A Microbiologist’s Guide to Yogurt + Instant Pot Yogurt Recipe

Last year, I made 26 batches of homemade yogurt and ate probably over 350 yogurt and granola breakfasts (or some variation of that). Since I left the world of laboratory bench work, the kitchen has become my lab, a place to create edible experiments to satisfy my microbial curiosities. From sourdough to kefir to kombucha to yogurt, I have found that yogurt is the one I’ve most consistently stuck to. Here, I’ll share with you how I make yogurt, some tips and tricks, and some of the science behind the scenes.

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What microbes are involved in yogurt and where do they come from?

The most common microbes in yogurt come from the bacteria Streptococcus thermophilus and Lactobacillus bulgaricus. Like many fermented foods, yogurt was probably first created by accident. Now, these bacteria are often cultured along with other lactic acid bacteria (for example, Lactobacillus acidophilus, Lactobacillus casei, and Bifidobacterium adolescentis) and if you look at the container of store bought yogurt, you’ll see these listed on the container.

(Fun fact: CRISPR technology has a yogurt origin story. It was in S. thermophilus that the CRISPR system was first identified. In 1987, scientists at the food company Danisco found that the CRISPR system defended this bacterium from viral attack.)

Do yogurt probiotics have any effect on the gut microbiome?

There’s mixed evidence about whether fermented foods have an effect on the gut microbiome. For yogurt, it’s the same story. 

• In one study, participants consumed yogurt for six weeks and found no significant shifts in bacterial abundance in the gut microbiome. In fact, some studies say that probiotics don’t have any known benefits in healthy individuals. 
• Another study finds that after four weeks, yogurt consumption reduced the ratio of intestinal E. coli to Bifidobacterium spp. and H. pylori levels in children infected with H. pylori.
• Another study found that two yogurt bacteria, Lactobacillus delbrueckii subsp. bulgaricus and Streptococcus thermophilus can be identified after passing through the human gut after eating yogurt. Viable bacteria was found in fecal samples suggesting that they can indeed survive passage through the stomach and intestines.

Despite these mixed results, a cup of yogurt does have other benefits: it’s a good source of protein, calcium, and other vitamins, lower in lactose, and potentially has other health benefits.

My yogurt making journey

When I first started making yogurt, I had a dedicated yogurt maker to do this. The yogurt maker could culture up to seven glass jars. While this method left me with one-serving sized portions, I found it to be a little limiting and more work than needed. I had to heat the milk in another pan, pour the mixture into the jars and then I was left with a lot of jars and lids to clean up. Plus, since I was eating it every morning, I needed to scale up and make more at one time.

I then moved onto the Instant Pot which we got as a gift a few years ago. With the Instant Pot, I could make half a gallon to one gallon of yogurt at a time, without needing to separate everything into individual jars. Over the years and many many batches, I’ve tweaked my method and now I’m excited to share it with you.

About the starter culture

First, the starter culture. To make a new batch of yogurt, you’ll need a starter culture to “seed” new batches of yogurt with bacteria. For simplicity sake, I use store bought yogurt. I fill up an ice cube tray with yogurt, and then freeze it. Once the cubes are frozen, I pop them out of the tray and put them into a ziploc bag to store in the freezer. This way I can easily take out one cube of frozen yogurt for a half gallon batch of fresh yogurt.

How to make yogurt in the Instant Pot… and the science behind it

To make yogurt in the Instant Pot, you’ll follow the general pattern as described below: warm the milk, cool it, add starter culture, and incubate for ~10 hours.

Ingredients and materials

• Instant Pot
• Instant read thermometer
• 2 tablespoons of yogurt starter culture (from previous batch or from the store)
• Half gallon of 1% milk
• Ice cube tray (for freezing the starter culture)

(1) Warm up milk to ~180°F

This is going to sound strange, but the first thing to do is add about a half cup of water into the Instant Pot and swirl it around to coat the bottom and the sides. This prevents the milk from sticking to the surface as it is heating. Once you’ve swirled the water around, pour out the excess. Now, pour the milk into the Instant Pot and secure the lid. (For all steps, you don’t need to include the sealing ring and it doesn’t matter if the pressure release is set to vent or not.) Then hit the yogurt button until the screen reads “boil.” Now you can step away for about 20-30 minutes. The Instant Pot will beep when the milk has heated up.

The science: Heating the milk disrupts the bonds normally found in whey proteins. Doing so allows the yogurt to coagulate better at a later step for a thicker texture. 

(2) Cool down to ~100°F

When the Instant Pot is done “boiling” the milk, cool it down to 100 – 105°F. You can do this in the Instant Pot itself or take the metal bowl out (it will be faster this way). If you don’t have a thermometer, you can judge the temperature by hand. Place your hand on the bottom half of the Instant Pot and if the temperature feels comfortably warm and you can keep your hand on it, you’re ready for step 4. It’ll take about an hour for the temperature to come down. Meanwhile, proceed to step 3.

The science: Putting the starter culture in too soon could kill the bacteria so you’ll need to wait until it is about 100 – 105°F. This is the ideal temperature for the bacteria to thrive.

(3) Prepare yogurt starter culture

While the yogurt is cooling, take the cube of yogurt out of the freezer if you have frozen portions of your starter culture (see the section above). This allows the starter culture to thaw out and get up to room temperature so that it is easier to mix into the milk. I usually put this in a covered container.

(4) Mix starter with a small amount of cooled milk

When the yogurt has cooled to 100 – 105°F, it’s time to mix the starter into the milk. First, add a couple tablespoons of the cooled milk into the starter and mix it in. This thins the starter yogurt enough so that it is more easily dispersed into the rest of the milk

(5) Pour slurry and mix into the rest of the milk

Before pouring the yogurt mixture into the cooled milk, remove the “skin” that has formed on the top using a spoon or a fork. Now you’re ready to pour the slurry in and mix it around in the milk.

The science: Inoculation! You’ve now introduced the helpful bacteria that will turn the milk to yogurt.

(6) Incubate for 10 hours

Place the insert containing your inoculated milk into the Instant Pot if you previously removed it. Close the lid to the Instant Pot. Then hit the yogurt button until it shows “10:00” as you will incubate it for 10 hours. Now you wait!

The science: This is where the microbial magic happens! The bacteria begins to metabolize the sugars in the milk (lactose) and turn it into lactic acid. The lactic acid gives yogurt its tangy taste and makes it thick. The acidity also prevents any potential contaminants from colonizing. The bacterial population grows in numbers up to 1 million bacteria per gram of yogurt, giving the yogurt its reputation as a probiotic.

(7) Place the yogurt in the fridge to cool and set further

When the 10 hours are up, the Instant Pot will beep. Your yogurt is finished! You’ll see that the yogurt has thickened and some of the whey might have separated out. Remove the insert containing the yogurt and cover. Place this into the fridge to cool and thicken further. My batch lasts me two weeks but I have not tried to see if it would keep longer.

Tips and tricks for the yogurt making process

• Place a plate over the Instant Pot insert while you’re cooling the milk. This keeps anything from falling into the milk and prevents the skin from forming on top.
• If you’re short on time for Step 2, you can fill a large bowl partway up with cool water and then place the Instant Pot insert with the hot milk into the bowl to cool faster. The heat will transfer to the water in the bowl. Once this water warms up, you can pour out the water and put cool water in. If you do this, keep in mind that the milk near the edges of the Instant Pot insert will be much cooler than the milk in the middle. Give it a good stir before taking the temperature.
• If you want to make more yogurt, increase the amount of starter proportionally. For example, if you’d like to make a gallon, use two cubes of frozen starter.

Yogurt making schedule

Because of the long incubation time, I’ve found two different schedules worked well for me so I didn’t have to wake up in the middle of the night to fetch my new batch of yogurt.

The first of this schedule involves making the yogurt completely during the day:

• 8 AM: Warm the milk, cool, and add starter culture.
• 10 AM: Start the 10 hour incubation.
• 8 PM: Place finished yogurt in the fridge.

For this method, I ideally would have the yogurt incubating by noon so that I can put it into the fridge before bed. This schedule allows you to eat the yogurt on the next morning as it has further cooled and set.

The second version of this schedule involves incubating the yogurt during the night:

• 8 PM: Warm the milk, cool, and add starter culture.
• 10 PM: Start the 10 hour incubation.
• 8 AM: Place finished yogurt in the fridge.

This schedule means that you won’t be able to eat it for breakfast that morning as ideally you’d give it a few hours in the fridge to cool and set up more. However, I’ve stuck a serving of yogurt in the freezer to chill before eating more immediately.

Alternatives: Making yogurt in a pot, Crock Pot, or yogurt maker

No Instant Pot? No problem. There’s so many other ways to make yogurt. After all, the first yogurts were made before these kitchen gadgets were created.

• Use the oven light
• Use the Crock pot

Further reading

Does Consumption of Fermented Foods Modify the Human Gut Microbiota? The Journal of Nutrition. 2020.

Yogurt Made Simple. Washington State University. 2015.

Yogurt. The Nutrition Source. Harvard T.H. Chan School of Public Health.