The newly sequenced gnome of non-sourdough-derived Kazachstania humilis MAW1 in terms of identification of factors inhibiting bacterial growth

Abstract

Background Ascomycetous budding yeasts are ubiquitous environmental microorganisms that are of great importance in food production and medicine. As a consequence of recent intensive genomic research, the taxonomy of yeast is becoming more organized based on the identification of monophyletic taxa, and 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. Results Previously, we isolated a yeast strain that impaired bio-hydrogen production in a dark fermentation bioreactor and also inhibited growth of Gram-positive (Clostridium butyricum, lactic acid bacteria strains) and Gram-negative (Escherichia coli, Citrobacter freundii, Klebsiella oxytoca, Pseudomonas putida) bacteria. Here, using next generation sequencing technologies, we sequenced the genome of this strain named K. humilis MAW1. This is the first sequenced genome of a K. humilis isolate not originating from a fermented food. This strain was examined by global phenotypic profiling, including carbon sources utilized and the influence of different stress conditions on growth. Using well-recognized bacterial model Escherichia coli AB1157 we show that K. humilis MAW1 cultivated in acidic medium inhibits bacterial growth by the disturbance of cell division, manifested by filament formation. Interestingly, under neutral (pH 7.0) conditions, stimulation of E. coli AB1157 growth was observed. To gain a greater understanding of 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 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. Conclusions We have characterized a non-sourdough-derived strain of K. humilis, including its genome sequence. The revealed here pH-dependent ability to inhibit bacterial growth has not been previously recognized in this species. Our study contributes to (i) the building of genome sequence-based classification and identification systems and (ii) the understanding of the bacteria-yeast interactions puzzle in the terms of food fermentation processes and search for novel antimicrobial factors.