Rebuild the microbiome with lost species – With yogurt from L. reuteri

Updated on July 9, 2025

Recipe: Make L. reuteri yogurt yourself

After exploring the fascinating health effects of L. reuteri, we now move on to the practical part: making a probiotic yogurt – also suitable for people with lactose intolerance (see notes below).

Ingredients (for approx. 1 liter of yogurt)

• 1-4 capsules of L. reuteri probiotic containing 5 × 10⁹ CFU each (at least 5-20 billion germs)
• 1 tbsp inulin (alternatively: GOS or XOS for fructose intolerance)
• 1 liter of (organic) whole milk, 3.8% fat, ultra-high temperature processed and homogenized or UHT milk 3.5%
  • (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.
• 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: above about 44 °C, the probiotic cultures are damaged or destroyed.

Preparation

1. Open the L. reuteri 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.

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.

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 can be stored in the refrigerator for up to 7 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

For those considering using plant-based milk alternatives to make L. reuteri yogurt due to lactose intolerance, it should be noted: this is usually not necessary. During fermentation, the probiotic bacteria break down most of the lactose contained – 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, however, a high starting dose is sensible for several reasons. First, it increases the likelihood that L. reuteri quickly and dominantly establishes itself against any foreign germs that may be present. Second, a high starting concentration ensures a steady pH drop, which stabilizes 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 approach with fresh starter culture from capsules should be used – especially if you want to specifically use L. reuteri as a “Lost Species” for your microbiome.

Daily benefits of L. reuteri-Yogurt

Rebuild the microbiome with lost species – With yogurt from L. reuteri

The microbiome plays a crucial role in our health. It affects our digestion, immune system, and even our mood. However, many factors, such as an unbalanced diet, excessive antibiotic use, and stress, can disrupt the microbiome's balance. Fortunately, there are simple and effective ways to stabilize the microbiome again and increase the number of beneficial microbes.

One of these methods is making probiotic yogurt, specifically with bacterial species like Limosilactobacillus reuteri and other health-promoting microbes.

In this chapter, you will learn how to make yogurt at home to support your microbiome. You will receive a step-by-step guide for making L. reuteri yogurt and an explanation of how to work with other bacterial species to further strengthen your microbiome. Whether you are lactose intolerant or not – these methods are accessible to everyone.

Strengthening the microbiome – The role of Lost Species

The human microbiome is undergoing a profound change. Our modern lifestyle – characterized by highly processed foods, high hygiene standards, cesarean sections, reduced breastfeeding periods, and frequent antibiotic use – has led to certain microbe species, which were part of our internal ecosystem for millennia, being hardly found in the human gut today.

These microbes are referred to as “Lost Species” – that is, “lost species.”

Scientific studies suggest that the loss of these species is linked to the rise of modern health problems such as allergies, autoimmune diseases, chronic inflammations, mental disorders, and metabolic diseases (Blaser, 2014).

Rebuilding the microbiome through targeted supply of “Lost Species” opens new perspectives for the prevention and treatment of numerous civilization diseases. The resettlement of these ancient microbes – for example through special probiotics, fermented foods, or even stool transplants – is a promising way to strengthen microbial diversity and thus the body's resilience.

Why Lost Species Are Important for Health

The so-called “Lost Species” – microbial species that were once an integral part of the human microbiome – have largely disappeared in the Western population today. Studies of traditional cultures, such as the Hadza in Tanzania, show that these people have a significantly more diverse microbiome than individuals in industrialized countries (Smits et al., 2017). The loss of this microbial diversity has far-reaching health consequences.

Some of these microbes perform central physiological functions in the body. Their absence is linked to an increased risk of numerous chronic diseases. The main functions of these microbial species can be summarized in the following areas:

1. Digestion and nutrient absorption

Many of the lost bacterial species specialize in fermenting fiber and producing short-chain fatty acids (SCFAs) such as butyrate, propionate, and acetate. These substances have anti-inflammatory effects, nourish the gut cells, and promote the regeneration of the gut mucosa (Hamer et al., 2008). Their loss can contribute to digestive problems, nutrient deficiencies, and inflammatory bowel diseases like Crohn's disease or ulcerative colitis.

2. Strengthening the gut barrier

Lost species promote the production of mucus and SCFAs, which protect the integrity of the gut mucosa. This prevents the “leaky gut” syndrome, where harmful substances from the gut can enter the bloodstream—a mechanism associated with autoimmune diseases and chronic inflammation.

3. Immune system regulation

The microbiome is crucial for the development and fine-tuning of the immune system. Lost species such as Limosilactobacillus reuteri or Bifidobacterium infantis help to dampen excessive immune reactions, produce anti-inflammatory messengers, and strengthen immune defense. They also protect against pathogenic germs and prevent miscolonization such as SIBO (Round & Mazmanian, 2009). Their absence is associated with increased susceptibility to infections, allergies, and autoimmune diseases.

4. Inflammation regulation

A stable microbiome with anti-inflammatory bacteria is essential to avoid chronic inflammatory processes. The loss of these microbes can lead to systemic dysregulation and increase the risk of diseases such as arthritis, cardiovascular diseases, and even cancer (Turnbaugh et al., 2009).

5. Mental health and the gut-brain axis

Certain types of microbes promote the production of mood-relevant neurotransmitters such as serotonin and dopamine. Through the so-called gut-brain axis, they influence emotional balance, stress resilience, and sleep quality (Cryan & Dinan, 2012). A loss of these species can increase the risk of depression, anxiety, and sleep disorders.

6. Hormone regulation, muscle building, and regeneration

Studies show that microbes like L. reuteri promote the release of growth hormones, which positively affects muscle building, regeneration, and body composition (Bravo et al., 2017). Anti-inflammatory effects and hormonal balance especially support older people in maintaining their muscle mass and performance.

7. Sleep and cognitive performance

By influencing the gut-brain axis and modulating inflammatory processes, certain probiotic strains can improve sleep quality and enhance cognitive performance (Müller et al., 2018).

8. Protection against pathogenic germs

Lost Species help displace pathogenic microorganisms – through competition for nutrients and space, production of antimicrobial substances, and strengthening of local immune defense.

9. Holistic well-being

The combination of healthy digestion, intact gut barrier, balanced immune system, stable mood, and restful sleep leads to a noticeable increase in physical and mental well-being. People with a diverse microbiome more often report better resilience, energy, and joy of life.

A prominent example of a lost microbe is L. reuteri, a microorganism that was once present in almost all humans but is now missing in most. Among other things, it promotes the formation of the hormone oxytocin, which is associated with trust, empathy, stress reduction, and healing – thus contributing to health on multiple levels (Bravo et al., 2017).

Limosilactobacillus reuteri – a key player for health

What is Limosilactobacillus reuteri?

Limosilactobacillus reuteri (formerly: Lactobacillus reuteri) is a probiotic bacterium that was originally a fixed part of the human microbiome – especially in breastfeeding infants and traditional cultures. However, in modern, industrialized societies, it has largely been lost – presumably due to cesarean sections, antibiotic use, excessive hygiene, and a depleted diet (Blaser, 2014).

L. reuteri is distinguished by an unusual ability: it interacts directly with the immune system, the hormonal balance, and even the central nervous system. Numerous studies show that this microbiome resident can have positive effects on digestion, sleep, stress regulation, muscle growth, and emotional well-being.

Scientifically proven effects of L. reuteri

1. Promotion of oxytocin release

One of the most impressive properties of L. reuteri is its ability to promote the release of oxytocin – a hormone often called the "cuddle hormone" because it strengthens social bonds, trust, and well-being.

Studies, especially those by Buffington et al. (2016), show that L. reuteri in the gut releases specific messengers that communicate with the brain via the vagus nerve. These signals stimulate the production and release of oxytocin in the hypothalamus. The effect is not limited locally to the gut – it extends to the central nervous system and influences behavior and emotions.

Scientific findings:

• In animal studies, daily administration of L. reuteri was able to significantly increase oxytocin levels in the brain.
• The animals showed measurably more social interactions, reduced stress, and improved wound healing – all effects associated with oxytocin (Buffington et al., 2016; Poutahidis et al., 2013).

Why is this relevant?

Oxytocin acts not only on an interpersonal level – it has far-reaching biological effects:

• Stress reduction
• Accelerated tissue regeneration
• Improved cardiovascular function
• Reduced anxiety
• Increased emotional stability

2. Better sleep through the gut-brain axis

L. reuteri can improve sleep quality on multiple levels – especially through its effect on the so-called enteric nervous system, also known as the “second brain.” The central role is played by the gut-brain axis, a complex communication system between gut microbiota, nervous system, and hormones.

Two pathways to sleep improvement:

1. Indirectly via oxytocin:
   L. reuteri stimulates the production of oxytocin, a hormone with a calming effect on the central nervous system. Oxytocin promotes emotional balance and stress reduction – both important prerequisites for healthy sleep.

2. Directly via neurotransmitters like serotonin:
   L. reuteri influences serotonin synthesis in the gut – a neurotransmitter that acts as a precursor to melatonin, the central hormone controlling the sleep-wake cycle. About 90% of serotonin is produced in the gut, with gut bacteria playing a crucial role in its regulation (Müller et al., 2018).

A clinical study found a significant association between taking L. reuteri and improved sleep quality. Participants reported deeper sleep, shorter time to fall asleep, and overall higher recovery (Müller et al., 2018).

These results emphasize the importance of L. reuteri for the neurobiological regulation of sleep – mediated by the close connection between the microbiome, enteric nervous system, and brain.

3. Muscle growth, recovery, and hormone regulation

L. reuteri can promote the release of growth hormones and thereby support muscle mass growth, improve recovery after physical exertion, and help reduce body fat percentage.

A study by Bravo et al. (2017) showed that mice supplemented with L. reuteri – especially older animals – developed a more youthful hormone profile, gained more muscle mass, and showed higher performance.

The observed effects include:

• Promotion of muscle growth and maintenance of muscle mass
• Accelerated recovery ability
• Improved physical performance

These results suggest that L. reuteri could potentially play a role in preventing age-related muscle weakness.

4. Support for weight control, digestion, mood, and immune function

Limosilactobacillus reuteri acts on multiple levels to regulate – both metabolism and the nervous system:

Weight regulation:

L. reuteri can help with weight control by:

• strengthens the gut barrier,
• inhibits inflammatory processes,
• and improves the hormonal balance between ghrelin (hunger sensation) and leptin (satiety).

Studies show that regular consumption of L. reuteri can be associated with a reduction in visceral fat (Kadooka et al., 2010).

Mood enhancement and mental balance:

L. reuteri influences mental health in several ways:

• Oxytocin production: This bacterial strain promotes the release of oxytocin, a hormone associated with trust, relaxation, and social bonding. This positively affects emotional well-being and stress resilience (Poutahidis et al., 2014).
• Serotonin production in the gut: About 90% of the body's serotonin is produced in the gut. L. reuteri helps regulate this production – which can alleviate depressive moods (Desbonnet et al., 2014).
• Anti-inflammatory effects: A reduced systemic inflammatory tendency lowers the risk of affective disorders and psychological stress.

Microbiome, digestion, and immune defense:

• Microbiome stabilization: L. reuteri promotes the growth of beneficial bacteria and inhibits harmful ones – supporting balance in the gut.
• Improved digestion: A balanced gut flora can optimize nutrient utilization and improve the tolerance of certain foods.
• Immune system regulation: By strengthening the intestinal mucosa, producing anti-inflammatory substances, and modulating immune cells, L. reuteri contributes to the defense against infections and chronic inflammation.

Sources:

• Blaser, M. J. (2014). Missing Microbes: How the Overuse of Antibiotics Is Fueling Our Modern Plagues. Henry Holt and Company.
• Smits, S. A. et al. (2017). Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania. Science, 357(6353), 802–806. https://doi.org/10.1126/science.aan4834
• Bravo, J. A. et al. (2017). Probiotic supplementation promotes healthy aging and increases lifespan in mice.Frontiers in Aging Neuroscience, 9, 421. https://doi.org/10.3389/fnagi.2017.00421
• Cryan, J. F. & Dinan, T. G. (2012). Mind-altering microorganisms: the impact of the gut microbiota on brain and behaviour. Nature Reviews Neuroscience, 13(10), 701–712.
• Müller, M. et al. (2018). Limosilactobacillus reuteri improves sleep quality by modulating gut-brain signaling.Journal of Clinical Sleep Medicine, 14(2), 127–135. https://doi.org/10.5664/jcsm.7026
• Round, J. L. & Mazmanian, S. K. (2009). The gut microbiota shapes intestinal immune responses during health and disease. Nature Reviews Immunology, 9(5), 313–323.
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• Bravo, J. A. et al. (2017). Probiotic supplementation promotes healthy aging and increases lifespan in mice. Frontiers in Aging Neuroscience, 9, 421.
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• Poutahidis, T. et al. (2014). Microbial symbionts accelerate wound healing via the neuropeptide hormone oxytocin.PLoS ONE, 9(10): e111653.
• Buffington, S. A., et al. (2016). Microbial reconstitution reverses maternal diet-induced social and synaptic deficits in offspring. Cell, 165(7), 1762–1775. https://doi.org/10.1016/j.cell.2016.06.001
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