Exploring the microbiome of the built environment: A primer on four biological methods available to building professionals

Building professionals are increasingly being called upon to conduct indoor microbial investigations as they remediate moisture-damaged buildings and design new, healthy, sustainable buildings. Characterizing the indoor microbial community present in the built environment is challenging and complicated by the vast array of biological methods available to building professionals. Furthermore, the particular biological technique employed to study an indoor environment can have a significant impact on the results obtained. This study evaluates the advantages and disadvantages of four biological methods suitable for indoor microbial investigations: culturing, quantitative polymerase chain reaction (qPCR), Sanger sequencing, and pyrosequencing. The results obtained from a study of four buildings are used to evaluate the merits of each bioanalytical approach. In each of the four study sites, the microbial-laden dust recovered on HVAC filters was used to provide a passive, long-term sample of the indoor air. Culturing of the microorganisms recovered from the dust was the least expensive method tested but provided a limited characterization of the microbial community present. qPCR provided the most specific information about the presence and quantity of target microorganisms but this method requires a priori knowledge of the species of interest and specifically designed primers that may not enumerate unanticipated species. Sanger sequencing provided microbial identification at the species level but lacked coverage to fully describe the microbial community present. Pyrosequencing provided in-depth sequence coverage of the microbial community present (to the genus level) but the vast dataset generated required increased computational analysis and data storage. Nevertheless, pyrosequencing when coupled with qPCR for target species quantification represents a viable approach that should become more accessible to building professionals as user-friendly software for analyzing sequencing results becomes available and more commercial laboratories offer these services.