Department of Biology, Tufts University, Medford, Massachusetts, USA.
Committee on Microbiology, University of Chicagogrid.170205.1, Chicago, Illinois, USA.
mSystems. 2022 Jun 28;7(3):e0015722. doi: 10.1128/msystems.00157-22. Epub 2022 Jun 7.
Despite the popularity of kombucha tea, the distribution of different microbes across kombucha ferments and how those microbes interact within communities are not well characterized. Using metagenomics, comparative genomics, synthetic community experiments, and metabolomics, we determined the taxonomic, ecological, and functional diversity of 23 distinct kombuchas from across the United States. Shotgun metagenomic sequencing demonstrated that the bacterium Komagataeibacter rhaeticus and the yeast Brettanomyces bruxellensis were the most common microbes in the sampled kombucha communities. To determine the specificity of bacterium-yeast interactions, we experimentally quantified microbial interactions within kombucha biofilms by measuring densities of interacting species and biofilm production. In pairwise combinations of bacteria and yeast, and individual strains of spp. were sufficient to form kombucha fermentations with robust biofilms, but Zygosaccharomyces bisporus, another yeast found in kombucha, did not stimulate bacteria to produce biofilms. Profiling the spent media of both yeast species using nuclear magnetic resonance spectroscopy suggested that the enhanced ability of to ferment and produce key metabolites in sucrose-sweetened tea may explain why it stimulates biofilm formation. Comparative genomics demonstrated that spp. with >99% genomic similarity can still have dramatic differences in biofilm production, with strong producers yielding five times more biofilm than the weakest producers. Through an integration of metagenomic and experimental approaches, our work reveals the diversity and nature of interactions among key taxa in kombucha microbiomes through the construction of synthetic microbial pairs. Manipulation of these microbes in kombucha has the potential to shape both the fermentation qualities of kombucha and the production of biofilms and is valuable for kombucha beverage producers, biofilm engineers, and synthetic ecologists.
尽管康普茶广受欢迎，但不同微生物在康普茶发酵中的分布情况以及这些微生物在群落中的相互作用方式尚不清楚。本研究采用宏基因组学、比较基因组学、合成群落实验和代谢组学方法，对来自美国各地的 23 种不同康普茶进行了研究，以确定其分类学、生态学和功能多样性。 高通量宏基因组测序表明，细菌科特氏菌（Kombagataeibacter rhaeticus）和酵母布鲁塞尔假丝酵母（Brettanomyces bruxellensis）是样本中康普茶群落中最常见的微生物。为了确定细菌-酵母相互作用的特异性，我们通过测量相互作用物种的密度和生物膜的产生，实验量化了康普茶生物膜内微生物的相互作用。在细菌和酵母的两两组合中， 和 种的单个菌株足以形成具有健壮生物膜的康普茶发酵，但在康普茶中发现的另一种酵母 Zygosaccharomyces bisporus 不能刺激细菌产生生物膜。使用核磁共振波谱对两种酵母物种的废培养基进行分析表明， 能够发酵和产生蔗糖甜茶中的关键代谢物的能力增强，这可能解释了它为什么能刺激生物膜的形成。比较基因组学表明，基因组相似度 > 99%的 种仍可能在生物膜产生方面存在显著差异，强生产者的生物膜产量是最弱生产者的五倍。 通过整合宏基因组学和实验方法，我们的工作揭示了康普茶微生物组中关键类群之间相互作用的多样性和性质，通过构建合成微生物对。在康普茶中对这些微生物进行操纵有可能改变康普茶的发酵特性以及生物膜的产生，这对于康普茶饮料生产商、生物膜工程师和合成生态学家都具有重要价值。
