movie, one of the main characters was born with the power to freeze her surroundings, which she struggles to control. By the time, ‘Let It Go’ was playing, I couldn’t help but wonder how the repeated freezing of the castle was impacting the indoor microbiology, which led to Google Scholar (I am a terrible movie watcher) to investigate what we know about the microbial ecology of refrigerators and freezers.

The amount of cold storage we use is staggering (at least to me) – the USDA reports that the US has ~4 billion cubic feet of refrigerated storage. Searching for information on the microbial ecology of refrigerators is difficult – imagine how many studies use some formation of the word ‘refrigerated’ or ‘frozen’ when referring to sample storage and processing.  However, The microbiology of psychrophiles (cold-loving microorganisms) dates back to at least 1902, when Schmidt-Nelson coined the term ‘psychrophile’. Psychrophiles include members of the genera Pseudomonas, Psychrobacter, Staphylococcus, Photobacterium, and Halomonas, among others. The biology behind these microbes is fascinating (anti-freeze proteins!) and they are widely distributed in the environment. Almost all psychrophile ecology research that I was able to identify investigated the impact on food storage and spoilage – however I can’t help but wonder about the microbial ecology of the refrigerated spaces themselves. I’m starting the search in the back of the grad student lunchroom fridge.


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