Environmental sponge sampling: We are only scraping the surface

Abstract

Drains located in retail deli departments are known harborage points for pathogenic and spoilage microorganisms. Previous studies have used sequencing approaches to study the microbial consortia found in drains and biofilms in various food processing environments. None of these studies, however, have focused on retail. The primary objective of this study was to characterize the microbiome of retail deli drain sponge samples and drain biomass samples through shotgun metagenomic and 16S rRNA amplicon sequencing approaches. Sponge samples were collected from the surfaces of retail deli drain covers and biomass samples were harvested from inside deli drain trenches from fourteen retail delis in three major US cities. All samples were subjected to 16S rRNA gene sequencing, and shotgun metagenomic sequencing was performed on a subset of samples. In the majority of samples, Pseudomonas was the most abundant; the remaining genera differed by sample, city, and sequencing method. Common sanitizer tolerance genes (qacE∆1 and qacE) were observed in all biomass samples which were subjected to shotgun metagenomic sequencing. While mean alpha diversity indices were similar between biomass and sponge samples evaluated via 16S RNA amplicon sequencing, a greater range of diversity was observed between biomass scrapes than sponge samples. Beta diversity differed significantly (P < 0.01) between biomass scrapes and sponges. Additionally, some taxa, such as the opportunistic pathogen Elizabethkingia, were virtually absent from sponge samples, but present at low abundance in biomass scrape samples. While studies traditionally have focused on detection of specific microorganisms of interest, this study indicates that drain trenches may harbor microorganisms that are not observed through traditional methods of environmental sampling (i.e. surface sponge samples). Collection of drain biofilms or biomass scrapes and use of culture-independent approaches would provide a more complete picture of the deli drain microbiome.