by Christina Agapakis

Scoop a spoonful of yogurt into a pot of warm milk and soon bacteria will start to bloom. The billions of Lactobacilli from the yogurt are surrounded by the rich milky environment. There are plenty of nutrients, sugars, proteins and fats that help the bacteria grow strong and multiply fast.

As they grow and divide they turn the milk sugar lactose into lactic acid (that’s why Lactobacilli are often called “lactic acid bacteria”). Lactic acid is a waste product for Lactobacillus cells and it’s what gives you a muscle cramp when you’re exercising hard, but it’s also the molecule that turns milk into yogurt. The acid has a tart taste and makes proteins stick together, turning milk into tangy, thick and creamy yogurt. Most important of all, the acid stops other bacteria from growing, protecting the milk from spoiling and protecting you from food poisoning. Lactic acid bacteria are so effective for preserving food that the same process is used to make cheese, sauerkraut, kimchi, pickles, and many other fermented foods.

Yogurt is alive, reproducing generation after generation from one batch to the next. Yogurt is also the longest running experiment on bacterial evolution, stretching thousands of years and millions of bacterial generations. Each batch of yogurt selects for bacteria that are better able to digest milk and better able to produce lactic acid. This selective pressure means that over the years Lactobacillus has evolved for life in milk.

To understand how Lactobacillus evolved, imagine starting with your fresh pot of yogurt and rewinding back through every batch backwards through time. Trillions of bacteria condensing back into single cells, spoonfuls of yogurt jumping out of fresh milk and back to the older batch. Now imagine all the way back to the very first time someone was brave enough to taste milk that had gotten thick and tart after being left out for too long. How was this first batch of yogurt made? Where did the first yogurt bacterium come from?

We can guess that the earliest yogurts were made thousands of years ago by accident. We can speculate about bacteria getting into the milk from the udder of a cow or from a dirty milking bucket. But we can also look deep into the DNA of different strains of Lactobacillus for clues about how they evolved for life in yogurt. In the genomes of different Lactobacillus strains we can see evolution in action.

There are over one hundred different species in the Lactobacillus genus, each specialized for the different environments where they’re found, from milk to cabbage to the human body. Lactobacillus bulgaricus is the most common type of yogurt bacteria, and its genome has evolved through the millennia of yogurt making to be specialized for digesting lactose. While the ancestral species lives on plants and can survive in many different conditions, L. bulgaricus slowly lost the genes that aren’t strictly necessary for life in milk and its genome is much smaller and simpler than other species.

There are other species of Lactobacillus that are equally specialized for a rich environment that is very hospitable to bacteria: your large intestine. The Lactobacilli living in your gut keep your digestion and your immune system healthy in many ways, including keeping away more dangerous bacteria, like how Lactobacilli protect yogurt from spoiling. Eating yogurt and other probiotic foods (the word probiotic comes from the Latin and Greek words pro–“for” and biotic–“life”) with live cultures can help to keep the microbes in your gut happy, keeping you healthy and strong.


1. Van de Guchte M, Penaud S, Grimaldi C, Barbe V, Bryson K, Nicolas P, Robert C, Oztas S, Mangenot S, Couloux A: The complete genome sequence of Lactobacillus bulgaricus reveals extensive and ongoing reductive evolution. Proc Natl Acad Sci USA 2006, 103:9274–9279.

2. Ventura M, O’Flaherty S, Claesson MJ, Turroni F, Klaenhammer TR, van Sinderen D, O’Toole PW: Genome-scale analyses of health-promoting bacteria: probiogenomics. Nat Rev Micro 2008, 7:61–71.

About the Author

Christina Agapakis is a synthetic biologist at UCLA interested in the structure, evolution and design of the microbial communities that help us to produce and digest our food. Her research is collaborative and multidisciplinary, working with engineers, artists, and designers and ranging from the ecology of soil to skin to cheese. She blogs at the Oscillator on Scientific American and tweets at @thisischristina.