Sequencing of Kombucha-associated microbes

Kombucha Tea (KT), a fermented tea with roots in traditional Chinese medicine, has surged in worldwide popularity due to its purported health benefits. KT contains a symbiotic culture of yeast and bacterial species, many of which are considered human probiotics. The molecular basis of the health benefits of KT has yet to be thoroughly explored in any animal model. We establish C. elegans as a model to query the molecular interactions between Kombucha-associated microbes (KTM) and the host. To identify Kombucha-associated microbes, we isolated 1) the microbes from the fermenting Kombucha culture, 2) the pool of microbes fed to the C. elegans animals on NGM plates, and 3) the microbes that colonize the gut of the nematodes feeding on KTMs. We then performed 16S and 18S rDNA sequencing of the Kombucha Tea microbiome and the KTMs seeded to NGM plates, as well as whole genome sequencing of the individual microbial isolates. We find that the gut microbiome of nematodes consuming a KTM-exclusive diet closely mirrors the microbial community found in the fermenting culture. Moreover, the whole genome sequencing of individual microbes revealed that the core microbial species in our Kombucha culture are Komagataeibacter rhaeticus, Acetobacter tropicalis, and Zygosaccharomyces bailli.

康普茶（Kombucha Tea, KT）是一款起源于中医药的发酵茶饮，因据称具备健康益处而在全球范围内迅速走红。康普茶含有酵母与细菌构成的共生培养体系，其中多数菌株被视为人类益生菌。目前尚未有任何动物模型能够完整阐明康普茶健康益处的分子机制。本研究以秀丽隐杆线虫（C. elegans）为模型，探究康普茶相关微生物（Kombucha-associated microbes, KTM）与宿主之间的分子互作关系。为明确康普茶相关微生物的组成，本研究分别分离了三类样本中的微生物：1）发酵中的康普茶培养物内的微生物；2）接种于NGM培养基平板、用于饲喂秀丽隐杆线虫的微生物群落；3）以KTM为食的线虫肠道内定殖的微生物。随后，本研究对康普茶微生物组以及接种至NGM平板的KTM进行了16S及18S rDNA测序，同时对分离得到的单株微生物开展全基因组测序。研究发现，以纯KTM为食的线虫肠道微生物组与发酵培养物中的微生物群落结构高度相似。此外，单株微生物的全基因组测序结果显示，本研究使用的康普茶培养物的核心微生物类群为葡糖醋杆菌（Komagataeibacter rhaeticus）、热带醋酸杆菌（Acetobacter tropicalis）以及拜耳接合酵母（Zygosaccharomyces bailli）。