Deciphering the microbiome shift during fermentation of medicinal plants

As the importance of the human microbiome for health and the well-being of each individual is becoming more and more apparent, it awakes the desire of influencing it. Fermented food and lactic acid bacteria (LAB) display the possibility to prevent microbial dysbioses and diseases, but their ecology on plants is less understood. To get insight into the microbiome of original and fermented medicinal plants, Matricaria chamomilla L. and Calendula officinalis L. leaves were fermented and the process was monitored over a period of six weeks. The starting samples were characterized by a distinct phyllosphere microbiome, while the endosphere revealed a high similarity. During fermentation, significant microbial shifts were observed, whereby LAB were enhanced in all approaches but never dominated. Among the LAB, Enterococcaceae were identified as the most dominant family in both plants. The remaining LAB community differed remarkably: M. chamomilla revealed higher relative abundances of Lactobacillaceae and Carnobacteriaceae, while C. officinalis showed higher presence of Leuconostocaceae and Streptococcaceae. The natural leaf microbiome and the indigenous LAB communities of field-grown Asteraceae medicinal plants are plant-specific and habitat-specific and are subjected to significant shifts during fermentation. Besides the leaf surfaces, also the leaf endosphere was identified as source for biopreservative LAB.

随着人体微生物组对个体健康与福祉的重要性日益凸显，调控该微生物组的诉求也随之浮现。发酵食品与乳酸菌（lactic acid bacteria, LAB）具备预防微生物群落失调与相关疾病的潜力，但目前学界对其在植物表面的生态特征仍知之甚少。为探究原生与发酵药用植物的微生物组特征，本研究对母菊（Matricaria chamomilla L.）与金盏花（Calendula officinalis L.）的叶片开展发酵实验，并对发酵过程进行为期六周的监测。初始样本呈现出独特的叶围（phyllosphere）微生物组结构，而叶内（endosphere）微生物组则表现出较高的相似性。发酵过程中，微生物群落发生了显著演替：所有实验组的乳酸菌丰度均得到提升，但始终未成为优势类群。在乳酸菌类群中，肠球菌科（Enterococcaceae）被确定为两种植物叶片中最优势的菌科。其余乳酸菌类群则存在显著差异：母菊叶片中乳杆菌科（Lactobacillaceae）与肉杆菌科（Carnobacteriaceae）的相对丰度更高，而金盏花叶片中明串珠菌科（Leuconostocaceae）与链球菌科（Streptococcaceae）的占比更高。田间种植的菊科（Asteraceae）药用植物的天然叶部微生物组与土著乳酸菌群落具有植物特异性与生境特异性，且在发酵过程中会发生显著的群落演替。除叶表生境外，叶内微生物组同样被证实为生物防腐用乳酸菌的潜在来源。