味噌是黃豆發酵製品。黃豆有豐富植物性蛋白質，其經自然發酵伴隨產生的次代謝物使味噌具獨特風味。味噌含不少種類乳酸菌、酵母菌及米麴菌類微生物，這些微生物發酵作用產生的多種酵素能幫助人體消化食物與吸收。味噌的健康美味以及方便性，已成為東亞人民生活中重要的食材。味噌依麴菌發酵時間與原料比例不同發展出多樣化類型的味噌；有米味噌、豆味噌、麥味噌及特殊味噌等，其風味、顏色、口感與香氣也不盡相同。為了深入了解台灣及日本幾種代表性味噌，本研究藉由多源基因體學結合DNA條碼的分析，探討台灣、日本不同地區、不同種類味噌的細菌相及真菌相，以了解菌種的分佈對味噌發酵過程的影響。本研究依Illumina 技術進行大規模定序，選取十二種味噌(含淡黃味噌、甜白味噌、紅味噌)進行16S rRNA以及ITS片段定序以解析各實驗組間菌相，結果顯示，十二個味噌樣本中，以日本青森KANESA甜白味噌含細菌物種豐度最高，名古屋豆味噌細菌物種豐度最低。以主成分分析台灣味噌與日本味噌，兩產地味噌的細菌相不具明顯差異。另外，針對淡黃味噌、甜白味噌及紅味噌探討，此三種類味噌之間的細菌相也不具明顯差異。台灣產味噌菌相的組成較日本產味噌單純，主要菌相組成以葡萄球菌科 (Staphylococcaceae)、明串珠菌科 (Leuconostocaceae)及乳酸桿菌科 (Lactobacillaceae)為主。而日本味噌除了含有上述菌科外，還富含鞘脂單胞菌科 (Sphingomonadaceae)、叢毛單胞菌科 (Comamonadaceae)、腸內球菌 (Enterococcaceae)以及鏈球菌科(Streptococcaceae)等細菌。台灣味噌明串珠菌科細菌占的比例較日本味噌多出許多，此現象和台灣悶熱潮溼氣候有關。藉由細菌類群差異分布分析，可初步看出味噌樣本有因產地接近而細菌相組成較相似的趨向。但其中一個意外的發現是，台灣十全味噌與鹿兒島麥味噌細菌相組成非常相似，此兩種味噌產地間距離遠，也屬於不同類型的味噌，推論製造過程中有人為製麴交流之可能性。此外，各味噌樣本中之真菌組成單純，平均95%以上序列對應至米麴菌(Aspergillus oryzae)，為味噌發酵最主要作用之真菌。此外，有非常少比例的假絲酵母菌屬(Candida)及黃麴黴菌(Aspergillus flavus)存在，其中黃麴黴菌所產生的黃麴毒素可能會污染味噌，因此，味噌在使用中的保存環境是需要非常留意的。

Miso is a fermented soybean paste widely used in Eastern Asia. The benefits of miso are associated with its tremendous nutrient profile, including iron, calcium, B vitamins, isoflavones, and essential amino acids. Noticeably, there are probiotics in miso. Koji (cereal grains with the mold Aspergillus oryzae) is as a major source of the microorganisms involved in miso fermentation. Many secondary metabolites are released from fermentation process and make miso flavorful. However, the diversity of microbiome in miso has not been comprehensively investigated, especially for different types of miso. In this study, twelve samples covered three types of miso, white, light yellow, and red miso, were chosen for microbiome examination. The composition of microbiome in miso was determined by Illumina sequencing with bacterial 16S and fungal ITS amplicons. Here, Staphylococcaceae, Leuconostocaceae and Lactobacillaceae were detected with high relative abundance in all Taiwanese miso. On the other hand, in Japanese Miso, besides the 3 predominant bacterial families, a more diverse composition was detected, including Sphingomonadaceae, Comamonadaceae, Enterococcaceae and Streptococcaceae. We found that Leuconostocaceae was significantly more abundant in Taiwanese miso than in Japanese miso, possibly resulting from the humid climate of Taiwan. Surprisingly, one Taiwanese miso shared large proportion of the microbiome with a Japanese miso, implying that a possible flow of koji from Japan to Taiwan. Furthermore, in the fungal composition, except for the predominant fermentation agent A. oryzae, some bad fungi such as Candida and A. flavus were detected. Therefore, the storage conditions of miso should be carefully noticed.

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