This study aims to investigate the microbial composition of koumiss made via traditional methods in Kyrgyz mountain pastures. We collected koumiss samples produced in plastic (P), wood (T), and leather (D) containers at household settings. These samples were subjected to shotgun metagenomic sequencing. As a result of the metagenome analyses, we identified a diversity of bacteria, yeasts, bacteriophages, and archaea in koumiss produced within different containers. Koumiss' microbial community was predominantly composed of lactic acid bacteria (LAB), particularly Lactobacillus helveticus and Lactococcus lactis. Additional LAB species such as Lactobacillus kefiranofaciens, Lactococcus raffinolactis, Lactiplantibacillus plantarum, and Lactococcus cremoris, as well as non-LAB taxa such as Kluyvera intermedia, Raoultella planticola, and Hafnia alvei were also identified as part of the koumiss microbiota. Nonetheless, the opportunistic pathogen, Enterobacter hormaechei, was among the detected species. The most abundant yeast species was identified as Brettanomyces bruxellensis. Other yeast species involving Monosporozyma unispora, Monosporozyma servazzii, and Yarrowia lipolytica were also detected within the metagenome. Despite the type of container material not significantly affecting the microbial diversity, Bifidobacterium spp. and bacteriophages were identified at higher levels in plastic containers. We detected various antimicrobial resistance genes and gene clusters that produce bioactive compounds within koumiss samples. This study highlights koumiss' rich microbial composition and its potential health impacts. It underscores the importance of effectively utilizing metagenomic and bioinformatics methods for better comprehension of the microbiota of koumiss.