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The microbial community of industrially produced Canadian Cheddar cheese was examined from curd to ripened cheese at 30–32 months using a combination of viable plate counts of SLAB (GM17) and NSLAB (MRSv), qPCR and 16S rRNA gene amplicon sequencing. Cell treatment with propidium monoazide excluded DNA of permeable cells from amplification. The proportion of permeable cells of both <i>Lactococcus</i> spp. and <i>Lacticaseibacillus</i> spp. was highest at 3–6 months. While most remaining <i>Lacticaseibacillus</i> spp. cells were intact during later ripening stages, a consistent population of permeable <i>Lactococcus</i> spp. cells was maintained over the 32-month period. While <i>Lactococcus</i> sequence variants were significant biomarkers for viable cheese curd communities at 0–1 m, <i>Lacticaseibacillus</i> was identified as a distinctive biomarker for cheeses from 7 to 20 months. From 24 to 32 months, <i>Lacticaseibacillus</i> was replaced in significance by four genera (<i>Pediococcus</i> and <i>Latilactobacillus</i> at 24 m and at 30–32 m, <i>Secundilactobacillus</i> and <i>Paucilactobacillus</i>). These results underscore the importance of monitoring potential defects in cheeses aged over 24 months, which could be diagnosed early through microbial DNA profiling to minimize potential waste of product. Future perspectives include correlating volatile flavor compounds with microbial community composition as well as the investigation of intra-species diversity.