Exploring the rare and abundant bacterial community structures and their metabolic differences in various types of qula cheese

Abstract

Qula is a fermented cheese-like product made from yak milk. Although the bacterial communities in qula have been well documented, the diversity and functions of both abundant and rare bacterial subcommunities are still unclear. Here, our study examines the community structures of abundant and rare taxa, as well as their metabolite profiles, in the distinct qula samples from Tibet, China, employing high-throughput sequencing and untargeted metabolomics. Our results indicate that rare bacterial taxa account for 98.15 % of total operational taxonomic units and 48 % of total sequences. Dominant bacteria from abundant taxa consist of Lactococcus, Lactobacillus, and Acetobacter, while rare taxa contain Prevotella, Ruminococcus, and Butyrivibrio. Furthermore, we show that stochastic processes predominantly influence bacterial assembly in qula microbial communities. Specifically, stochastic processes have a more significant impact on community assembly for rare taxa, while deterministic processes are more important for abundant taxa. Moreover, we evaluate the contributions of rare taxa to network complexity and community stability, identifying potential keystone species. By analyzing metabolic profiles, we further compared the differences in metabolic functions between rare and abundant taxa in the qula microbiome. Our study shows that, along with abundant taxa, rare taxa in the qula microbiome play a significant role in community assembly and interactions, offering valuable insights into the microbial ecosystems of traditional fermented foods.