Purpose: The purpose of this study was to use shotgun metagenomic and 16S rRNA amplicon sequencing to identify the microbial communities in foods suspected of adulteration.
Methods: Eight cilantro samples (distributor or retail), five masala spice mixes (imported), seven cucumbers (retail), and two brands of mung bean sprouts (retail) were sequenced. 16S rRNA gene amplicon and shotgun metagenomic data were analyzed with Resphera Insights and COSMOSID, respectively.
Results: Enterobacteriaceae were significantly higher in cucumber, masala, and sprouts relative to cilantro (P<0.002; Mann-Whitney test), with sprouts maintaining the highest relative abundance (mean 55.2%). Observed species were the highest in the masala (~983) and lowest in mung bean sprouts (~277). Sprout brands were further distinguished by a predominance of spoilage associated Leuconostoc (54%) and Lactococcus (29%) species in brand A. Flavobacterium species were only present in cilantro; abundances ranged from 7% to 34%, depending on the source. The cucumber samples had approximately 340 observed species, with a high variability in abundance distributed among individual samples. For example, the average proportional abundance of Rhizobium was 12%; however, one cucumber sample contained a 50% proportional abundance and, Paenibacillus ranged from 5% to 31%. Lastly, three of the masala spice mixes were contaminated with Plautia stali, a bacterial symbiont specific to “stink” bugs, at proportional abundances ranging from 1.5 to 3.2% suggesting contamination with filth.
Significance: Metagenomic methods can identify the bacteria harbored in foods to improve culture methods and food quality. Our data reveal the diversity of microbial communities in different commodity types and sources such as, Paenibacillus that can hinder pathogen detection, spoilage bacteria, and food adulterants such as P. stali.