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Related Experiment Video

Updated: Jan 12, 2026

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
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Differences between second- and third-generation sequencing in capturing microbial community dynamics during

Xiaopeng Guo1, Qinglin Li2, Bo Zhang3

  • 1School of Life Science and Engineering, Lanzhou University of Technology, 287 Langongping Road, Lanzhou, Gansu Province, 730050, PR China; Gansu Industrial Technology Center for Food and Pharmaceutical Resources Development and Biomanufacturing, 287 Langongping Road, Lanzhou, Gansu Province, 730050, PR China.

International Journal of Food Microbiology
|October 30, 2025
PubMed
Summary

This study compares second- and third-generation sequencing for analyzing Baijiu Daqu microbes. Third-generation sequencing offers higher resolution for rare species, aiding in discovering functional strains for improved Baijiu quality.

Keywords:
Functional insightsMethodological comparisonMicrobial communitiesNongxiangxing Daqu

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Area of Science:

  • Microbiology and Fermentation Science
  • Genomic Sequencing Technologies

Background:

  • Baijiu Daqu microbial community analysis traditionally relies on second- or third-generation sequencing.
  • Understanding microbial dynamics is crucial for Baijiu quality and traditional fermentation processes.

Purpose of the Study:

  • To systematically compare second- and third-generation sequencing platforms for microbial community analysis of Nongxiangxing Daqu.
  • To propose a framework for selecting appropriate sequencing platforms based on research objectives.
  • To enhance microbial community profiling accuracy and facilitate functional strain discovery in traditional fermentation systems.

Main Methods:

  • Comparative analysis of microbial communities in Nongxiangxing Daqu using second-generation (Next-Generation Sequencing) and third-generation sequencing platforms.
  • Correlation analysis with nontargeted metabolomics data.
  • Evaluation of sequencing accuracy, reproducibility, sequence quality, and taxonomic resolution.

Main Results:

  • Second-generation sequencing demonstrated higher accuracy for dominant species and intragroup reproducibility.
  • Third-generation sequencing yielded higher quality sequences, better resolution of low-abundance taxa, and increased species-level sequencing depth.
  • Third-generation sequencing identified additional rare or unique species strongly associated with specific metabolites.

Conclusions:

  • Third-generation sequencing provides superior resolution for rare taxa and deeper taxonomic insights in Baijiu Daqu analysis.
  • The choice of sequencing platform should align with specific research goals, such as identifying dominant species versus rare functional strains.
  • Enhanced microbial profiling accuracy and functional strain discovery contribute to improving Baijiu quality and expanding applications in fermentation.