Differences between second- and third-generation sequencing in capturing microbial community dynamics during...

Current investigations of Baijiu Daqu predominantly utilize second- or third-generation sequencing technologies to characterize microbial community dynamics during storage. We conducted the systematic comparison of second- and third-generation sequencing platforms for the microbial community analysis of Nongxiangxing Daqu and proposed a framework for selecting the appropriate platform based on specific research objectives. Second-generation sequencing, also known as next-generation sequencing, more accurately detected dominant species and higher intragroup reproducibility; third-generation sequencing produced higher-quality sequences, provided higher resolution of low-abundance taxa, and had increased species-level sequencing depth and taxonomic resolution under the prevailing sequencing throughput. Correlation analyses with nontargeted metabolomics indicated that third-generation sequencing detected additional rare or unique species strongly associated with metabolites. Therefore, this study enhances microbial community profiling accuracy and facilitates functional strain discovery, thereby contributing to Baijiu quality enhancement and broader applications in traditional fermentation systems.