How to Rebuild Your Microbiome with Lost Species – Homemade Yogurt with L. reuteri, L. rhamnosus and B. infantis

Updated on 17 August 2025

Recipe: Make Your Own L. reuteri, L. rhamnosus and B. infantis Yogurt

Also suitable for people with lactose intolerance (see notes below)

Ingredients (for approximately 1 liter of yogurt)

• 4 capsules L. reuteri (5 billion CFU each)
• 2 capsules L. rhamnosus (10 billion CFU each)
• 2 capsules B. infantis (1 billion CFU each)
• 1 tablespoon inulin (alternative: GOS or XOS for those with fructose intolerance)
• 1 liter (organic) whole milk, 3.8% fat, ultra-high temperature treated and homogenized (UHT) or shelf-stable milk
• The higher the fat content, the thicker the yogurt

Note

• 1 capsule of L. reuteri = at least 5 × 10⁹ CFU (colony-forming units)
• CFU is a unit that indicates how many live microorganisms are present in a preparation

Milk and Temperature Guidelines

• Do not use fresh milk because it is not sterile and cannot support long fermentation times
• UHT milk is ideal as it is germ-free and ready to use
• The milk should be at room temperature or gently warmed in a water bath to about 38 °C (100 °F).

Avoid higher temperatures because probiotics start to get damaged at around 44 °C

Preparation

1. Open all 8 capsules and pour the powder into a small bowl
2. Add 1 tablespoon of inulin per liter of milk to support bacterial growth
For people with fructose intolerance, GOS or XOS are good alternatives
3. Add 2 tablespoons of milk to the bowl and stir well until smooth
4. Add the remaining milk and mix thoroughly
5. Pour the mixture into a fermentation-safe container such as a glass jar
6. Place the container in a yogurt maker, set it to 38 °C (100 °F), and ferment for 36 hours

From the second batch onward use 2 tablespoons of yogurt from the previous batch as starter

Prepare the first batch with the bacteria capsules.

From the second batch onward use 2 tablespoons of yogurt from the previous batch as starter. This also applies if the first batch is still thin or not perfectly firm. Use it as a starter as long as it smells fresh tastes mildly sour and shows no signs of spoilage no mold no unusual discoloration no sharp odor.

Per 1 liter of milk

• 2 tbsp yogurt from the previous batch

• 1 tbsp inulin

• 1 liter UHT milk or ultra heat treated homogenized whole milk

How to do it

1. Put 2 tbsp yogurt from the previous batch into a small bowl.

2. Add 1 tbsp inulin and mix with 2 tbsp milk until smooth with no lumps.

3. Stir in the remaining milk and mix well.

4. Pour the mixture into a fermentation safe container and place it in the yogurt maker.

5. Ferment at 38 °C 100 °F for 36 hours.

Note Inulin is the food for the cultures. Add 1 tbsp inulin per liter of milk to every batch.

If you have any questions email team@tramunquiero.com or use our contact form.

Why 36 hours

This duration is scientifically based
L. reuteri doubles approximately every 3 hours
Over 36 hours this allows for 12 doubling cycles, resulting in exponential growth and a high concentration of active probiotics
Longer fermentation also stabilizes lactic acid and strengthens the cultures

Important

• The first batch may not turn out well
• Do not throw it away
• Instead use 2 tablespoons from the first batch to start a second one
• If that still fails, check your yogurt maker’s temperature setting
• Devices with precise temperature control usually yield good results from the first try

Tips for Best Results

• The first batch is often thinner or more grainy
• Use 2 tablespoons of it as a starter for the next batch
• Each new batch will improve in consistency
• Higher fat content makes for creamier yogurt
• The finished yogurt can be stored in the fridge for up to 9 days

Suggested Use

Enjoy about half a cup (roughly 125 ml, 4 US fl oz.) daily, ideally in the morning or as a snack.

Regular use helps the beneficial microbes thrive and support your microbiome over time.

Yogurt Making with Plant-Based Milk – A Coconut Milk Alternative

If you're considering using plant-based milk for making SIBO yogurt due to lactose intolerance, there's good news: in most cases, this isn't necessary. During fermentation, probiotic bacteria break down most of the lactose, making the final yogurt often well tolerated even by those with lactose intolerance.

However, if you avoid dairy for ethical reasons (e.g., vegan lifestyle) or due to concerns about hormones in animal milk, you can use plant-based alternatives like coconut milk. Making yogurt with plant-based milk is technically more demanding because it lacks natural sugars (like lactose), which bacteria use as an energy source.

Advantages and Challenges

One benefit of plant-based milk is that it doesn't contain hormones, which can be present in cow’s milk. However, many people report that fermentation with plant-based milk is often unreliable. Coconut milk, in particular, tends to separate during fermentation into watery and fatty phases, which negatively affects the texture and taste.

Recipes using gelatin or pectin sometimes yield better results, but they remain inconsistent. A promising alternative is guar gum, which not only promotes the desired creamy consistency but also acts as a prebiotic fiber for the microbiome.

Recipe: Coconut Milk Yogurt with Guar Gum

This base allows for successful fermentation of yogurt using coconut milk and can be inoculated with the bacterial strain of your choice, such as L. reuteri or a starter from a previous batch.

Ingredients

• 1 can (approx. 400 ml) coconut milk (without additives like xanthan or gellan, guar gum is allowed)
• 1 tablespoon sugar (sucrose)
• 1 tablespoon raw potato starch
• ¾ teaspoon guar gum (not the partially hydrolyzed form)
• Probiotic culture of your choice (for example, the contents of one L. reuteri capsule with at least 5 billion CFU) or 2 tablespoons yogurt from a previous batch

Instructions

1. Heat the coconut milk in a small saucepan over medium heat to about 82°C (180°F) and hold that temperature for 1 minute.
2. Stir in the sugar and potato starch, then remove the saucepan from the heat.
3. After about 5 minutes of cooling, add the guar gum. Blend thoroughly using an immersion blender or stand mixer for at least 1 minute. This ensures a smooth and thick consistency similar to cream.
4. Let the mixture cool to room temperature.
5. Gently stir in the probiotic culture. Do not blend.
6. Pour the mixture into a glass jar and ferment at around 37°C (99°F) for 48 hours.

Why Guar Gum?

Guar gum is a natural dietary fiber derived from the guar bean. It consists mainly of the sugar molecules galactose and mannose (galactomannan) and serves as a prebiotic fiber that is fermented by beneficial gut bacteria to produce short-chain fatty acids such as butyrate and propionate.

Benefits of Guar Gum

Guar gum stabilizes the yogurt base by preventing the separation of fat and water. It has a prebiotic effect that supports the growth of beneficial bacterial strains such as Bifidobacterium, Ruminococcus, and Clostridium butyricum. It also improves microbiome balance, which can help people with irritable bowel syndrome or loose stools. Additionally, studies have shown that guar gum can enhance the effectiveness of antibiotics, leading to a 25 percent higher success rate in the treatment of small intestinal bacterial overgrowth (SIBO).

It is important not to use the partially hydrolyzed form of guar gum. This version has no gelling properties and is not suitable for yogurt preparation.

Why We Recommend 3 to 4 Capsules per Batch

For the initial fermentation with Limosilactobacillus reuteri, we recommend using 3 to 4 capsules per batch, which provides 15 to 20 billion colony-forming units (CFU).

This dosage follows the guidelines of Dr. William Davis, who explains in his book Super Gut (2022) that a starting dose of at least 5 billion CFU is needed for a successful fermentation. A higher initial quantity of 15 to 20 billion CFU has proven especially effective.

The reason is that under ideal conditions, L. reuteri doubles every 3 hours. During a typical 36-hour fermentation, around 12 doubling cycles take place. In theory, even a small initial dose can produce a large bacterial count.

In practice, however, a higher starting dose makes sense for several reasons. First, it increases the chances that L. reuteriquickly becomes dominant over other microbes. Second, it helps stabilize the fermentation environment by ensuring a steady drop in pH. Third, too low a starting dose can delay the fermentation process or lead to poor bacterial growth.

That’s why we recommend using 3 to 4 capsules for the first batch to ensure a strong and reliable start. After a successful fermentation, the yogurt can usually be reused up to 20 times to start new batches before fresh starter cultures are needed.

Restart after 20 fermentations

A common question when fermenting with Limosilactobacillus reuteri is: How many times can you reuse a yogurt starter before you need a fresh starter culture? Dr. William Davis recommends in his book Super Gut (2022) not to reproduce a fermented L. reuteri yogurt continuously for more than 20 generations (or batches). But is this number scientifically justified? And why exactly 20—not 10, not 50?

What happens when you reuse the starter?

Once you have made a L. reuteri yogurt, you can use it as a starter for the next batch. This transfers live bacteria from the finished product into a new nutrient medium (e.g., milk or plant-based alternatives). This is ecological, saves capsules, and is often done in practice.

However, repeated reuse leads to a biological problem:
Microbial drift.

Microbial drift—how cultures change

With each transfer, the composition and properties of a bacterial culture can gradually change. Reasons for this include:

• Spontaneous mutations during cell division (especially with high turnover in warm environments)

• Selection of certain subpopulations (e.g., faster growers displacing slower ones)

• Contamination by unwanted microbes from the environment (e.g., airborne microbes, kitchen flora)

• Nutrient-based adaptations (bacteria “adapt” to certain milk species and alter their metabolism)

The result: after several generations, it is no longer guaranteed that the same bacterial species—or at least the same physiologically active variant—is present in the yogurt as at the start.

Why Dr. Davis recommends 20 generations

Dr. William Davis originally developed the L. reuteri yogurt method for his readers to specifically utilize certain health benefits (e.g., oxytocin release, better sleep, skin improvement). In this context, he writes that a starter “works reliably for about 20 generations” before a new starter culture from a capsule should be used again (Davis, 2022).

This recommendation is not based on systematic lab tests but on practical experience with fermentation and reports from his community.

“After about 20 generations of re-use, your yogurt may lose potency or fail to ferment reliably. At that point, use a fresh capsule again as starter.”
— Super Gut, Dr. William Davis, 2022

 

He justifies the number pragmatically: after about 20 rounds of reuse, the risk of unwanted changes increases—such as thinner consistency, altered aroma, or reduced health effects.

Are there scientific studies on this?

No specific scientific studies exist yet on L. reuteri yogurt across 20 fermentation cycles. However, there is research on the stability of lactic acid bacteria over multiple passages:

• In food microbiology, it is generally accepted that genetic changes can occur after 5–30 generations—depending on species, temperature, medium, and hygiene (Giraffa et al., 2008).

• Fermentation studies with Lactobacillus delbrueckii and Streptococcus thermophilus show that after about 10–25 generations, changes in fermentation performance (e.g., lower acidity, altered aroma) can occur (O’Sullivan et al., 2002).

• For Lactobacillus reuteri specifically, it is known that its probiotic properties vary greatly depending on subtype, isolate, and environmental conditions (Walter et al., 2011).

These data suggest that 20 generations is a conservative, sensible guideline to preserve the culture’s integrity—especially when aiming to maintain health effects (e.g., oxytocin production).

Conclusion: 20 generations as a practical compromise

Whether 20 is the “magic number” cannot be scientifically determined exactly. But:

• Discarding after fewer than 10 batches is usually unnecessary.

• Exceeding 30 batches increases the risk of mutations or contamination.

• 20 batches correspond to about 5–10 months of use (depending on consumption)—a good timeframe for a fresh start.

Practical recommendation

After a maximum of 20 yogurt batches, a new starter culture from capsules should be used, especially if you want to specifically utilize L. reuteri as a “Lost Species” for your microbiome.

Daily Benefit