Ascomycetous budding yeasts are ubiquitous environmental microorganisms important in food production and medicine. Due to recent intensive genomic research, the taxonomy of yeast is becoming more organized based on the identification of monophyletic taxa. This includes genera important to humans, such as Kazachstania. Until now, Kazachstania humilis (previously Candida humilis) was regarded as a sourdough-specific yeast. In addition, any antibacterial activity has not been associated with this species. Previously, we isolated a yeast strain that impaired bio-hydrogen production in a dark fermentation bioreactor and inhibited the growth of Gram-positive and Gram-negative bacteria. Here, using next generation sequencing technologies, we sequenced the genome of this strain named K. humilis MAW1. This is the first genome of a K. humilis isolate not originating from a fermented food. We used novel phylogenetic approach employing the 18 S-ITS-D1-D2 region to show the placement of the K. humilis MAW1 among other members of the Kazachstania genus. This strain was examined by global phenotypic profiling, including carbon sources utilized and the influence of stress conditions on growth. Using the well-recognized bacterial model Escherichia coli AB1157, we show that K. humilis MAW1 cultivated in an acidic medium inhibits bacterial growth by the disturbance of cell division, manifested by filament formation. To gain a greater understanding of the inhibitory effect of K. humilis MAW1, we selected 23 yeast proteins with recognized toxic activity against bacteria and used them for Blast searches of the K. humilis MAW1 genome assembly. The resulting panel of genes present in the K. humilis MAW1 genome included those encoding the 1,3-β-glucan glycosidase and the 1,3-β-glucan synthesis inhibitor that might disturb the bacterial cell envelope structures. We characterized a non-sourdough-derived strain of K. humilis, including its genome sequence and physiological aspects. The MAW1, together with other K. humilis strains, shows the new organization of the mating-type locus. The revealed here pH-dependent ability to inhibit bacterial growth has not been previously recognized in this species. Our study contributes to the building of genome sequence-based classification systems; better understanding of K.humilis as a cell factory in fermentation processes and exploring bacteria-yeast interactions in microbial communities.

中文翻译：

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解锁非酵母 Kazachstania humilis MAW1 的基因组：深入了解抑制因子和表型特性

子囊菌芽殖酵母是普遍存在的环境微生物，在食品生产和医学中发挥着重要作用。由于最近深入的基因组研究，基于单系类群的鉴定，酵母的分类学变得更加有组织。这包括对人类重要的属，例如哈萨克斯坦。到目前为止，Kazachstania humilis（以前的 Candida humilis）被认为是酸面团专用酵母。此外，尚未发现任何抗菌活性与该物种有关。此前，我们分离出了一种酵母菌株，该菌株会损害暗发酵生物反应器中的生物氢生产并抑制革兰氏阳性菌和革兰氏阴性菌的生长。在这里，我们利用下一代测序技术，对这种名为 K. humilis MAW1 的菌株的基因组进行了测序。这是第一个非源自发酵食品的矮堇菜分离株的基因组。我们使用新颖的系统发育方法，利用 18 S-ITS-D1-D2 区域来显示 K. humilis MAW1 在哈萨克斯坦属其他成员中的位置。通过整体表型分析对该菌株进行了检查，包括利用的碳源以及应激条件对生长的影响。使用公认的细菌模型大肠杆菌 AB1157，我们发现在酸性培养基中培养的 K. humilis MAW1 通过扰乱细胞分裂（表现为细丝形成）来抑制细菌生长。为了更好地了解 K. humilis MAW1 的抑制作用，我们选择了 23 种具有公认的细菌毒性活性的酵母蛋白，并将它们用于 K. humilis MAW1 基因组组装的 Blast 搜索。由此产生的 K. humilis MAW1 基因组中存在的基因组包括编码 1,3-β-葡聚糖糖苷酶和可能扰乱细菌细胞包膜结构的 1,3-β-葡聚糖合成抑制剂的基因。我们对非酵母来源的矮矮酵母菌株进行了特征分析，包括其基因组序列和生理方面。 MAW1 与其他 K. humilis 菌株一起显示了交配型基因座的新组织。这里揭示的 pH 依赖性抑制细菌生长的能力以前在该物种中尚未被认识到。我们的研究有助于建立基于基因组序列的分类系统；更好地了解 K.humilis 作为发酵过程中的细胞工厂，并探索微生物群落中细菌-酵母的相互作用。