Must read paper of the week: Tools to improve built environment data collection for indoor microbial ecology investigations

Got alerted to a very interesting paper because I have subscribed to Google Scholar automated updates for Brent Stephens (see a full list of Google Scholar pages for researchers working on microbiology of the built environment here). The paper is: Tools to improve built environment data collection for indoor microbial ecology investigations by Tiffanie Ramos and Brent Stephens and it is in the journal Building and Environment under a Creative Commons license.


Recent studies have greatly increased our knowledge of microbial ecology of the indoor environments in which we live and work. However, the number of studies collecting robust, long-term data using standardized methods to characterize important building characteristics, indoor environmental conditions, and human occupancy — collectively referred to as “built environment data” — remain limited. Insufficiently described built environment data can limit our ability to compare microbial ecology results from one indoor environment to another or to use the results to assess how best to control indoor microbial communities. This work first reviews recent literature on microbial community characterization in indoor environments (primarily those that utilized molecular methods), paying particular attention to the level of assessment of influential built environment characteristics and the specific methods and procedures that were used to collect those data. Based on those observations, we then describe a large suite of indoor environmental and building design and operational parameters that can be measured using standardized methods to inform experimental design in future studies of the microbial ecology of the built environment. This work builds upon the recently developed MIxS-BE package that identifies high-level minimal built environment metadata to collect in microbial ecology studies, primarily by providing more justification, detail, and context for these important parameters and others from the perspective of engineers and building scientists. It is our intent to provide microbial ecologists with knowledge of many of the tools available for built environment data collection, as well as some of the constraints and considerations for these tools, which may improve our ability to design indoor microbial ecology studies that can better inform building design and operation.

One thing I like about this paper is it reviews recent DNA-based studies of the microbiology of the built environment in relation to how much built environment data was collected as part of the study.

Another thing that is useful is the presentation of tools that should help improve the collecting of built environment data associated with such studies.  There is a VERY comprehensive Table presenting this information including references with extra details.  And this Table is bolstered by discussion in the main text.

This is a critically important paper for studies of microbiology of the built environment and would be of use to others working on microbial ecology and thinking about how to collect metadata for one’s studies.

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Jonathan Eisen

I am an evolutionary biologist and a Professor at U. C. Davis. My lab is in the UC Davis Genome Center and I hold appointments in the Department of Medical Microbiology and Immunology in the School of Medicine and the Department of Evolution and Ecology in the College of Biological Sciences. My research focuses on the origin of novelty (how new processes and functions originate). To study this I focus on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis (see my lab site here which has more information on lab activities).  In addition to research, I am heavily involved in the Open Access publishing and Open Science movements.