茶飲料在全世界廣受消費者喜愛。以發酵程度分成不發酵、部分發酵、全發酵與後發酵茶，不同發酵程度的茶葉具有獨特的風味和口感，而影響茶葉品質的原因繁多，製作過程、氣候地理環境因素、茶樹品種等。後發酵茶因製作過程中經過微生物發酵(渥堆)而產生獨特風味，然而微生物在部分發酵與全發酵茶的製茶步驟影響的研究相對較少。本實驗的茶葉製程研究取樣自阿里山石棹茶園，而茶葉產品的真菌相研究則購自市面產品。本研究採用多源基因體學方法了解茶葉真菌相，較傳統培養法可呈現更完整的菌相組成。結果顯示，真菌物種數與多樣性從原料、萎凋至發酵步驟逐漸增加。主成份分析發現部分發酵與全發酵呈現兩個不同的真菌變動趨勢，且在萎凋步驟就已經出現顯著差異。比較製程各階段的真菌相發現，各階段共有的真菌 OTU 有193種，占總菌相比例達到97%，顯現萎凋和發酵步驟的優勢菌種為原本就存在於茶葉上的真菌。在茶葉成品中的真菌菌相在各樣本間差異大，真菌分佈與茶葉發酵程度關聯性低。而產地對於原料上真菌的影響可能也在殺菁後與成品產生區隔。本研究針對茶葉中的有益成分茶黃素、GABA與洛伐他丁 (Lovastatin)，將茶葉上與其生合成相關的真菌菌種視為潛在的有益真菌。結果顯示潛在有益菌集中在麴黴菌屬 (Aspergillus)，主要出現在全發酵茶與後發酵茶中。綜合以上發現，參與茶葉製程萎凋與發酵步驟的真菌多數來自原料，在茶菁發酵後到成品的過程真菌種類大幅降低，而全發酵與後發酵茶可能含有更多能合成有益成份的真菌。

Tea is one of the most popular beverages consumed in the world and its biological activities and health benefits have been widely explored. According to the extent of fermentation, tea can be categorized to four groups, namely non-fermented, partially-fermented, completely-fermented, and post-fermented. Many factors, including manufacturing, climate, geography and tea races, affect the tea quality, whereas the role of microbiomes remains unclear. Here, the microbial communities in tea leaves were investigated by amplicon-based metagenomics. Multiple rarefactions showed a trend with species richness and Shannon diversity increasing from raw material, withered semi-product, to fermented semi-products. By using principal component analyses (PCA), I found that partially- and completely-fermented tea showed distinct microbial communities at the withering step. In total 193 OTU were shared among the tea manufacturing steps, counting for at least 97% of the relative abundance across all steps, indicating that the fungi involved in tea-making process mostly originated from tea leaves. Hierarchical clustering analyses suggested that the composition of tea microbiomes is related to the local flora. Interestingly, several Aspergillus species that may produce beneficial metabolites, including theaflavin, GABA, and lovastation, were found in tea leaves. Aspergillus spp were most abundant in the post-fermented tea.

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