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.

Assessment of Chicken Carcass Microbiome Responses During Processing in the Presence of Commercial Antimicrobials Using a Next Generation Sequencing Approach.

The purpose of this study was to 1) identify microbial compositional changes on chicken carcasses during processing, 2) determine the antimicrobial efficacy of peracetic acid (PAA) and Amplon (blend of sulfuric acid and sodium sulfate) at a poultry processing pilot plant scale, and 3) compare microbial communities between chicken carcass rinsates and recovered bacteria from media. Birds were collected from each processing step and rinsates were applied to estimate aerobic plate count (APC) and Campylobacter as well as Salmonella prevalence. Microbiome sequencing was utilized to identify microbial population changes over processing and antimicrobial treatments. Only the PAA treatment exhibited significant reduction of APC at the post chilling step while both Amplon and PAA yielded detectable Campylobacter reductions at all steps. Based on microbiome sequencing, Firmicutes were the predominant bacterial group at the phyla level with over 50% frequency in all steps while the relative abundance of Proteobacteria decreased as processing progressed. Overall microbiota between rinsate and APC plate microbial populations revealed generally similar patterns at the phyla level but they were different at the genus level. Both antimicrobials appeared to be effective on reducing problematic bacteria and microbiome can be utilized to identify optimal indicator microorganisms for enhancing product quality.