Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei, Taiwan.
Center for Biotechnology, National Taiwan University, Taipei, Taiwan.
J Sci Food Agric. 2024 Nov;104(14):8604-8612. doi: 10.1002/jsfa.13688. Epub 2024 Jun 25.
Microbiota succession determines the flavor and quality of fermented foods. Quantitative PCR-based quantitative microbiome profiling (QMP) has been applied broadly for microbial analysis from absolute abundance perspectives, transforming microbiota ratios into counts by normalizing 16S ribosomal RNA (16S rRNA) gene sequencing data with gene copies quantified by quantitative PCR. However, the application of QMP in fermented foods is still limited.
QMP elucidated microbial succession of Taiwanese pickled cabbage. In the spontaneous first-round fermentation (FR), the 16S rRNA gene copies of total bacteria increased from 6.1 to 10 log copies mL. The dominant lactic acid bacteria genera were successively Lactococcus, Leuconostoc and Lactiplantibacillus. Despite the decrease in the proportion of Lactococcus during the succession, the absolute abundance of Lactococcus still increased. In the backslopping second-round fermentation (SR), the total bacteria 16S rRNA gene copies increased from 7.6 to 9.9 log copies mL. The addition of backslopping starter and vinegar rapidly led to a homogenous microbial community dominated by Lactiplantibacillus. The proportion of Lactiplantibacillus remained consistently around 90% during SR, whereas its absolute abundance exhibited a continuous increase. In SR without vinegar, Leuconostoc consistently dominated the fermentation.
The present study highlights that compositional analysis would misinterpret microbial dynamics, whereas QMP reflected the real succession profiles and unveiled the essential role of vinegar in promoting Lactiplantibacillus dominance in backslopping fermentation of Taiwanese pickled cabbage. Quantitative microbiome profiling (QMP) was found to be a more promising approach for the detailed observation of microbiome succession in food fermentation compared to compositional analysis. © 2024 Society of Chemical Industry.
微生物群落演替决定了发酵食品的风味和品质。基于定量聚合酶链反应（qPCR）的定量微生物组分析（QMP）已广泛应用于从绝对丰度角度分析微生物，通过将 16S 核糖体 RNA（16S rRNA）基因测序数据与 qPCR 定量的基因拷贝数进行归一化，将微生物群落比例转化为计数。然而，QMP 在发酵食品中的应用仍然有限。
QMP 阐明了台湾泡菜的微生物演替。在自发的第一轮发酵（FR）中，总细菌的 16S rRNA 基因拷贝数从 6.1 增加到 10 对数拷贝/mL。优势乳杆菌属依次为乳球菌属、肠球菌属和植物乳杆菌属。尽管在演替过程中乳球菌属的比例下降，但乳球菌属的绝对丰度仍在增加。在回灌第二轮发酵（SR）中，总细菌的 16S rRNA 基因拷贝数从 7.6 增加到 9.9 对数拷贝/mL。回灌 starter 和醋的添加迅速导致以植物乳杆菌为主导的同质微生物群落。在 SR 过程中，植物乳杆菌的比例一直保持在 90%左右，而其绝对丰度则持续增加。在没有醋的 SR 中，肠球菌属一直占主导地位。
本研究强调，组成分析会错误地解释微生物动态，而 QMP 则反映了真实的演替谱，并揭示了醋在促进植物乳杆菌在台湾泡菜回灌发酵中占据主导地位方面的重要作用。与组成分析相比，QMP 被发现是一种更有前途的方法，可以更详细地观察食品发酵中的微生物群落演替。© 2024 化学工业协会。
