Journal of Tea Science Research, 2024, Vol.14, No.2, 92-101 http://hortherbpublisher.com/index.php/jtsr 93 communities and their functional roles in tea fermentation. By integrating results from various studies, this study enhances the understanding of microbial dynamics in tea fermentation and offers insights for improving tea yield and quality. 2 Metagenomic Techniques 2.1 Evolution of metagenomic methods The field of metagenomics has evolved significantly over the past few decades, transitioning from traditional culture-based methods to advanced sequencing technologies. Initially, the study of microbial communities relied heavily on the isolation and cultivation of individual species, which was time-consuming and often biased towards easily cultivable organisms. The advent of high-throughput sequencing technologies, such as pyrosequencing and shotgun metagenomics, has revolutionized our understanding of microbial diversity by allowing the comprehensive analysis of microbial communities directly from environmental samples without the need for cultivation (Lyu et al., 2013; Zhao et al., 2015). 2.2 Current tools and technologies in metagenomics Modern metagenomic studies employ a variety of advanced tools and technologies to analyze microbial communities. Shotgun metagenomic sequencing, for instance, enables the sequencing of all genetic material in a sample, providing insights into the taxonomic composition and functional potential of the microbiota (Li et al., 2018; Landis et al., 2022). Additionally, metaproteomics, which involves the large-scale study of proteins expressed by microbial communities, complements metagenomic data by offering a functional perspective on microbial activity (Xie et al., 2019). Techniques such as 16S rRNA sequencing are also commonly used to identify and classify bacteria within complex communities (Wu et al., 2022). 2.3 Challenges in metagenomic analysis Despite the advancements in metagenomic techniques, several challenges remain. One major issue is the complexity of data analysis, as metagenomic datasets are often large and require sophisticated bioinformatics tools for processing and interpretation. Another challenge is the accurate assembly of metagenomic sequences, which can be hindered by the presence of highly similar sequences from different organisms (Landis et al., 2022). Additionally, the functional annotation of metagenomic data is complicated by the vast diversity of microbial genes, many of which have unknown functions (Xie et al., 2019). The integration of metagenomic data with other omics approaches, such as metaproteomics and metabolomics, requires careful consideration to ensure comprehensive and accurate interpretations. 3 Microbial Profiles in Different Tea Types 3.1 Microbial composition in green tea fermentation Green tea fermentation involves a diverse microbial community, primarily dominated by lactic acid bacteria (LAB) and yeasts. In the fermentation of Miang, a traditional fermented tea from northern Thailand, LAB such as Lactobacillus and Acetobacter were found to be the predominant bacterial genera, while Candida and Pichia were the main fungal genera (Unban et al., 2020). Similarly, in industrial-scale green tea kombucha fermentations, the bacterial community was dominated by Acetobacteraceae, with Oenococcus oeni being strongly associated with green tea fermentations (Coton et al., 2017). These microbial communities play crucial roles in the biochemical properties of the tea, contributing to its flavor and health benefits. 3.2 Microbial dynamics in black tea fermentation Black tea fermentation, particularly in kombucha, is characterized by a dynamic microbial community that includes both bacteria and yeasts. Studies have shown that the bacterial genus Komagataeibacter and the yeast Brettanomyces bruxellensis are the most common microbes in kombucha communities (Landis et al., 2022). The microbial diversity in black tea kombucha is influenced by the fermentation process, with significant shifts in the yeast community from Candida to Lachancea during the fermentation period (Chakravorty et al., 2016). Additionally, the presence of Gluconacetobacter europaeus and Acetobacter peroxydans has been noted as dominant species in black tea fermentations (Coton et al., 2017).
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