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The importance of the microbiome – especially with regard to the first microbial colonization in newborns


Modern research repeatedly shows that our health is influenced not only by external factors such as diet and environment, but also significantly by the microbiome that populates our bodies. The timing and manner in which this complex ecosystem is first established in life play a crucial role. Birth—as the first and most intensive contact between mother and child—is a key focus here. While a vaginal delivery involves a natural transmission of microorganisms, the colonization during a cesarean section differs significantly. These differences have not only immediate but also long-term health consequences.

The microbiome: importance and initial colonization

The microbiome encompasses all microorganisms—bacteria, viruses, fungi, and other microbes—that live in and on our bodies. These communities fulfill important functions:

  • Training the immune system: A diverse microbial colonization helps to “train” the immune system early on so that it learns to distinguish between harmless and potentially harmful antigens.

  • Metabolism and nutrient absorption: A well-established microbiome supports metabolism and contributes to the production of vital substances.

  • Protection against pathogens: The microbes compete with pathogenic organisms and thus prevent their overgrowth.

The first colonization of the newborn represents a crucial moment. This depends on the transfer of the maternal microbiota – a process that varies greatly depending on the mode of birth.

Different microbiome colonization: Vaginal vs. Caesarean section

Vaginally delivered children

Studies, most notably the study by Dominguez-Bello et al. (2010, PNAS) , have shown that newborns born vaginally primarily receive microorganisms from the mother's birth canal. These pathogens include, for example, Lactobacillus and Bifidobacterium , which are typically found in the vagina. These bacteria are not only essential for a diverse microbiome structure but also contribute to optimally conditioning the immune system from the start.

Children born by cesarean section

In contrast, babies born by cesarean section primarily receive microorganisms from the mother's skin and the surrounding environment. These differences manifest themselves in the following aspects:

  • Reduced diversity: Microbial diversity in the first months of life is often reduced due to the lack of transmission of the vaginal microbiota – a key factor for early immune development.

  • Altered composition: Instead of the typical anaerobic bacteria from the birth canal, bacteria that are more commonly associated with the skin or the hospital environment dominate.

The meta-analysis by Bager et al. (2008, Clinical & Experimental Allergy) concludes that infants born by cesarean section have an approximately 20–30% increased risk of suffering from immune-mediated diseases such as asthma, allergies, and atopic diseases. Altered microbial colonization represents a key mechanism that can impair the normal development of the immune system.

Long-term health effects

The consequences of the initial microbial colonization affect health for years:

  • Asthma and respiratory diseases: An insufficiently trained immune system can impair the ability to distinguish between harmless and harmful antigens. Studies show that the risk of childhood asthma is significantly increased in children born by cesarean section.

  • Allergies and atopic diseases: A diverse and stable microbiome structure has a protective effect. However, a deficiency of important microorganisms can promote the development of allergies.

  • Metabolic disorders and chronic diseases: In addition to the direct influence on the immune system, microbial colonization also influences metabolism and thus the risk of later chronic diseases.

These findings underpin the basic idea of ​​the microbiome concept: not the blind elimination of germs, but the targeted promotion of a balanced, natural microbiome community is crucial for long-term health.

Caesarean section as a phenomenon of our time

Increasing number of caesarean sections

In recent decades, there has been a significant increase in cesarean sections worldwide. Several factors play a role:

  • Medical indications: In cases of risky situations or complications during pregnancy and childbirth, a cesarean section is often the safer alternative.

  • Planned cesarean sections: In addition to purely medical reasons, more and more women are consciously choosing to have a cesarean section. This can be due to various personal and psychosocial reasons.

Psychosocial dimensions of birth

Birth is far more than a medical act—it is a profound experience that profoundly shapes the mother's identity and self-confidence. Several studies have shown that:

  • The experience of natural birth is closely linked to the development of an intensive mother-child bond.

  • Oxytocin production , which is stimulated during vaginal births, plays an important role in postnatal healing and emotional bonding.

  • The experience of birth itself – as a ritual of transition – influences the woman’s self-confidence and psychological well-being.

These aspects shed light on the cultural problem that in our modern society there is often a “bacteria aversion”, while at the same time the natural processes and the interaction between mother and child are underestimated.

Cultural Perspectives: Bacteria as an Essential Part of Our Being

Many cultures have an ambivalent relationship with microorganisms. On the one hand, they are feared as pathogens, but on the other, they are essential to our health. The following aspects illustrate this dichotomy:

  • Stigmatization vs. Integration: While hygiene and disinfection are highly valued in modern society, it is often overlooked that excessive germ reduction can lead to a one-sided microbiome structure.

  • Bacteria as constant companions: Every touch, every kiss, and every hug leads to an exchange of microbes. These interactions are not random, but contribute to the constant refreshment and diversification of our microbiome.

  • Reorientation of the health concept: The knowledge of the importance of a diverse microbiome suggests that we should fundamentally rethink our attitude towards bacteria. The goal must be to promote a healthy and stable microbial ecosystem rather than destroying it through excessive disinfection.


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Practical implications and future perspectives

The findings from the studies have direct implications for clinical practice and future research:

  • Targeted microbiome remediation: Especially in cases of cesarean section, the targeted promotion of natural colonization – for example through probiotic applications or the so-called vaginal seeding method – could help to compensate for the initial microbiome deficiency.

  • Microbiome testing: Regular analysis of the microbiome could serve as a diagnostic tool in the future to detect imbalances early and take targeted countermeasures.

  • Education and prevention: A comprehensive understanding of the role of the microbiome should be incorporated into counseling for expectant parents. The benefits of natural childbirth, not only from a medical but also from a psychosocial perspective, should be emphasized in the context of the child's health.

  • Interdisciplinary research: The interface between microbiome research, psychology, and obstetrics offers an exciting field to further explore the long-term effects of birth mode on child development.

The way in which a newborn's microbiome establishes itself has far-reaching consequences for their future health.


Numerous studies show that children born vaginally benefit from a natural and diverse transfer of vital microorganisms, while cesarean births are associated with altered microbial colonization and an increased risk of diseases such as asthma, allergies and atopic diseases.
At the same time, it becomes clear that the trend toward increased and even voluntary caesarean sections is a phenomenon of our time—a phenomenon that encompasses not only medical but also psychosocial and cultural dimensions. Birth as an experience that strengthens the mother-child bond and supports postnatal healing takes a back seat when natural processes are artificially circumvented.
It therefore seems all the more important to place the concept of the microbiome at the center of healthcare: The goal is not to eliminate bacteria, but to promote a stable and diverse microbial environment that trains the immune system, optimizes metabolism, and provides long-term protection against chronic diseases. Future approaches in obstetrics and neonatal care should therefore be integrated—including targeted microbial interventions and increased education about the importance of natural microbiome transmission.

Overall, a deeper understanding of the role of the microbiome not only opens up new perspectives for the prevention and treatment of numerous diseases, but also challenges us to re-evaluate our cultural relationship with microbes and bring it into a health-promoting balance.


Many people today feel constantly exhausted, in pain, sleep poorly, or notice that their body isn't regenerating as well as it used to. They may even exercise, pay a little attention to their diet – but still lack energy and make no progress. What many don't realize is that the body is often in a state known as "catabolic." This means that it is primarily operating in breakdown mode – rather than building up.

The body has two basic functional states: anabolic and catabolic. The anabolic state represents building, regeneration, healing, and renewal. This is where muscles are built, hormones are produced, and damaged cells are repaired. This is the state in which we recover from exertion, in which we become healthier, stronger, and more resilient. The catabolic state, on the other hand, represents breakdown – here the body switches to generating energy by breaking down its own reserves. This makes sense in the short term, for example during acute stress, fasting, or intense physical exertion. It becomes problematic when the body remains in this breakdown mode permanently – and that is exactly the case for many people today.

A major cause of this is chronic stress. Whether it's professional pressure, constant availability, inner restlessness, or unresolved emotional issues – all of this keeps the nervous system in what's known as sympathetic mode, or the "fight or flight" response. The body releases increased amounts of cortisol, a stress hormone that, in high doses over the long term, inhibits muscle growth, disrupts sleep, and promotes inflammation in the body. This has direct consequences: Muscles are broken down, joints regenerate more slowly, and the immune system is weakened.

Lack of sleep also plays a major role. The most important anabolic processes take place during deep sleep. Growth hormones are released, cells are repaired, and tissue is built. Those who sleep poorly—or too little—lose precious regeneration time night after night. In the long term, this can lead to muscle loss, hormonal imbalances, and chronic fatigue.

Another often overlooked factor is lack of exercise. If you don't move enough in your daily life, you don't stimulate your body to build muscle. Your muscles aren't sufficiently stressed, which pushes your body into a catabolic state. At the same time, you lack the movement to activate your metabolism, stimulate lymph flow, and regulate your nervous system. The body falls into a kind of "standstill" that has nothing to do with true recovery.

And then there's the issue of nutrition and micronutrient deficiencies. Our cells need protein, vitamins, minerals, and healthy fats to repair and rebuild. If these building blocks are missing—for example, due to an unbalanced diet, frequent diets, or poor intestinal absorption—the body simply lacks the material it needs to stay healthy. Older people or people with chronic inflammation in particular often have what's known as anabolic resistance—meaning that even when the body receives stimuli, it can no longer respond well to them because it lacks the right conditions.


In addition, many people suffer from silent inflammation that spreads unnoticed throughout the body. This inflammation blocks important rebuilding processes and also keeps the body in a state of breakdown. Typical causes include a leaky gut, sugar, trans fats, environmental toxins, and chronic stress.

When all these factors come together, the body gradually loses its ability to regenerate. Muscles stop growing, joints heal poorly, skin ages faster, hair falls out—even thinking becomes more difficult. Energy is lacking, strength diminishes, and the joy of life fades.

But it doesn't have to stay that way. The good news is: The body can rebuild itself – if we create the right conditions for it. This primarily means reducing chronic stress, getting good, deep sleep again, exercising regularly – but in moderation and with targeted muscle stimulation – and providing the body with all the nutrients it needs. This also includes identifying and treating inflammation, for example, through gut health, a low-inflammatory diet, and targeted micronutrient therapy.

In functional medicine, this is referred to as an integrative strategy: We look not just at individual symptoms, but at the bigger picture. We strengthen the autonomic nervous system, promote energy metabolism in the mitochondria, and support the body's detoxification systems. This allows body, mind, and emotions to return to balance – and regeneration becomes possible again.

When the body returns to an anabolic state, not only do the muscles recover. Joints, connective tissue, the immune system, and even our mental clarity also benefit. It's a sign that a person is no longer just "surviving," but truly living.

A body under constant stress can't rebuild. It needs rest, nutrition, and exercise—but in the right amounts. Only then can it regenerate, build muscle, heal joints, and regain strength.

Catabolic = breakdown | Anabolic = build-up
The body constantly oscillates between these two states:

  • Catabolic: Stress, fasting, overtraining, inflammation, nutrient deficiency → muscle breakdown, cellular stress
  • Anabolic: Regeneration, deep sleep, muscle building, healing, cell repair. These phases alternate in a healthy balance.

But many people today are permanently catabolic:

  • Chronic stress (cortisol) inhibits anabolic signaling pathways (e.g. mTOR).
  • Inflammation triggers catabolic processes.
  • Insulin resistance, lack of exercise and malnutrition block anabolic stimuli.
  • In old age, anabolic resistance also occurs – the body no longer responds sufficiently to building stimuli.

What can you do? – Ways back to the rebuilding state

This is where functional medicine helps – it asks: What blocks the anabolic state?

And how can we specifically get back into regeneration?

This includes:

(breathing exercises, nature, sleep rituals)
(Muscle stimulation, but not too much – less is often more!)
(e.g. magnesium, B vitamins, amino acids, omega-3)
(Gut health, low-inflammatory diet)
(at least 7–8 hours, sleep hygiene, evening rituals)


1. Movement with building impulse

  • Strength training (progressive) activates mTOR and IGF-1 – both anabolic signaling pathways.
  • Short, intense, regenerative – not too much (avoiding training stress).

2. Eat protein-rich food – with rhythm

  • High-quality amino acids (especially leucine, glutamine, glycine).
  • Protein-dense meals in anabolic time windows (e.g. after training or in the morning).
  • HMB, Collagen, Creatine, BCAAs, Ashwagandha, Zinc, Magnesium, Omega-3
  • mTOR activators: insulin (targeted!), leucine, resistance training

Anabolic substances: The solution: Back to building mode

3. Reduce micro-inflammations

  • Silent inflammation inhibits anabolic signaling pathways and promotes muscle breakdown.

Measures:

  • Anti-inflammatory diet (omega-3, curcumin, polyphenols)
  • Gut health: Avoid leaky gut

Strengthen detoxification: Glutathione, bitter substances, lymph flow

4. Switch the autonomic nervous system

  • Construction occurs in the parasympathetic nervous system.
  • Ways to get there:
  • Breathing exercises, meditation, vagus nerve stimulation
  • Biofeedback, cold therapy, contact with nature

Integration of functional medicine

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1. Autonomic nervous system

  • Constant stress keeps us in the sympathetic nervous system (catabolic).
  • Only in the parasympathetic nervous system can the body build: sleep, digestion, cell healing.

2. Mitochondria & Energy Metabolism

  • Mitochondria are central players in the structure.
  • Anabolic phases require energy – without ATP there is no cell growth.
  • Support: Q10, NADH, B vitamins, carnitine, targeted ketosis/carb cycles3.

Detoxification Toxic load keeps the system catabolic.

  • Glutathione, sulfur compounds, fasting cycles activate autophagy – help in the transition to anabolic regeneration.

Consciousness & Relationships Those who are stuck in catabolism often also experience mental deterioration: anxiety, irritability, lack of motivation.

  • A consciously designed anabolic lifestyle (exercise, good food, relaxation) not only strengthens the body – it leads to a clearer mind and more self-confidence.
  • In relationships, differences become apparent immediately: people in the development mode are more creative, more approachable, and more productive.

The most important points:

Catabolism dominates in cases of chronic stress, inflammation, and deficiency.

Anabolic buildup requires targeted stimuli, proteins, and parasympathetic activation.

Functional medicine provides tools for diagnostics and targeted intervention. You aren't designed for constant stress—your body wants to grow, heal, and renew itself. Give it the chance to do so: with mindful movement, nourishing nutrition, and inner peace. Every muscle, every cell, every feeling can be rebuilt.

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