Global Analysis of Public Cheese Microbiomes Reveals Widespread Bacterial Taxa and Geographic Community Structure

Cheese microbiomes remain difficult to compare globally because public sequencing datasets are fragmented and methodologically heterogeneous. Here, we curated 14,203 sequencing records from 233 BioProjects and retained 8910 records from 112 BioProjects for standardized reanalysis, establishing a global comparative framework for cheese microbiome research. Three taxonomic profiling pipelines (QIIME2, Kraken2 and mOTUs) recovered broadly consistent genus-level patterns dominated by lactic acid bacteria, although quantitative concordance varied between methods and study collections. Whole-genome shotgun analysis identified 12 widespread bacterial species independently detected in at least 50% of BioProjects by both Kraken2 and mOTUs, with Lactococcus lactis, Streptococcus thermophilus and Lactococcus cremoris detected in at least 84% of BioProjects in both analyses. Geographic structure remained evident after accounting for dominant community composition: sample-origin country explained 36.6% of community variation in the primary analysis and remained associated with community composition in balanced subsampling and analyses removing or continuously adjusting for five dominant lactic acid bacterial genera. However, public datasets were strongly geographically imbalanced, with European BioProjects dominating the available collection. Together, these results establish a reproducible framework and comparative baseline for investigating cheese microbiome diversity, geographic structure and cross-study patterns across globally distributed public sequencing datasets.