Deciphering Bacterial Community Structure, Functional Prediction and Food Safety Assessment in Fermented Fruits Using Next-Generation 16S rRNA Amplicon Sequencing

• DOI: 10.3390/microorganisms9081574
• Publication Date: 2021-07-26T02:07:00Z
• Authors: Bashir Hussain; Jung-Sheng Chen; Bing-Mu Hsu; I-Tseng Chu; Suprokash Koner; Tsung-Hsien Chen; Jagat Rathod; Michael W. Y. Chan
• Keywords: Stenotrophomonas; Operational taxonomic unit; Pathogenic bacteria

Fermented fruits and vegetables play an important role in safeguarding food security world-wide. Recently, robust sequencing-based microbial community analysis platforms have improved safety assessment. This study aimed to examine the composition of bacteria evaluate bacterial fermented fruit products using high-throughput 16S-rRNA metagenomic analysis. The operational taxonomic unit-based classification DNA sequences revealed 53 genera. However, amplicon sequencing variant (ASV)-based clustering 43 classifiable Taxonomic classifications that abundance Sphingomonas, which was predominant genus majority tested samples, more than 85–90% among total identified most samples. Among these genera, 13 low genera were potential opportunistic pathogens, including Acinetobacter, Bacillus, Staphylococcus, Clostridium, Klebsiella, Mycobacterium, Ochrobactrum, Chryseobacterium, Stenotrophomonas, Streptococcus. Of major pathogenic species validated polymerase chain reaction. pathogens not detected samples different stages final fermentation, except one sample from first stage fermentation S. aureus detected. finding consistent with ASV-based according only fermentation. significantly correlated human disease pathways. These results indicated is a reliable safe process as products. hybrid method reported this can be used simultaneously diversity, their functional predictions assessment novel Additionally, does involve random detection markedly decrease time verification. Furthermore, for quality control identification external contamination.