Microbiology of the Built Environment: Day 2

Here’s my report from Day 2 of the Microbiology of the Built Environment Conference in Boulder… the 5th annual and last of its kind!  Storify of the tweets from the day below.

The opening talk on Day 2 was by Martin Taubel from the National Institute for Health and Welfare, Finland, “Of house dust and a crawling baby robot — indoor microbial exposure assessment”.  Coming from a public health perspective one of the main points was “we do not know how to measure exposure to indoor microbes properly”.  He talked largely about a comparison of rural and urban homes where they found (among other things) a lower diversity of bacteria with increasing urbanization.  A lot of the focus was on the problem of repeatability and how to sample dust to best measure human exposure.  The second half of his talk was about a crawling baby robot used to study re-suspension of particles in a controlled chamber.  Crawling on carpets creates a concentrated and localized cloud of particles around the infant that may be problematic.

Kati Huttunen, Department of Environmental and Biological Sciences, University of Eastern Finland, “A tricky task: assessing the toxicity of dust”.  One of her points was that the toxicity of a microbe is very dependent on context; other bugs, substrate, pH, etc.  Makes it very hard to pin down the problems.  To a significant extent her talk was about the various choices in a decision tree regarding experimental design when measuring the toxicity of dust.  I would love to see a flow chart of this entire space, seems like that would be super useful to people doing this kind of work.  I think she very much lived up to the “tricky task” part of her title.

Susan Lynch, University of California at San Francisco, “The gut-airway axis and its potential role in atopy”.  She talked at length about the importance of early life exposure to the latter development of asthma.  The model is that microbial exposure from the environment affects the development of the gut microbiome, which interacts in various ways with the human immune system that leads to disease (asthma) in some cases.   She had very compelling data about which commensal bacteria are missing in kids at risk of asthma and the fact that with decreasing bacterial diversity comes increased fungal richness.  They’re now moving into the intervention space… I’ll be very very curious to see how those trials work out!

Karen Dannemiller, The Ohio State University tag-teaming the next talk with Jordan Peccia from Yale University “The Association of indoor microbial communities on atopic and non-atopic populations”.   The first half of the talk focused on reducing environmental exposures that lead to asthma development.  She showed data that fungal richness in dust was inversely correlated with asthma development, which I thought was the opposite of what Susan Lynch just claimed but am now just confused.   Sounds like we need more data!  Jordan talked about the importance of considering mechanistic approaches, looking at factors such as re-suspension and deposition of microbes in the built environment.

Kerry Kinney and Steven Bourne from University of Texas, Austin “The monitoring of microbiological air quality in public schools — a longitudinal study”.  They described the results of a study of “portable” classrooms (which apparently are rarely removed).  They look in many ways like normal buildings but some differences include open crawl spaces, poor ventilation (though often leaky enough to offset this), poor maintenance.  Open attics are a major concern, positive pressurization has a big impact on microbial communities (pre versus post intervention).

Huan Gu from Syracuse University talked about “Characterization and Control of Biofilms in
the Built Environment”… in particular in hospitals.   Talked about the resistance of biofilms to removal and their persistence in the face of antibiotics.  They have a small chamber to test Pseudomonas biofilm formation and have a bunch of antibiotic resistant strains.   (Full disclosure:  our lab recently sequenced many of these strains).  She finished with a discussion about the importance of the topography of the surface itself, and how we might design surfaces that are resistant to biofilm formation.

Tod Merkel, US Food and Drug Administration, “Assessing functional genes on the
fly: RNA patterns reveal the Pertussis responses to atmospheric environments”.   Telling an interesting story about Pertussis… it’s human-human transmission only; no reservoir, no other host, doesn’t survive on surfaces/water/etc.  Talking about model of transcriptional activation where certain genes are turned on only for survival in respiratory droplets.  Has developed a baboon model for Pertussis transmission.

David Thaler, University of Basel, “Perspectives on indoor Prokaryote — Fungal
associations”.  David talked about the Neolithic Revolution and the major changes in microbiology precipitated therein (agriculture, built structures, cheese, wine, beer, etc.).   Making the analogy that we are entering a second Neolithic-style change where either we adapt to live with microbes or have an antibiotic-resistance disaster.  Hard to summarize this talk, he ranged across a wide variety of fascinating topics including phase variation in tuberculosis, water activity, the importance (or not) of bacterial diversity, autoimmunity, etc.

Bubba Brooks, University of California at Berkeley, Banfield lab, “Longitudinal
studies of developmental microbiomes neonatal intensive care units”.  Talking about the first wave of microbial colonization (usually the mother) and the second wave (normally the home of the infant).  In the case of low-birth weight pre-term infants, the second wave comes from the hospital.  Many strains persist in the NICU, some strains are very good an infecting co-housed infants.  Cleaning and occupancy are the main drivers of NICU bacterial diversity.

Brian Klein from Harvard University, “Microbiomes of Indoor Athletic Facilities”.   Studying indoor running tracks from the premise that athletes are an understudied population that are actually less healthy than average (more respiratory infections, lower immunity).  Gearing up for a large study but doesn’t have the data yet.  (full disclosure, our lab sequenced some strains from this project).

Amy Pruden, Virginia Polytechnic and State University “Microbiome reconnaissance in water infrastructure: Legionella, metagenomics and its co-occurrence with corrosion”.  Talking about premise plumbing, the idea of inoculating drinking water pipes, the variety of water-borne pathogens and more.   Made the interesting point that regulatory framework is not setup for non-fecal inhaled pathogens.   Raising temp of hot water one of the best control methods, but uses more energy and risks scalding. Talked at length about the Flint water crisis and about the resulting Legionella outbreaks as a result in changed water chemistry.   Concluded that our water infrastructure “sucks” and a call to action.

And that wraps up 5 years of these talks!   Storify of the day below.


2 thoughts on “Microbiology of the Built Environment: Day 2

  1. I recommend Thaler’s article, specifically Table 3 and its explanation, to those who wonder why results from NGS methods applied to the indoor microbiome are not reproducible.

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David Coil

David Coil is a Project Scientist in the lab of Jonathan Eisen at UC Davis. David works at the intersection between research, education, and outreach in the areas of the microbiology of the built environment, microbial ecology, and bacterial genomics. Twitter