Impact of sampler selection on the characterization of the indoor microbiome via high-throughput sequencing

• This study compared six different indoor microbial samplers in a retail store.
• Pyrosequencing was used for the comparison with both bacterial and fungal targets.
• Microbial communities in settled dust and HVAC filter dust were more diverse than in active bioaerosol samplers.
• Little overlap in the microbial community was observed in the collocated bioaerosol samplers.
• Sampler selection affects the microbiome recovered.

Concerns regarding the potential health effects of microorganisms in the indoor environment paired with recent advances in DNA sequencing technologies have led to a rapid expansion in microbial studies of the built environment. The objective of this study is to compare the microbial communities recovered from six different samplers placed in the same building to assess how sample selection can impact the interpretation of the indoor microbiome. To this end, pyrosequencing was used to delineate the fungal and bacterial communities recovered from six samplers placed in an occupied retail building over two consecutive sampling events spaced one week apart. The microbial communities (335K+ sequences) were much more diverse in the settled dust and heating, ventilation, and air-conditioning (HVAC) filter dust samples than the communities recovered from the shorter term, composite samples collected in four different bioaerosol samplers. The bacterial communities recovered from a given sampler were in general more similar to communities from the same samplers than to communities recovered during the same sampling event. Only 14% of the bacterial OTUs and 44% of the fungal OTUs detected were shared in all four bioaerosol samplers, despite the fact that the samplers were collocated and sampled the indoor air simultaneously. These results indicate that sample type should be considered when interpreting results, particularly when comparing results across multiple studies that use different sampling techniques.