Rebuild the microbiome with lost species – With yogurt from L. reuteri, L. rhamnosus, and B. infantis

Updated on August 16, 2025

Recipe: Make L. reuteri, L. rhamnosus, and B. infantis yogurt yourself

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

Ingredients (for approx. 1 liter of yogurt)

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

Note:

• 1 capsule L. reuteri, at least 5 × 10⁹ (5 billion) CFU (en)/KBE (de)
• CFU stands for colony forming units – in German, kolonie-bildende Einheiten (KBE). This unit indicates how many viable microorganisms are contained in a preparation.

Notes on milk choice and temperature

• Do not use fresh milk. It is not stable enough for the long fermentation times and not sterile.
• Ideal is H-milk (long-life, ultra-high temperature milk): It is sterile and can be used directly.
• The milk should be at room temperature – alternatively, gently warm it in a water bath to 38 °C (100 °F). Please avoid higher temperatures: from about 44 °C, the probiotic cultures are damaged or destroyed.

Preparation

1. Open all 8 capsules and put the powder into a small bowl.
2. Add 1 tbsp of inulin per liter of milk – this serves as a prebiotic and promotes bacterial growth. For people with fructose intolerance, GOS or XOS are suitable alternatives.
3. Add 2 tbsp of milk to the bowl and stir thoroughly to avoid lumps.
4. Stir in the remaining milk and mix well.
5. Pour the mixture into a fermentation-suitable container (e.g., glass)
6. Place in the yogurt maker, set the temperature to 38 °C (100 °F), and let ferment for 36 hours.

From the second batch onwards, use 2 tablespoons of yogurt from the previous batch as a starter

You prepare the first batch with the bacteria capsules.

From the second batch onwards, use 2 tablespoons of yogurt from the previous batch as a 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 discolorations, no pungent odor).

Per 1 liter of milk:

• 2 tbsp yogurt from the previous batch

• 1 tbsp inulin

• 1 liter UHT milk or ultra-high temperature treated, homogenized whole milk

Here’s how:

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

2. Add 1 tablespoon of inulin and stir smooth with 2 tablespoons of milk until no lumps remain.

3. Stir in the remaining milk and mix well.

4. Pour the mixture into a fermentation-suitable container and place it in the yogurt machine.

5. Let ferment at 38 °C (100 °F) for 36 hours.

Note: Inulin is the food for the cultures. Add 1 tablespoon of inulin per liter of milk for each batch.

If you have questions, we are happy to assist you via email at team@tramunquiero.com or through our contact form.

Why 36 hours?

The choice of this fermentation duration is scientifically based: L. reuteri requires about 3 hours per doubling. In 36 hours, there are 12 doubling cycles – this corresponds to exponential growth and a high concentration of probiotic active germs in the finished product. Additionally, the longer maturation stabilizes the lactic acids and makes the cultures particularly resilient.

!Important to note!

The first batch often does not succeed for many users. However, it should not be discarded. Instead, it is recommended to start a new batch with two tablespoons of the first batch. If this also fails, please check the temperature of your yogurt maker. For devices where the temperature can be set precisely to the degree, the first batch usually succeeds well.

Tips for perfect results

• The first batch is usually still a bit more liquid or grainy. Use 2 tablespoons of the previous batch as a starter for the next round – with each new batch, the consistency improves.
• More fat = thicker consistency: The higher the fat content of the milk, the creamier the yogurt becomes.
• The finished yogurt is shelf-stable in the refrigerator for up to 9 days.

Consumption recommendation:

Enjoy about half a cup (approx. 125 ml) of the yogurt daily – preferably regularly, ideally at breakfast or as a snack in between. This allows the contained microbes to develop optimally and sustainably support your microbiome.

Yogurt making with plant-based milk – an alternative with coconut milk

If you are considering using plant-based milk alternatives to make SIBO yogurt due to lactose intolerance, be advised: this is usually not necessary. During fermentation, the probiotic bacteria break down most of the lactose present – the finished yogurt is therefore often well tolerated, even with lactose intolerance.

However, those who want to avoid dairy products for ethical reasons (e.g., as vegans) or due to health concerns about hormones in animal milk can turn to plant-based alternatives like coconut milk. Making yogurt with plant-based milk is technically more demanding because the natural sugar source (lactose), which the bacteria use as an energy source, is missing.

Advantages and Challenges

An advantage of plant-based dairy products is that they contain no hormones, as can be found in cow's milk. However, many people report that fermentation with plant-based milk often does not work reliably. Especially coconut milk tends to separate during fermentation – into watery phases and fat components – which can affect texture and taste experience.

Recipes with gelatin or pectin sometimes show better results but remain unreliable. A promising alternative is the use of 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 successful fermentation of yogurt with coconut milk and can be started with the bacterial strain of your choice – for example with 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 tbsp sugar (sucrose)
• 1 tbsp raw potato starch
• ¾ tsp guar gum (not the partially hydrolyzed form!)
• Bacterial culture of your choice (e.g., the contents of an L. reuteri capsule with at least 5 billion CFU)
  or 2 tbsp yogurt from a previous batch

Preparation

1. Heating
   Heat coconut milk in a small pot over medium heat to about 82°C (180°F) and maintain this temperature for 1 minute.
2. Stirring in the starch
   Mix sugar and potato starch while stirring. Then remove from heat.
3. Incorporate guar gum
   After about 5 minutes of cooling, stir in guar gum. Now blend with an immersion blender or in a stand blender for at least 1 minute – this ensures a homogeneous and thick consistency (similar to cream).
4. Let cool
   Let the mixture cool to room temperature.
5. Add bacteria
   Gently stir in the probiotic culture (do not blend).
6. Fermentation
   Pour the mixture into a glass container and ferment for 48 hours at about 37°C (99°F).

Why guar gum?

Guar gum is a natural fiber derived from the guar bean. It mainly consists of the sugar molecules galactose and mannose (galactomannan) and serves as a prebiotic fiber fermented by beneficial gut bacteria – for example, into short-chain fatty acids like butyrate and propionate.

Benefits of guar gum:

• Stabilization of the yogurt base: It prevents the separation of fat and water.
• Prebiotic effect: Promotes the growth of beneficial bacterial strains such as Bifidobacterium, Ruminococcus, and Clostridium butyricum.
• Better microbiome balance: Supports people with irritable bowel syndrome or loose stools.
• Enhancement of antibiotic effectiveness: Studies observed a 25% higher success rate in the treatment of SIBO (small intestinal bacterial overgrowth).

Important: Do not use the partially hydrolyzed form of guar gum – it has no gel-forming effect and is not suitable for yogurt.

Why we recommend 3–4 capsules per batch

For the first fermentation with Limosilactobacillus reuteri, we recommend using 3 to 4 capsules (15 to 20 billion CFU) per batch.

This dosage is based on the recommendations of Dr. William Davis, who describes in his book “Super Gut” (2022) that a starting amount of at least 5 billion colony-forming units (CFU) is necessary to ensure successful fermentation. A higher starting amount, about 15 to 20 billion CFU, has proven to be particularly effective.

The background: L. reuteri doubles approximately every 3 hours under optimal conditions. During a typical fermentation time of 36 hours, about 12 doublings occur. This means that even a relatively small starting amount could theoretically be sufficient to produce a large number of bacteria.

In practice, a high initial dosage is sensible for several reasons. First, it increases the likelihood that L. reuteri quickly and dominantly establishes itself against any foreign germs present. Second, a high starting concentration ensures a steady pH drop, stabilizing the typical fermentation conditions. Third, too low an initial density can lead to delayed fermentation onset or insufficient growth.

Therefore, we recommend using 3 to 4 capsules for the first batch to ensure a reliable start of the yogurt culture. After the first successful fermentation, the yogurt can usually be used up to 20 times for re-culturing before fresh starter cultures are recommended.

Restart after 20 fermentations

A common question in fermentation 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 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 during backslopping?

Once you have made a 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 solution (e.g., milk or plant-based alternatives). This is ecological, saves capsules, and is often done in practice.

However, repeated backslopping 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 are:

• Spontaneous mutations during cell division (especially with high turnover in warm environments)
• Selection of certain subpopulations (e.g., faster growers displace slower ones)
• Contamination by unwanted microbes from the environment (e.g., airborne germs, kitchen microflora)
• Nutrient-related adaptations (bacteria "acclimate" to certain milk species and change 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 beginning.

Why Dr. Davis recommends 20 generations

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

This 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 times of re-culturing, the risk increases that unwanted changes become noticeable – for example, thinner consistency, altered aroma, or reduced health effect.

Are there scientific studies on this?

Concrete scientific studies specifically on L. reuteri yogurt over 20 fermentation cycles do not yet exist. 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, a change 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 can vary greatly depending on subtype, isolate, and environmental conditions (Walter et al., 2011).

These data suggest: 20 generations is a conservative, sensible guideline to preserve the integrity of the culture – especially if you want to maintain the 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 fewer than 10 batches is usually unnecessary.
• Drawing more than 30 batches increases the risk of mutations or contamination.
• 20 batches correspond to about 5–10 months of use (depending on consumption) – a good period for a fresh start.

Recommendation for practice

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

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