The bacterial and fungal microbiome of retail stores

Abstract

Microorganisms found in the indoor environment of retail stores are not well studied, despite potentially serious human exposure implications. In this study, filters from central heating, ventilation, and air-conditioning (HVAC) units were used to collect a time-integrated sample of the airborne indoor microbiome in 14 U.S. retail stores. The microbial communities recovered from the filter dust samples were analyzed with pyrosequencing to characterize the fungal and bacterial microbiome present. The objectives of this work were to: (1) characterize the microbial communities present in retail stores, (2) delineate relationships between the indoor microbiome and building or environmental parameters, and (3) evaluate the use of HVAC filter dust as a sample location for indoor microbial investigations. The microbiome in retail stores was observed to be diverse with 4,771 and 1,577 unique operational taxonomic units for bacteria and fungi, respectively. The diverse microbial community detected over time in the same store could not be fully explained by seasonal trends. That indicates that even when utilizing a long-term sampling approach like HVAC filter samples, the indoor microbiome cannot be completely characterized by a single sampling event. The bacterial community in retail stores was influenced by the outdoor microbiome and microbiota commonly associated with human skin. Physical location of the retail stores had some influence on the bacterial microbial community present and strongly impacted the fungal community recovered. Air exchange rate did not influence the observed bacterial or fungal communities. In a comparison to five other indoor air samplers, passive samplers including HVAC filter dust and settled dust captured a higher diversity of the microbial community. The collection of a more diverse sample may allow detection of potentially pathogenic microorganisms. However, there was significant difference in the microbial community structures recovered between samplers in the same sampling event which suggests sampling methodology has an impact on the inferred microbiome recovered. The overall results from this study indicate that retail stores harbor a diverse microbial community that varies over time.