Discovery of an intracellular parasite in Saccharomyces cerevisiae and Kluyveormyces marxianus, a novel case report

Saccharomyces cerevisiae, a key organism in industrial fermentation, is vulnerable to microbial contaminants causing stuck fermentation. During anaerobic fermentation optimization with baker’s yeast, recurrent fermentation arrest prompted microscopic analysis, revealing a novel coccoid, cocci-like, highly shaking intracellular parasiteparasite within S. cerevisiae and Kluyveromyces marxianus. The parasite exhibited intra- and extracellular localization, with intrinsic autofluorescence) enabling visualization via fluorescence microscopy without staining. Contaminated yeast samples were filtered (0.45 µm) and treated with lyticase to isolate the parasite. While filtration yielded extracellular parasites with diminished motility, lyticase-liberated intracellular forms lost motility rapidly, confirming host dependence. The parasite failed to grow axenically on YPD, NA, or blood agar. Phenotypic characterization identified it as Gram-positive, catalase-negative, and non-hemolytic, with transient susceptibility to streptomycin but no complete eradication. Parasite proliferation correlated with yeast growth phases, peaking during stationary phase and coinciding with fermentation failure. Notably, motility ceased upon yeast removal, implicating metabolic reliance on host-derived factors, while new yeast buds remained parasite-free, suggesting targeted invasion of mature cells. This symbiotic, bacteria-like organism’s autofluorescence provided a unique diagnostic marker, distinguishing it from prior fungal-bacterial associations. Its obligate pseudo-parasitic behavior and disruption of fermentation efficiency underscore its potential role in industrial fermentation challenges. These findings highlight the need for revised contamination control strategies and further research into its biology, transmission mechanisms, and host interactions to mitigate fermentation inefficiencies. The discovery emphasizes the underexplored complexity of microbial contaminants in industrial yeast systems and opens avenues for developing targeted interventions to safeguard fermentation productivity.