Yogurt is a cultured food, which means that it relies on live microbes to transform it from fresh milk into yogurt. It is generally made by mixing a small amount of active yogurt with milk, where the microbes are allowed to flourish and begin the process again. As with sourdough, this perpetuation means that individual strains may survive for a very long time. The microbes themselves have a very specialized and important role to play in the production of yogurt.

The two strains of bacteria used to make yogurt are Lactobacillus bulgaricus and Streptococcus thermophilus. It is theorized that these bacteria were accidentally introduced to fresh milk along with plant matter, since L. bulgaricus are closely related to a strain of plant-dwelling bacteria. Once the advantages of yogurt were seen, these bacteria were intentionally cultured in fresh milk to make more yogurt. S. thermophilus appears to have a symbiotic relationship with L. bulgaricus, since both are always present in successfully cultured yogurt.

Yogurt has several advantages over fresh milk, especially for a pre-industrial society. Most importantly, yogurt is far less perishable than fresh milk, particularly when no refrigeration is available. It is thicker than milk, which makes it easier to store and broadens its cooking applications. It gains a tart flavor that many people find appealing. Finally, since it contains less lactose than fresh milk, it is easier to digest, particularly for people with some form of lactose intolerance.

The basis of yogurt is the transformation of lactose into lactic acid by L. bulgaricus. This process makes the yogurt more acidic, which thickens the proteins in the milk and causes it to become more viscous. The acidity prevents colonization from other microbes, which aids in preservation. By breaking down lactose to make the lactic acid, the microbes lower the levels of lactose in the yogurt. It is unclear what role S. thermophilus plays in all of this, and it may be there simply to help L. bulgaricus fight off outside microbial invaders during the early stages of the process.

Since yogurt is cultured by mixing a bit of yogurt with milk, all yogurt-producing strains essentially share a common ancestor, stretching back from batch to batch. Living in fresh milk and yogurt was a striking change in environment from feeding off plant material, and the bacteria have altered their genetic makeup to match. Modern L. bulgaricus lacks several mechanisms for breaking down plant sugars that its wild cousins retain, while both L. bulgaricus and S. thermophilus have substantially altered their biology to fit more easily into the world of yogurt. In essence, the two species have been domesticated by long human cultivation.