PRJNA476777
Carrots 16S rRNA gene amplicon Raw sequence reads
Determine the effect of post-harvest interventions (sanitizer washing, storage temperature, and storage period) on the bacterial community composition of carrot surfaces and survival of antibiotic-resistant inoculated pathogens, spoilage-associated bacteria, and heterotrophic aerobic bacteria capable of growth on media containing antibiotics. Retail carrots were inoculated with composted manure generated from antibiotic-dosed cows and further inoculated with two ARBs relevant to fresh produce, E.coli O157:H7 and Pseudomonas aeruginosa. The survival and re-growth of known inoculated pathogens and Pseudomonas spp. present on carrot surfaces after washing with commercial food grade sanitizers was determined by serial dilution and spread plating. Culture-independent 16S rRNA gene amplicon sequencing was carried out to profile and compare the microbiota among the different conditions. While amplicon sequencing provided information on relative abundances of various bacterial populations, including non-culturable members, culture-based methods allowed for comparison and characterization of ARB, including a human pathogen and an opportunistic human pathogen that is also associated with food spoilage.