Microbiome shifts in sprouts (alfalfa, radish, and rapeseed) during production from seed to sprout using 16S rRNA microbiome sequencing

Sprouts harbor high levels of bacteria and have been implicated in massive outbreaks of foodborne illnesses. The elucidation of microbial profiles in sprouts is important; however, little is known about the changes in the microbial composition during production. The present study aimed to define the microbial ecology of sprouts during the stages of production using 16S rRNA metagenome sequencing and culture-dependent methods. Samples of three types of sprouts (alfalfa, radish, and rapeseed) were collected from each stage of production (seed, soaking, germination 1 (Germ 1), germination 2 (Germ 2), sprouting, unwashed, and washed sprouts; n = 105) and subjected to microbiome analyses as well as quantitative and qualitative analyses. Aerobic plate count (APC) and coliforms levels significantly increased within one day (Germ 1) by 3.9–4.4 and 4.2–5.2 log CFU/g, respectively, and levels up to 8.0–9.0 and 6.9–9.0 log CFU/g, respectively, were recorded at the final stage. During production, the microbial communities in alfalfa sprouts simplified into Enterobacteriaceae (80.97–99.29%), whereas the radish and rapeseed sprouts were dominated by microbial communities belonging to two families, the Enterobacteriaceae (radish: 32–43.4%, rapeseed: 24.11–38.39%) and Pseudomonadaceae (radish: 30.53–46.45%, rapeseed: 41.51–57.34%). This suggests that the sprout manufacturing conditions could promote the growth of particular bacterium. Alpha diversity analysis revealed a diverse bacterial community structure in the seeds; however, the diversity sharply declined until Germ 1 and recovered during the production steps thereafter. Beta diversity results suggested that the pattern of microbial composition, and the major shifts in composition, differed by seed type. Significant changes in the bacterial community were observed during the soaking (alfalfa), Germ 1 (radish), and Germ 2 (rapeseed) stages. The present study is the first fundamental report to investigate microbial changes by during the various stages of the sprouting process. The results highlight the potential risk of sprouts regarding foodborne illness and facilitate the determination of effective intervention points during sprout production.