本研究旨在探討發酵畢赤酵母 Pichia fermentans（Pf菌）與嗜酸球乳桿菌 Pediococcus acidilactici（Pa菌）應用於台灣東山地區阿拉比卡鐵皮卡品系咖啡生豆二次發酵中的潛力與實際影響，並針對發酵過程中微生物菌相動態、特定內含物變化，以及最終風味品質進行綜合性分析與評估。東山地區雖擁有良好氣候與栽培條件，但當地咖啡普遍缺乏風味辨識度與品牌價值，因此本研究以控制型二次發酵作為風味提升策略，藉由選用具發酵潛力之Pf與Pa菌株，進行生豆的發酵處理。實驗設計分為單菌組(僅Pf菌)與共發酵組(Pf+Pa菌共施用)，透過次世代定序技術（NGS）分析菌相組成變化，並與未發酵組作為對照進行HPLC定量，分析咖啡因與綠原酸含量，同時搭配甜度與感官杯測進行風味表現評估。結果顯示，在特定處理組別中，微生物群落的穩定性與組成出現差異，Pf菌為真菌群中的絕對優勢菌種，而Pa雖佔比不高，仍能穩定定殖。部分菌株可能透過代謝作用參與綠原酸等酚類物質的轉化，進一步影響酸質表現。感官分析則顯示，發酵處理後於甜度與平衡度上表現相對穩定，風味表現趨於集中一致。整體而言，本研究證實Pf與Pa菌共發酵技術可穩定咖啡豆發酵過程中之菌相結構，提升甜感與酸質表現，改善整體感官品質，對於提升東山咖啡的市場辨識度與附加價值具有潛力，並為未來台灣特色咖啡之差異化開發與機能性加工提供具體應用依據。

This study explores the application of Pichia fermentans (Pf) and Pediococcus acidilactici (Pa) in the secondary fermentation of Arabica Typica green coffee beans from Dongshan, Taiwan. Through next-generation sequencing (16S and ITS), HPLC, °Brix sweetness, and sensory evaluation, the effects on microbial dynamics, chemical composition, and flavor quality were assessed. Results showed that Pseudomonas antarctica dominated the bacterial community, while Pa remained stably present and potentially contributed to acidity and flavor modulation. In the fungal community, Pf showed over 99% relative abundance across treatments, indicating strong adaptability and dominance. Although overall microbial diversity was low, the Pf+Pa group exhibited more stable fungal diversity. HPLC results showed little change in caffeine levels, but chlorogenic acid slightly increased in the Pf group and significantly decreased in the Pf+Pa group, suggesting enzymatic degradation by Pa. Sensory analysis revealed that the Pf+Pa group achieved the highest scores in aroma, sweetness, flavor, aftertaste, balance, and overall impression, with the highest °Brix and lowest pH. These findings suggest that Pf and Pa co-fermentation can improve flavor complexity and offer a promising strategy for enhancing the quality and market identity of Taiwanese specialty coffee.

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