Impact of DNA extraction, PCR amplification, sequencing, and bioinformatic analysis on food-associated mock communities using PacBio long-read amplicon sequencing.

ABSTRACT:

Background

Long-read 16S rRNA gene amplicon sequencing has a high potential for characterizing food-associated microbiomes. The advantage results from sequencing the full-length (1,500 bp) gene, enabling taxonomic resolution at species level. Here we present a benchmarking study using mock communities representative of milking machine biofilms and raw meat, revealing challenges relevant to food-associated habitats. These were varying species abundances, reliable intra-genus differentiation of species, and detection of novel species with < 98.7% sequence identity to type strains. By using mock communities at different levels of preparation - as mixed whole cells, mixed extracted DNA, and mixed PCR products - we systematically investigated the influence of DNA extraction using two di

SUBMITTER: Baer M 

PROVIDER: S-EPMC11622462 | biostudies-literature | 2024 Dec

REPOSITORIES: biostudies-literature