Impact of Sampler Selection on the Characterization of the Indoor Microbiome via High-Throughput Sequencing

The potential health effects of microorganisms in the indoor environment paired with recent advances in sequencing technology have led to a rapid expansion in indoor microbial studies employing a multitude of sampling approaches. Although the effect of sampler selection on the microbial community recovered has been examined previously via culture-based methods, high-throughput sequencing techniques allow a more thorough analysis of the impact of sampler type on the microbioata inferred. The objective of this study was to use pyrosequencing to compare the fungal and bacterial communities recovered from six different samplers (two passive and four active) placed in the same occupied building over two consecutive sampling events spaced one week apart. The microbial communities (represented by 335K+ sequences) collected from the passive samplers (settled dust and heating, ventilation, and air-conditioning filter dust samplers) were much more diverse than the shorter term samples collected by the active bioaerosol samplers. There were differences in the fungal and bacterial community structures recovered by the six samplers. The bacterial communities recovered from a given sampler were most closely related to samples collected at different times from the same sampler versus those collected during the same sampling event with a different sampler. For the short- term bioaerosol samplers, only 14% of the bacterial OTUs and 44% of the fungal OTUs detected were common in all four samplers, despite the fact that the samples were located and sampled the indoor air simultaneously. Fewer than 1% of the bacterial OTUs and fewer than 6% of the fungal OTUs recovered from the building were detected in all six samplers. These results indicate that caution is recommended when comparing results from multiple studies that use different sampling techniques, as each sampler may be collecting a different microbial community.