Meeting Report: Microbiomes of the Built Environment – Meeting #3: Day 1

Today was the first day of the 3rd meeting in the NAS-sponsored series of “Microbiomes of the Built Environment:  From Research to Application” meetings.  This meeting was held at UC Irvine and the goal was to provide information for the NAS committee that will subsequently produce a report on the status of the field.  For anyone that missed the talks, everything was recorded and will be available online.   We’ll post here at microBEnet when that happens.  The Storify of Twitter is at the end of this post.

Session #1 “How the Built Environment Microbiome Responds to Context and Perturbations”

The first speaker was Janet Jansson “Microbial Community Response to Environmental Conditions and the ‘Microbiomes in Transition (MinT)’ Initiative”.  She described a changing world (climate change, disease, chemical/drug exposure) where the impact on microbial communities is largely unknown.  Talked about a “multi-omics” approach for studying complex and changing environments.   Gave a few examples including permafrost and mice.

Next was Sarah Evans who talked about “Soil Microbial Responses to Climate Perturbations”.  Showed examples in soil, where manipulation of drought conditions causes a major shift in the microbiome.  Microbial communities show a change in ecological strategy, via taxonomic shifts.  Most of these shifts are caused by the arrival of new taxa to the system. Talked about rain microbial communities which I hadn’t though much about, however doesn’t see a large signature of those things in soils.

Last in the intro session was Shelly Miller “The Effect of Geographic Location on the Composition and Function of Indoor Microbiomes”.  Talked about their 1200 US homes study, their detailed Boulder dorm study, and the Boulder flood study.  Summarized part of their results with “If you want to change the fungi you live with, move somewhere else, preferably far away.  If you want to change the bacteria, change who you live with”.  Showing data that only a few fungi were more present inside homes than outside, more for bacteria but still only a few % of the total.  Broad scale metadata (climate, geography) predict fungal composition but not bacterial composition.  The dorm study showed that they could predict the sex of occupants from the bacterial communities.   The flood study showed that flood homes have different bacterial/fungal communities even after remediation.

Individual talks

Rob Knight gave a special talk called “The Current Toolkit for Studying Microbiome/Built Environment Interfaces”.  Talked about the big data aspect of microbiology and the dramatic changes in the field over the last 15 years.  Started with a lot of discovery data, early microbiome studies, etc.  Talked about the need for more accurate taxonomic assignments (examples of subway anthrax study, and the high abundance of platypus samples in Finland).  Hard to summarize his talk, he summarized the entire field!  Some data I hadn’t seen before about the spatial distribution of metabolic products and their relationship to bugs.

Another special talk about Scott Jackson “Microbiome and Metagenomic Standards at NIST”.  Gave some background on NIST.   Talked about various standards they’ve developed, including a human DNA standard for clinical diagnostics and an RNA spike-in standard for microarrary experiments.  They even have a highly characterized antibody molecule as a standard.  Describing the transition to a world where microbes themselves are therapeutics (as opposed to proteins or isolated molecules).  Talked about the fact that microbiome studies have so many places for error, from collection to extraction to analysis.  They are potentially interested in developing a mock community standard, but make the point that existing ones aren’t used.

Session #2 “Expanding the Toolkit: Studying Microbial Functions”

First talk was by Jay Lennon “A trait-based approach to microbial diversity”.  Pointing out the limitation of studying lists of taxa.  Asking about the phylogenetic conservation of traits, trade-offs between traits, and different kinds of traits.  Talked about bacterial persistence and longevity.  Claimed that 90% of skin bacteria were either dead or dormant.

Other talk in this session was from Pieter Dorrestein “Chemistry of the human habitat…”.  Started off describing the significant lack of knowledge regarding indoor chemistry.  Need that groundwork before we can relate that to microbes and the whole system. Talked mostly about what I would call chemical forensics, matching chemical signatures on between people and the objects that surround them.

Session #3 “Expanding the Toolkit: Modeling the Microbiome”

First up was Jennifer Martiny “Microbial biogeography in light of traits”  As with Jay Lennon’s talk, an emphasis on traits versus lists of taxa.  Mentioned the Doolittle argument that because of HGT and rapid evolution, taxonomy might not be as informative as we hope.  However, she went on to show data that in fact there is a strong phylogenetic signal among microbes.  Gave some neat examples about microbial traits.

Next in session was Patricia Fabian (remotely) “Modeling the Built Environment, Indoor Air Quality, and Health: A Systems Science Approach”.  Talked about the challenges facing models, including multi-factorial nature, rare diseases, insufficient power in most studies, etc.  But, did show the advantages of the modeling approach… giving some interesting examples including influenza survival and impact of weatherization on low income multi family housing.

Session #4 “Analyzing What’s Known from Case Examples: Comparing and Contrasting Results”

Tiina Reponen “Microbiomes of the Built Environment: Homes”.  She started of by listing those attributes that make homes different from hospitals and the ISS (this is a comparative session).  Those were pets, influence of outdoor fungi, humidity, and building materials.  Showed the effects of various home characteristics on microbial richness, abundance, spores, etc.  Then made the point that what we really want to know is the relationship to health effects.  Talked in depth about the CCAAPS study, where they looked at homes over a long time. Also discussed the ERMI index (Environmental Relative Moldiness Index) which is a PCR-based assay that appears to be predictive in infants of later development of asthma.

Next was Brandon “Bubba” Brooks, “Reviewing major themes in hospital microbiome research”.  Gave a good background on hospital work.  Talked about the NICU as both and important and tractable study system.  Showed source-tracking data about where microbes on touch surfaces in the hospital come from.  Emphasized the need for genome sequencing, strain-level differences are important.  Summarized differences between hospitals and houses.  Hospitals are more sourced from humans, more spatial separation, etc.

Last talk in this group was Kasthuri Venkateswaran “Venkat” talking about “Environmental “omics on the ISS”.  Talking about Planetary Protection and why NASA cares about the microbiome.  NASA has access to some really cool closed systems, not just the ISS but various testing facilities including underwater.  Gave some geography of the ISS.  Talked about the results of a large-scale survey of the ISS, did both culture-dependent and culture-independent methods.  Looked at both bacteria and fungi.

Afterwards we had breakout sessions for discussing the status of the field and then a poster session.  Here is the Storify of tweet for the day:

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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