Microbiologic surveys for Baijiu fermentation are affected by experimental design

Area of Science:

• Microbiology
• Metagenomics
• Fermentation Science

Background:

• Baijiu, a traditional Chinese alcoholic beverage, relies on spontaneous grain fermentation under anaerobic conditions.
• The microbial succession mechanisms in Baijiu brewing remain unclear, and the evaluation of metagenomic strategies for microecology surveys is incomplete.
• Understanding the microbiome is crucial for optimizing Baijiu production.

Purpose of the Study:

• To compare different sequencing methodologies for analyzing bacterial communities in Baijiu fermentation.
• To evaluate the impact of technology selection on phylogenetic and functional profiles.
• To provide insights for selecting appropriate methods for studying fermentation systems.

Main Methods:

• Utilized strong-flavor Baijiu fermentation as a model system.
• Compared bacterial community data from short-read 16S rRNA (V3-V4 regions), full-length 16S rRNA (V1-V9 regions), and whole metagenomic shotgun sequencing (WMS).
• Analyzed phylogenetic and functional profiles, including metabolic pathways.

Main Results:

• Sequencing methods yielded differences in bacterial composition and their correlation with volatiles and physicochemical variables.
• The V3-V4 16S rRNA dataset showed a higher positive correlation with WMS data at genus and family levels compared to the V1-V9 dataset.
• WMS identified significant changes in metabolic pathways (e.g., starch metabolism, fatty acid biosynthesis), which were largely uncorrelated with functional predictions from 16S data.

Conclusions:

• Whole metagenomic shotgun sequencing offers more comprehensive insights into Baijiu microbial communities and metabolic functions than 16S rRNA sequencing.
• The V3-V4 region of 16S rRNA sequencing demonstrates better concordance with WMS data for bacterial community analysis.
• This study provides valuable technical guidance for selecting optimal methodologies in fermentation research.