One of the hurdles in linking microbial ecology with building science has been incorporating quantitative information about the microorganisms encountered in indoor environments, mainly because the standard high-throughput amplicon approach for community analysis is semi-quantitative, at best. Over the summer, there was a Twitter conversation related to this topic.
My take-away from this (what I view as a productive) Twitter exchange is the idea that community analysis is one way to identify the important taxa and generate hypotheses. Those relevant taxa would then be further explored with, for example, qPCR. Seems like a solid approach to me. The hard part, of course, is in identifying the functionally relevant taxa that should be revisited with quantitative approaches. Which brings me to this year-old paper:
Rosen, Connor E., and Noah W. Palm. “Functional classification of the gut microbiota: the key to cracking the microbiota composition code: functional classifications of the gut microbiota reveal previously hidden contributions of indigenous gut bacteria to human health and disease.” BioEssays 39.12 (2017): 1700032.
The authors detail many reasons why, outside of infectious disease and satisfying Koch’s postulate, identifying the microbiota responsible for the disease state is challenging. Once a particular function or trait has been identified (they use the example of the production and secretion of immunoglobulin A), they discuss a new approach, relying on fluorescence-based cell sorting followed by 16S gene amplicon sequencing, to isolate those taxa associated with that trait.
In applying this approach to the built environment, the challenge (and opportunity!) comes from identifying specific microbial traits or functions that we’d like to either promote (e.g. those present in farming environments which protect respiratory health) or minimize (e.g. those present in water damaged buildings which are associated with ill respiratory health). Then quantity can also be incorporated to create a more complete picture of the roles that environmental indoor microbiota play in occupant and building health.