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Cheese Fermentation: Lactic Acid Bacteria, Rennet, Aging & the Microbial Transformation of Milk

Clinical overview, safety guidelines, and evidence-graded applications for Cheese Fermentation: Lactic Acid Bacteria, Rennet, Aging & the Microbial Transformation of Milk.

Evidence Based Editorial Team: NutritionColours Editorial Team

Overview

Cheese is milk transformed by bacteria (and sometimes mold) working alongside coagulation. Starter cultures — most commonly Lactococcus lactis, Streptococcus thermophilus, and various Lactobacillus species — acidify the milk and set the flavor base, while secondary cultures shape the finished cheese: Propionibacterium produces the characteristic holes (“eyes”) in Swiss-style cheeses, Penicillium strains create the blue veining in Roquefort and Gorgonzola or the white bloomy rind on Brie and Camembert, and Brevibacterium linens produces the orange-red washed rinds and pungent aroma of cheeses like Limburger and Taleggio.

Coagulation: acid vs. rennet

Milk solids can be set two ways. Acid coagulation (used for fresh cheeses like ricotta, queso blanco, and paneer) relies on lowering the pH until casein proteins clump. Rennet coagulation uses the enzyme chymosin — traditionally sourced from calf stomach, but now commonly produced as microbial or fermentation-derived (vegetarian) rennet — to form a firmer curd, which is the basis for most aged cheeses.

Cheese categories

  • Fresh, unaged: ricotta, mozzarella, feta, queso fresco, cottage cheese, mascarpone — high moisture, mild, short shelf life.
  • Aged hard cheeses: cheddar, Parmigiano-Reggiano, Gruyère, Pecorino Romano — lower moisture, concentrated flavor, months to years of aging.
  • Blue-veined: Roquefort, Gorgonzola, Stilton — inoculated with Penicillium roqueforti and aged with air channels that let mold develop.
  • Soft-ripened (bloomy rind): Brie, Camembert — surface-ripened by Penicillium camemberti, softening from the outside in.
  • Washed rind: Limburger, Époisses, Munster — rinds washed in brine or alcohol during aging, encouraging B. linens growth.

Nutritional changes during fermentation and aging

Fermentation and aging alter cheese’s nutrient profile compared with fluid milk. Lactose is substantially broken down by bacterial fermentation — well-aged hard cheeses (such as cheddar or Parmesan) contain only trace amounts and are often tolerated by people with lactose intolerance. Protein and calcium become more concentrated per gram as whey and moisture are removed. Some cheeses, particularly soft and surface-ripened varieties, also contain vitamin K2 (as MK-8 and MK-9) produced by bacteria during fermentation.

Safety notes

Soft, mold-ripened, and unpasteurized cheeses carry a higher risk of Listeria monocytogenes contamination than hard, aged, or processed cheeses. The U.S. FDA and CDC advise that pregnant people, older adults, young children, and immunocompromised individuals avoid soft cheeses (such as brie, Camembert, blue-veined, feta, and queso fresco) unless the label confirms they are made from pasteurized milk.

Sources

  • U.S. FDA / CDC — food safety guidance on Listeria risk and soft cheeses during pregnancy
  • USDA FoodData Central — fdc.nal.usda.gov

Clinically reviewed by Dr. Shilpa Thakur. Last reviewed 2026-07-20. Educational information, not medical advice.