How to Improve Your Microbiome: A Practical Guide from Diet to Lifestyle

To improve the state of the gut microbiome, the most important steps are to increase the diversity of plant products and fiber in your daily diet, regularly consume fermented foods, and get adequate sleep, exercise, and stress management – these five areas have the strongest and best-documented impact on the composition and function of the microbiota. Initial effects, such as reduced bloating or more regular digestion, can be noticed within a few weeks, but a lasting change in the microbiome’s composition requires months of consistent habits. Probiotic and prebiotic supplementation can be a helpful addition in specific situations but does not replace these fundamentals.

This step-by-step guide covers all factors influencing the microbiome – from diet and supplementation, through sleep, physical activity, and stress, to practical ways of monitoring effects. You will find specific data, comparative tables, and references to scientific research. Whether you are starting to build healthy habits from scratch or looking to supplement your existing knowledge about the gut – each chapter can be read independently or you can go through the entire guide.

1. What is the microbiome and why is its condition important?

The gut microbiome is a collective name for billions of microorganisms – mainly bacteria, but also viruses, fungi, and archaea – that inhabit our digestive system, primarily the colon. It is not a passive "tenant": this internal ecosystem actively participates in digestion, produces certain vitamins, shapes the functioning of the immune system, and communicates with the brain. The composition and diversity of the microbiome influence how we digest food, how we respond to stress, and how efficiently our immunity works.

1.1. How many microorganisms make up the gut microbiome?

The scale of the gut microbiome is hard to imagine, but a few numbers illustrate it well:

• Approximately 38 trillion bacterial cells inhabit the adult human body – a number of a similar order of magnitude to the number of human body cells (around 30 trillion).
• In a single individual, 300 to 500 species of bacteria dominate, although the total catalog of species identified in global population studies currently numbers over 4600 species.
• The genome of gut bacteria alone contains at least several million unique genes – by comparison, the human genome has approximately 20,000 genes.
• Nearly 90% of the microbiota in a healthy adult belongs to two groups of bacteria: Firmicutes and Bacteroidetes.

1.2. What is the gut-brain axis?

The gut-brain axis is a bidirectional communication system between the gut and the brain. Signals flow in both directions – the brain influences motility and secretion in the gut (hence "butterflies in the stomach" before a stressful event), and the gut microbiome affects brain function through several parallel pathways:

• Vagus nerve – a direct neural connection between the gut and the brain, transmitting signals about the state of the microbiota.
• Immune system – gut bacteria modulate inflammation, which is reflected in the functioning of the nervous system.
• Short-chain fatty acids (SCFAs) – products of fiber fermentation by gut bacteria, which can affect the permeability of the blood-brain barrier and regulate gene expression in neurons.
• Neurotransmitters – gut bacteria participate in the metabolism and production of compounds such as serotonin, GABA, and dopamine, which play a key role in mood regulation.

Research on the gut-brain axis is developing very dynamically, and observed links between microbiota composition and mood disorders or cognitive functions are increasingly well-documented. However, causal mechanisms are still the subject of active research – science confirms the existence of this communication, but not all its consequences are yet fully understood.

1.3. What does the microbiome really affect? What is confirmed by science, and what is preliminary?

Many simplifications have arisen around the microbiome – we distinguish what is well-established from what is still being clarified.

Scroll right to see the full table (on mobile devices) →

Some of the mechanisms listed – especially those concerning specific strains of probiotic bacteria – are described in more detail in the article Probiotics and prebiotics – what they are, how they work, and how to use them?.

1.4. Diversity or abundance – what matters more for gut health?

In the context of the microbiome, it's not just about how many bacteria we have in our intestines, but primarily how diverse their composition is. This diversity is referred to as alpha diversity, most often measured by the Shannon index, which considers the number of different species and the proportions between them.

Reduced microbiota diversity is one of the most frequently recurring signals in research on intestinal disorders, including inflammatory bowel diseases and bacterial infections. For this reason, diversity is often treated as one of the practical indicators of microbiome health.

However, it should be noted that the "more diversity = better" relationship is not that simple – some studies indicate that very high diversity does not always translate into better health outcomes, and the optimal level may depend on individual characteristics of the body. Despite these nuances, from a practical perspective, the best-documented strategy for increasing microbiota diversity is a diverse diet rich in plant-based foods – this topic is explored further in chapter 3.2.

2. What harms the microbiome? Dysbiosis risk factors

Dysbiosis, or an imbalance of the gut microbiota, is rarely the result of a single event. More often, it is the sum of daily factors – some unavoidable (e.g., necessary antibiotic treatment), others largely dependent on lifestyle. Below we present six factors that most strongly influence the composition and diversity of the microbiome.

2.1. How do antibiotics affect the microbiome and how long does regeneration take?

Antibiotics are currently one of the strongest factors disrupting the gut microbiome. They act non-selectively – they reduce bacterial populations by several orders of magnitude and decrease species diversity after just a few days of use.

The good news: the microbiome is surprisingly resilient, and in healthy individuals, species diversity returns to a level close to baseline most often within 2 months. However, full recovery to the baseline state takes longer, and some studies indicate that some strains may not recover even after 6 months after the end of treatment. The pace and extent of regeneration depend on several factors:

• Type and spectrum of antibiotic – broad-spectrum antibiotics are more destructive than narrow-spectrum, targeted ones
• Frequency of use – repeated antibiotic courses hinder full regeneration
• Diet before treatment – a fiber-poor diet before antibiotic treatment is associated with slower microbiota regeneration after its completion
• Age – in older people and young children, the recovery of bacterial flora to the baseline state can be slower

2.2. Does a diet low in fiber and high in ultra-processed foods harm the microbiome?

This is one of the most important and best-documented factors affecting the microbiome – so significant that we dedicate an entire chapter 3 to it.

Highly processed foods (from the UPF group, ultra-processed food) are characterized by a low fiber content and a high content of additives, such as emulsifiers, preservatives, and artificial flavorings. Research indicates that a diet rich in such products is associated with:

• reduced microbiota diversity (alpha-diversity)
• lower levels of beneficial bacteria, such as Akkermansia muciniphila and Faecalibacterium prausnitzii
• an increase in the proportion of pro-inflammatory bacteria
• decreased production of short-chain fatty acids (SCFAs)

This correlation results from a simple mechanism: fiber is the main "fuel" for gut bacteria that produce SCFAs. If the diet provides too little of it, these beneficial strains have nothing to "live on," and their place is taken by microorganisms that thrive better in a fiber-poor environment – often with a pro-inflammatory profile.

2.3. How do stress and cortisol affect the microbiome?

The microbiome and the stress response system (HPA axis – hypothalamus-pituitary-adrenal) communicate bidirectionally. Chronic stress and high cortisol levels can increase the permeability of the gut barrier and shift the composition of the microbiota towards dysbiosis – with a decrease in diversity and a reduction in the proportion of anti-inflammatory bacteria.

We describe this mechanism, along with practical strategies for managing stress as an element of gut care, in detail in chapter 7.

2.4. Do alcohol and tobacco smoking disrupt the microbiome?

Alcohol – even moderate, regular alcohol consumption is associated with changes in the composition of the gut microbiota. Studies observe a decrease in the number of anti-inflammatory bacteria (Akkermansia muciniphila, Faecalibacterium prausnitzii) and an increase in the proportion of pro-inflammatory bacteria, as well as increased permeability of the intestinal barrier ("leaky gut"). In individuals with alcohol use disorders, dysbiosis can persist for several weeks after cessation, indicating that regeneration in this case is not immediate.

Tobacco smoking – the impact of smoking on the gut microbiome is less clear-cut than in the case of alcohol. Studies show that smoking changes the composition of the microbiota, but these effects vary depending on the health context – in some studies, they were linked to different risks for various inflammatory bowel diseases. Regardless of the impact on the microbiome, the negative effects of smoking on digestive health and overall body condition are well-documented for other reasons.

2.5. Does an overly sterile environment harm the microbiome? The hygiene hypothesis

The hygiene hypothesis, in its original form, posited that limited contact with microorganisms in childhood "insufficiently trained" the immune system, increasing the risk of allergies. This most literal version of the hypothesis – that a lack of infections is the problem – has been largely revised.

The contemporary version of this concept, sometimes referred to as the biodiversity hypothesis, emphasizes not infections, but the microbiological diversity of the environment – contact with nature, animals, soil, and a diverse microbiological environment in early childhood. Cohort studies consistently indicate that lower gut microbiota diversity in infancy is associated with a higher risk of allergic diseases (e.g., atopic dermatitis, allergic rhinitis) in later life.

For adults, the practical conclusion is that excessive sterilization of the daily environment (e.g., widespread use of strong antibacterial agents for everything) has no health justification, and contact with a naturally diverse environment – including fermented foods, pets, and outdoor activities – supports microbiota diversity.

2.6. How does sleep deprivation affect the gut microbiome?

The composition of the gut microbiota follows a circadian rhythm, and its disruption—due to sleep deprivation, shift work, or irregular meal times—can shift this composition in an unfavorable direction. This relationship also works in reverse: the state of the microbiome affects sleep quality. This bidirectional mechanism, along with practical implications, is explored in Chapter 5.

The table below summarizes all six factors from this chapter.

Scroll right to see the full table (on mobile devices) →

3. Diet as the Foundation of a Healthy Microbiome

Of all factors influencing the gut microbiome, diet is the most significant and rapidly impactful—changes in microbiota composition after dietary modification can be observed within a few days. In this chapter, we move from general mechanisms to specific, practical dietary choices.

3.1. Which fractions of prebiotic fiber best support the microbiome?

Prebiotic fiber is not a single compound but an entire group of different substances sharing one characteristic: they are not digested by human enzymes but serve as food for gut bacteria. However, different fiber fractions are fermented by different groups of bacteria, at different rates, and with varying effects.

Scroll right to see the full table (on mobile devices) →

The practical conclusion from this comparison is simple: diversity of fiber sources is more important than maximizing a single fraction. Combining different types of fiber (e.g., resistant starch with pectins) allows for nourishing a broader range of gut bacteria with a lower risk of digestive discomfort than focusing solely on inulin or FOS.

More about resistant starch itself – including how to easily increase it in your diet by cooling starchy foods – can be found in the article Resistant starch – what it is and in which foods it is found?

BICAPS Butyric Sodium Butyrate 60 capsules - ForMeds

3.2. Does the "30 different plant foods a week" rule really work?

Yes – and it is one of the best-documented principles in microbiome nutrition. It comes from the American Gut Project, one of the largest microbiome research projects, which analyzed stool samples and dietary habits of over 10,000 people from the USA, UK, and Australia.

The results were clear: individuals consuming more than 30 different types of plant foods per week had a significantly more diverse microbiome than those eating 10 or fewer types of plants – regardless of whether they followed a vegan, vegetarian, or mixed diet. The group eating more plants also had fewer antibiotic resistance genes in their microbiome.

Significantly, "30 different plants" does not mean 30 large servings of vegetables. This number includes:

• vegetables and fruits (each type counted separately)
• herbs and spices (e.g., basil, turmeric, ginger, garlic)
• nuts and seeds
• groats, flakes, and whole grain products
• legumes (each type – beans, lentils, chickpeas – counted separately)

3.3. How do polyphenols affect the microbiome through bacterial fermentation?

Polyphenols – compounds found in berries, citrus fruits, green tea, cocoa, red wine, olive oil, and herbs – are another group of ingredients whose action is inextricably linked to the microbiome. This relationship works both ways:

• Polyphenols influence the microbiome – they can promote the growth of beneficial bacteria and limit the development of some potentially harmful bacteria.
• The microbiome transforms polyphenols – most polyphenols, when consumed, are poorly absorbed by the body. It is gut bacteria that metabolize them into smaller, much more absorbable, and biologically active compounds.

An example is urolithins – metabolites formed from ellagitannins (compounds found in pomegranates, walnuts, and some berries) exclusively through the action of specific gut bacteria (e.g., from the genus Gordonibacter). Similarly, equol, a metabolite of soy isoflavones, is produced only in individuals whose microbiota contains appropriate bacterial strains.

From a practical point of view, this means that regular consumption of polyphenol-rich foods – including herbal teas, green tea, or cocoa – supports the microbiome in two ways: it provides substrates for fermentation and simultaneously promotes the proliferation of bacteria capable of producing beneficial metabolites.

3.4. What fermented products support the microbiome and how to introduce them into your diet?

Fermented products – pickles, yogurt, kefir, kombucha, fermented cottage cheese – are a natural source of live microorganisms and compounds formed during the fermentation process. In 2021, researchers from Stanford University compared the effect of a diet rich in fermented products with a fiber-rich diet on the microbiome of 36 healthy individuals over 10 weeks.

The results were surprising: a diet rich in fermented products increased microbiota diversity and lowered the level of 19 inflammatory markers in the blood, while a fiber-rich diet – contrary to the researchers' expectations – did not significantly affect microbiota diversity in this short period. The effect of increased diversity was stronger with larger servings of fermented products.

However, this is not an argument against fiber – both strategies (fiber and fermentation) act on different aspects of the microbiome and complement each other best, which is reflected in the very structure of this chapter.

A detailed overview of the properties of individual fermented products, including vegetable pickles, can be found in the article Pickles and gut health – what properties do natural fermented products have?

3.5. What should you limit in your diet to avoid harming the microbiome?

Just as certain products support the microbiome, others can act in the opposite direction. Three groups deserve special attention.

Sugar and Trans Fats

A diet high in simple sugars and trans fats is typical of highly processed foods, which we already described in Chapter 2 – it limits fiber availability, promotes the proliferation of pro-inflammatory bacteria, and reduces SCFA production. Limiting these ingredients is one of the most universal steps, regardless of the dietary model you choose.

Emulsifiers

Emulsifiers – substances added to food to improve texture and extend shelf life (e.g., carboxymethylcellulose E466 and polysorbate 80 E433) – are among the most frequently studied additives for their impact on the microbiome. Studies on gut models and in humans have shown that they can:

• thin the protective intestinal mucus layer
• increase intestinal barrier permeability
• reduce microbiota diversity and SCFA levels
• promote the proliferation of bacteria with pro-inflammatory potential

These emulsifiers are most commonly found in products such as sauces, dressings, ice cream, confectionery, and industrial bread – reading labels and choosing products with shorter ingredient lists naturally helps limit their consumption.

Sweeteners

The impact of sweeteners on the microbiome is a topic where research is not clear. Some studies – including one of the most frequently cited – indicate that saccharin can change the composition of the gut microbiota and worsen glucose tolerance. However, newer systematic reviews emphasize that the results of studies on sweeteners and emulsifiers are inconsistent – the same additive is described in different studies as harmful, neutral, or even beneficial, depending on the dose, study duration, and methodology.

A practical conclusion: both for emulsifiers and sweeteners, the safest approach is moderation, not complete elimination at all costs – especially since the evidence is not clear enough to justify drastic restrictions in healthy individuals.

4. Probiotic and Prebiotic Supplementation – When and How

The diet and lifestyle described in previous chapters are the foundation of a healthy microbiome – for most people, these bring the greatest and most lasting effects. Probiotic and prebiotic supplementation is an additional tool that can be helpful in specific situations but does not replace daily dietary habits.

The mechanisms of probiotic action, their classification into strains, types of prebiotics, and detailed indications are extensively described in the article Probiotics and prebiotics – what they are, how they work, and how to use them? – in this chapter, we focus on the practical aspect: when to consider supplementation in the context of microbiome restoration and how to choose a preparation.

4.1. When should you consider probiotic or prebiotic supplementation?

Supplementation has the best documented applications in several specific situations:

• During and after antibiotic therapy – this is the most thoroughly researched indication. Meta-analyses of clinical trials indicate that using specific probiotic strains during antibiotic therapy can reduce the risk of antibiotic-associated diarrhea. In one meta-analysis covering over 11,000 adult patients, the risk of such diarrhea was lower in the probiotic group than in the control group.
• After gastrointestinal infections – as a supportive element for restoring microbiota balance.
• For occasional digestive discomfort – bloating, irregular bowel movements, or a feeling of heaviness after meals can be indications to try supplementation, although effects are individual and depend on the specific strain.
• During periods of dietary change, travel, or increased stress – situations that can temporarily disrupt microbiota balance (as described in Chapter 2).

Probiotic research consistently points to strain specificity – efficacy demonstrated for one strain does not automatically mean efficacy for an entire bacterial genus or species. This is one of the main reasons why the results of various "probiotic" studies can be ambiguous.

4.2. How to choose a good probiotic? What to look for when selecting a product

The market for probiotic supplements is very diverse, and merely the word "probiotic" on the label says little about the product's actual effectiveness. When choosing, pay attention to several elements:

• Specific strain, not just species – the label should include the full name of the strain (e.g., Lactobacillus rhamnosus GG, Saccharomyces boulardii CNCM I-745), and not just the genus and species. The strain, not the species, is the unit for which clinical trials are conducted.
• Number of CFUs (colony-forming units) – most clinical studies use preparations ranging from several to several tens of billions of CFUs per dose. A high CFU count alone does not guarantee efficacy if the strain has no research confirmation for a given application.
• Form of preparation – enteric-coated capsules protect bacteria from the stomach environment, which is important for strains sensitive to stomach acid. Some strains (e.g., Saccharomyces boulardii, which is a yeast, not a bacterium) are naturally resistant to stomach conditions.
• Connection to clinical studies – check if the given strain has been tested in a context similar to your situation (e.g., supporting the microbiota after antibiotic therapy), and not just generally described as a "probiotic."
• Storage conditions – some preparations require refrigeration, which affects bacterial viability until the expiration date.

5. Sleep and the Microbiome – An Underestimated Connection

Sleep rarely appears on the list of "things that affect the microbiome" – yet research into this connection has been intensely developing in recent years. The relationship between sleep and the gut microbiota is bidirectional: how we sleep affects the composition of bacteria in our gut, and the composition of the microbiota affects how we sleep.

5.1. How does the circadian rhythm affect the microbiome composition?

The gut microbiome is not static over time – its composition undergoes rhythmic, daily fluctuations, closely related to the feeding and fasting cycle, i.e., the hours when we eat and sleep. In people with a regular daily routine, these fluctuations are predictable and synchronized with the body's biological clock.

Problems arise when this rhythm is constantly disrupted – by shift work, frequent travel across time zones (known as jet lag), or simply irregular meal and sleep times. In such situations, the diurnal rhythmicity of the microbiota "blurs," and its composition shifts in an unfavorable direction – for example, a change in the proportion between two dominant groups of bacteria (Firmicutes and Bacteroidetes) is observed, which has been linked in studies to metabolic disorders.

Interestingly, studies indicate that this effect can be partially reversed by a regular, time-restricted eating window (eating within fixed, limited hours during the day) – such regularity helps restore the natural rhythm of the microbiota even with a disturbed circadian rhythm.

5.2. How do sleep deprivation and sleep disorders lead to dysbiosis?

Sleep deprivation and fragmentation (frequent waking at night) are consistently linked to gut dysbiosis in studies. This mechanism involves several interconnected elements:

• Increased intestinal barrier permeability – circadian rhythm disturbances lead to "loosening" of the intestinal epithelium, which facilitates the penetration of bacterial components into the bloodstream and exacerbates inflammation.
• Activation of the HPA axis – sleep deprivation stimulates the same stress response axis (involving cortisol) that we describe in more detail in Chapter 7 in the context of stress.
• Decrease in anti-inflammatory, butyrate-producing bacteria – with a simultaneous increase in the proportion of pro-inflammatory bacteria.

Studies on shift workers show that a disturbed sleep rhythm is associated with changes in the composition and function of the gut microbiota, which in cohort studies have been linked to a higher risk of metabolic syndrome, gastrointestinal ailments, and mood swings.

5.3. How does the microbiome affect sleep quality? A bidirectional relationship

The other side of this relationship is equally important: the composition of the gut microbiota affects sleep regulation. Some gut bacteria, including those from the genera Lactobacillus and Bifidobacterium, are involved in the metabolism of serotonin precursors and the production of GABA – neurotransmitters of key importance for regulating the sleep-wake cycle and the process of falling asleep.

The microbiota also influences the expression of biological clock genes in the brain and liver, meaning its disruption can dysregulate the body's central circadian rhythm – not just the "local," intestinal one. In several interventional studies, probiotic supplementation has been associated with improved subjectively assessed sleep quality, however, this area of research is still at an early stage and requires confirmation in larger, well-controlled studies.

In practice, these two dependencies create a loop – in both possible directions. Good sleep supports a healthy, diverse microbiome, and a healthy microbiome supports good sleep. Similarly, disturbed sleep exacerbates dysbiosis, and dysbiosis can further hinder falling asleep and recovery – meaning that improvement in one of these areas often translates to the other.

The mechanism of the HPA axis and cortisol, which appears with sleep disorders, is part of a broader picture of the impact of stress on the microbiome – in Chapter 7, we expand on this topic and present specific stress reduction strategies.

6. Physical Activity and the Microbiome

Movement is one of the factors that – alongside diet – most strongly and rapidly influence the composition of the gut microbiota. At the same time, this is an area where it is worth distinguishing the effect of moderate, regular activity from the effect of very intense, prolonged training – because these two scenarios affect the gut in completely different ways.

6.1. What do studies say about the impact of endurance and strength training on the microbiome?

Most data concerns endurance training. Studies consistently indicate that regular, long-term endurance training is associated with an increase in microbiota diversity and an increased proportion of bacteria such as Prevotella, Akkermansia, and Faecalibacterium – i.e., genera linked to SCFA production and improved gut barrier integrity. Competitive athletes (e.g., professional rugby players) show higher microbiota diversity in studies than individuals with a sedentary lifestyle.

Strength training is much less studied in this regard. Available data are ambiguous – some studies indicate changes in the microbiota related to strength results, while others show no significant differences compared to non-training individuals. In a mouse model study, endurance training more strongly increased microbiota diversity than strength training, although both types of training led to distinct, specific changes in the composition of individual bacterial groups.

Scroll right to see the full table (on mobile devices) →

6.2. How does training intensity affect the intestinal barrier?

This is where physical activity can work in two opposite directions – depending on intensity and duration.

Moderate activity supports the intestinal barrier – it improves gut blood supply, increases butyrate production, and aids in the regeneration of the intestinal epithelium.

Very intense or prolonged exertion can temporarily increase gut permeability ("leaky gut"). Even an hour of intense treadmill running increases small intestine permeability in tested runners, while low-intensity running does not cause this effect. In endurance athletes (marathon runners, triathletes), an increase in markers such as LPS, I-FABP, and zonulin – indicators of increased intestinal permeability – is observed during and after exercise.

The mechanism is physiological: during intense exercise, the body directs blood to muscles and the heart, limiting blood flow to the intestines (known as splanchnic hypoperfusion). With prolonged duration or high intensity, this leads to hypoxia of intestinal epithelial cells and loosening of the tight junctions between them. High ambient temperature exacerbates this effect.

Important nuance: increased permeability after exercise is usually temporary and does not necessarily involve digestive symptoms – in many people, it occurs "silently," without bloating or abdominal pain. Its scale also depends on the recovery time between training sessions – too short intervals between intense workouts do not give the intestinal epithelium time to repair.

6.3. How to train to support the microbiome? Practical conclusions

• Regularity is more important than maximum intensity – from the microbiome's perspective, several sessions of moderate activity per week provide benefits without the risk associated with gut barrier overload.
• Very long and intense workouts require adequate recovery – both for muscles and the gut. Too frequent, closely spaced high-intensity sessions do not give the intestinal epithelium time to rebuild.
• Strength training is less studied in terms of the microbiome, but general physical activity – regardless of its form – is associated with higher microbiota diversity compared to a sedentary lifestyle.
• Diet supports gut resilience to exertion – an adequate intake of fiber and polyphenols (sections 3.1 and 3.3) helps regenerate the intestinal barrier stressed by intense training.

7. Stress and the Microbiome – The Gut-Brain Axis in Practice

In Chapter 2, we mentioned that chronic stress and cortisol are one of the factors disturbing the microbiome. In this chapter, we expand on this mechanism and – more importantly – move on to practical strategies that can help break this cycle.

7.1. How does the cortisol mechanism lead to stress-induced dysbiosis?

The stress response proceeds through the hypothalamus-pituitary-adrenal (HPA) axis and the sympathetic nervous system, leading to an increase in cortisol and catecholamine levels. These hormonal changes affect the gut in several ways:

• Altered intestinal transit time – stress can speed up or slow down the movement of contents through the intestines.
• Reduced mucus production – the protective layer of the intestinal epithelium becomes weaker.
• Increased intestinal barrier permeability – cortisol affects tight junction proteins between epithelial cells, "loosening" the barrier.
• Changes in microbiota composition – studies on students under chronic stress showed a decrease in the number of health-beneficial bacteria compared to periods of lower stress.

What is important for understanding why stress can be so difficult to "cure" with a dietary approach alone: a vicious cycle is created here. Increased intestinal permeability and dysbiosis exacerbate inflammation, and inflammation, in turn, can intensify the perception of stress and deepen the HPA axis response. In human studies – for example, a public speaking test – small intestine permeability significantly increased, but only in individuals who actually experienced a cortisol response to the stressor. This shows that it is not the stressful situation itself, but the body's physiological response to it that is significant for the gut.

7.2. What stress reduction strategies support the microbiome?

Good news: since the mechanism works both ways, stress-reducing actions can genuinely support microbiome rebuilding – whether they act "from the brain" or "from the gut." The best-documented strategies include:

• Regular physical activity – lowers HPA axis reactivity and simultaneously supports the microbiome through the mechanisms described in Chapter 6.
• Adequate quantity and quality of sleep – sleep and stress share the same hormonal axis (HPA), as described in Chapter 5.
• Relaxation and mindfulness techniques – regular practice of breathing techniques, meditation, or relaxation training is associated with reduced reactivity to stress.
• Contact with nature and offline time – limiting constant stimulation (including excessive use of devices) supports nervous system regeneration.

If you are looking for a more detailed guide on how to naturally lower cortisol – including specific habits, herbs, and supplements – you will find it in the article How to naturally lower cortisol? Diet, herbs, supplements and lifestyle.

7.3. How can adaptogens indirectly influence the microbiome?

Adaptogens – a group of herbs and mushrooms such as ashwagandha, rhodiola (Rhodiola rosea), and reishi – have long been used to support the body's resilience to stress. Their connection with the microbiome is primarily indirect: by influencing the reactivity of the HPA axis and cortisol levels, adaptogens can limit the mechanism of stress-induced dysbiosis described in 7.1.

Some preclinical studies (mainly in animal models) also indicate a direct effect of certain adaptogens on the composition of the gut microbiota. However, evidence from human studies in this area is still limited, and preclinical results do not automatically translate to effects in humans. For this reason, in the context of the microbiome, adaptogens should be treated as a component supporting stress reduction – and indirectly, through this mechanism, as support for the gut – rather than as a direct "microbiome therapy."

An overview of adaptogens, their applications, and mechanisms of action in the context of stress resilience can be found in the article Top 5 adaptogens for better immunity and energy.

8. How quickly can the microbiome be rebuilt?

This is one of the most frequently asked questions – and the answer depends on what we actually mean by "rebuilding." Changing the composition of the microbiota and permanently altering its function are two different time scales.

8.1. How quickly does diet change microbiome composition? What do studies say?

One of the most well-known studies on this topic showed that the composition of the gut microbiota reacts to dietary changes within a single day. American researchers asked volunteers to switch to a diet consisting exclusively of animal products or exclusively plant-based products – changes in the composition and activity of the microbiota were visible almost immediately, resembling profiles typical of carnivorous or herbivorous animals.

This is good news, but with an important caveat: these rapid changes are also quickly reversible. When the diet returns to its previous pattern, the microbiota largely returns to its former composition. In other words, a one-time "detox" or a week-long dietary change can have a short-term effect, but it will not permanently change the "baseline" of the microbiota. Other studies even indicate that the effects of long-term dietary patterns can accumulate across generations – a fiber-poor diet leads to a progressive loss of certain bacterial species that are difficult to restore even after returning to a fiber-rich diet.

8.2. Realistic expectations: days, weeks, months, years

Scroll right to see the full table (on mobile devices) →

The practical conclusion is that the first effects (e.g., less bloating, more regular bowel movements) can be felt within a few days to a few weeks, but a lasting change in the composition and function of the microbiota is a process measured in months – and requires consistency, not one-off interventions.

8.3. What biomarkers can be observed without laboratory tests?

You don't need a microbiome test to notice that something is changing. Here are a few practical indicators you can observe on an ongoing basis:

• Regularity and consistency of bowel movements – a stable rhythm and consistency similar to a "formed sausage" (type 3-4 on the Bristol stool scale) is a good sign
• Frequency of bloating and gas – their reduction after dietary changes is often one of the first noticeable effects
• Energy levels after meals – fewer energy "crashes" after eating
• Skin condition – for some people, dietary changes are associated with an observed improvement in skin condition, although this relationship is complex and individual
• Frequency of infections – fewer seasonal infections may (though not necessarily) be an indirect signal of better immune system function

None of these signals alone is "proof" of a specific microbiome composition, but together they provide a practical picture of whether the changes introduced are having an effect. If you are looking for plant-based support during microbiome restoration, read the article Herbs for gut cleansing – which ones really work?

9. How to monitor the state of the microbiome?

With the growing popularity of the microbiome topic, many tests "examining the microbiome" have appeared on the market – find out what they actually measure and what they cannot replace.

9.1. What do microbiome tests measure and what are their limitations?

Most microbiome tests available on the market are based on sequencing the 16S rRNA gene from a stool sample. This method allows determining which groups of bacteria (and in what proportions) are present in the sample – this is real and valuable scientific information.

The problem lies elsewhere – in the interpretation of the results:

• Lack of standardized reference ranges – unlike blood tests (e.g., glucose or cholesterol levels), there are no universally approved "norms" against which the microbiome result can be definitively assessed
• High day-to-day variability – the composition of the microbiota fluctuates depending on recent meals, hydration, or even the time of sample collection
• The result itself does not diagnose a disease – the presence or absence of specific bacteria may correlate with various health conditions, but it is not an independent diagnostic criterion

Microbiome tests can be an interesting tool for tracking changes over time in the same person (e.g., before and after dietary changes) – in this context, they are more useful than as a one-time "diagnosis."

9.2. What clinical symptoms can indicate the state of the microbiome?

In everyday practice, the most information about the state of the microbiome comes from observing one's own body – in four main areas:

• Digestion – regularity of bowel movements, bloating, gas, feeling of heaviness after meals
• Skin – changes in skin condition are sometimes linked to the state of the microbiota, although the mechanism of this relationship (the gut-skin axis) is still under investigation and should not be treated as an unequivocal diagnostic indicator
• Mood and concentration – as described in chapters 1 and 5, the gut-brain axis means that mood swings or "brain fog" can be partly related to the state of the gut, although there are usually many causes for such symptoms
• Immunity – frequency of infections and seasonal allergies

None of these symptoms alone is specific to the microbiome – all can also have other causes. However, when considered together and observed over time, they provide a practical picture of the direction in which changes are occurring.

9.3. When should you consult a doctor or dietitian?

Caring for the microbiome through diet and lifestyle is safe for most healthy people, but there are situations where self-experimentation is not the appropriate approach.

These symptoms require medical diagnosis – they should not be resolved solely by dietary changes or supplementation. Beyond "alarm" indicators, consulting a dietitian is also a good solution if, despite implementing the changes described in this guide, digestive ailments do not subside after a few weeks – in such a situation, a more individualized approach may be needed, e.g., temporary elimination of certain food groups and their controlled reintroduction.

10. FAQ

10.1. Does microbiome composition change with age?

Yes. The diversity of the gut microbiota is usually highest in adulthood and tends to decrease in old age, accompanied by a decrease in the proportion of SCFA-producing bacteria and an increase in pro-inflammatory bacteria. However, the rate and scale of these changes are highly individualized – diet and physical activity remain important factors modifying the microbiome regardless of age.

10.2. Does the mode of delivery (C-section) affect the baby's microbiome?

Studies consistently indicate that babies born by C-section have a different microbiota composition in the first months of life than babies born naturally – most often a lower proportion of bacteria from the genera Bacteroides and Bifidobacterium. These differences are partially mitigated by exclusive breastfeeding, and over time (after the first year of life), differences between groups become less pronounced for many bacterial species.

10.3. Does intermittent fasting support the microbiome?

As mentioned in Chapter 5, the gut microbiota exhibits a natural circadian rhythm associated with the feeding and fasting cycle, and a regular, time-restricted eating window can support this rhythm. However, research on intermittent fasting in the context of the microbiome is still in its early stages – current data suggest potential benefits related to regularity, but do not yet allow for definitive recommendations regarding specific fasting protocols.

10.4. Does a vegetarian or vegan diet automatically mean a healthier microbiome?

Not necessarily. As the American Gut Project showed (described in Chapter 3.2), it was the number of different plant products in the diet, rather than the diet label itself (vegan, vegetarian, or mixed), that was most strongly associated with microbiome diversity. A vegetarian diet based primarily on highly processed meat substitutes may fare worse in this regard than a varied mixed diet rich in vegetables, fruits, herbs, and legumes.

10.5. Will one slip-up on an unhealthy diet destroy the effects of previous work on the microbiome?

No. As we described in Chapter 8, the microbiota reacts quickly to dietary changes, but these short-term fluctuations are largely reversible. A single meal or even a few days of deviation from the usual eating pattern will not reverse months of consistent habits. Long-term, repetitive dietary patterns are what matter – not single episodes.

10.6. Is it worth taking probiotics preventively, permanently, without a specific reason?

The best-documented indications for probiotic supplementation – described in Chapter 4 – concern specific situations, such as antibiotic therapy. Long-term, "preventive" probiotic intake without a specific indication is not harmful for most healthy individuals, but there is also no strong evidence that it provides additional benefit compared to a diet rich in fiber and fermented foods (Chapter 3), which form the foundation of a healthy microbiome regardless of potential supplementation.

11. Summary

A healthy gut microbiome is not the result of one "magic" intervention, but the sum of daily habits – and that's good news, because it means you have a real influence over it. Key takeaways from this guide:

• Diversity is more important than single "superfoods" – both in the context of fiber (Chapter 3.1) and the overall number of different plant products per week (Chapter 3.2)
• Diet is the foundation – prebiotic fiber, polyphenols, and fermented products have the greatest, best-documented impact on the microbiome (Chapter 3)
• Sleep, movement, and stress are just as important as diet – all three areas are linked by the gut-brain axis mechanism and its impact on intestinal barrier permeability (Chapters 5-7)
• Supplementation is an addition, not a foundation – probiotics and prebiotics have the best-documented use in specific situations, e.g., after antibiotic therapy (Chapter 4)
• Regeneration requires time and consistency – the first effects can be felt within a few weeks, but a lasting change is a process measured in months (Chapter 8)
• Observing your own body is a good starting point – regularity of digestion, energy levels, and well-being tell you more than a one-time microbiome test (Chapter 9)

If you were to choose just one change to start with – the greatest, best-documented effect will come from increasing the diversity of plant products in your daily diet and regularly incorporating fermented foods. The rest – sleep, physical activity, stress reduction – should be built gradually, as a complement to this foundation.

12. Sources

1. Sender R, Fuchs S, Milo R. (2016). Revised Estimates for the Number of Human and Bacteria Cells in the Body. PLoS Biology, 14(8): e1002533. PMID: 27541686. DOI: 10.1371/journal.pbio.1002533 (section 1)
2. McDonald D. et al. (2018). American Gut: An Open Platform for Citizen Science Microbiome Research. mSystems, 3(3): e00031-18. PMID: 29795809. DOI: 10.1128/mSystems.00031-18 (section 3.2)
3. Wastyk H.C. et al. (2021). Gut-microbiota-targeted diets modulate human immune status. Cell, 184(16): 4137-4153. PMID: 34256014. DOI: 10.1016/j.cell.2021.06.019 (section 3.4)
4. Chassaing B. et al. (2015). Dietary emulsifiers impact the mouse gut microbiota promoting colitis and metabolic syndrome. Nature, 519(7541): 92-96. PMID: 25731162. DOI: 10.1038/nature14232 (section 3.5)
5. Suez J. et al. (2014). Artificial sweeteners induce glucose intolerance by altering the gut microbiota. Nature, 514(7521): 181-186. PMID: 25231862. DOI: 10.1038/nature13793 (section 3.5)
6. Palleja A. et al. (2018). Recovery of gut microbiota of healthy adults following antibiotic exposure. Nature Microbiology, 3(11): 1255-1265. PMID: 30349083. DOI: 10.1038/s41564-018-0257-9 (section 2.1)
7. Blaabjerg S. et al. (2017). Probiotics for the Prevention of Antibiotic-Associated Diarrhea – systematic reviews and meta-analyses. Nutrients, 9(12): 1321. PMID: 29214004. DOI: 10.3390/nu9121321 (section 4.1)
8. McFarland L.V. et al. (2018). Strain-Specificity and Disease-Specificity of Probiotic Efficacy: A Systematic Review and Meta-Analysis. Frontiers in Medicine, 5: 124. PMID: 29868573. DOI: 10.3389/fmed.2018.00124 (section 4.1)
9. Smith R.P. et al. (2020). Sleep, circadian rhythm, and gut microbiota. Sleep Medicine Reviews, 53: 101340. PMID: 32668369. DOI: 10.1016/j.smrv.2020.101340 (section 5)
10. Wang T. et al. (2024). Gut microbiota and sleep: Interaction mechanisms and therapeutic prospects. Open Life Sciences, 19(1): 20220317. PMID: 39035457. DOI: 10.1515/med-2022-0317 (section 5)
11. Yang D. et al. (2023). Acute sleep deprivation exacerbates systemic inflammation and psychiatry disorders through gut microbiota dysbiosis and disruption of circadian rhythms. Microbiological Research, 268: 127292. PMID: 36608535. DOI: 10.1016/j.micres.2022.127292 (section 5.2.)
12. Bona P. et al. (2023). Exercise-Induced Modulation of the Gut Microbiota: Mechanisms, Evidence, and Implications for Athlete Health. Journal of Functional Morphology and Kinesiology, 8(1): 1. PMID: 36648215. DOI: 10.3390/jfmk8010001 (section 6.1)
13. Liu X. et al. (2021). Resistance and Endurance Exercise Training Induce Differential Changes in Gut Microbiota Composition in Murine Models. Frontiers in Physiology, 12: 791953. PMID: 35002744. DOI: 10.3389/fphys.2021.791953 (section 6.1)
14. Ribeiro F.M. et al. (2021). Is There an Exercise-Intensity Threshold Capable of Avoiding the Leaky Gut? Frontiers in Nutrition, 8: 627289. PMID: 33763440. DOI: 10.3389/fnut.2021.627289 (section 6.2)
15. Madison A.A. et al. (2024). Exploring the complex relationship between psychosocial stress and the gut microbiome: implications for inflammation and immune modulation. Journal of Applied Physiology, 137(4): 855-867. PMID: 39361101. DOI: 10.1152/japplphysiol.00652.2024 (section 7.1)
16. Mika A., Fleshner M. (2015). Breaking Down the Barriers: The Gut Microbiome, Intestinal Permeability and Stress-related Psychiatric Disorders. Frontiers in Cellular Neuroscience, 9: 392. PMID: 26528141. DOI: 10.3389/fncel.2015.00392 (section 7.2)
17. David L.A. et al. (2014). Diet rapidly and reproducibly alters the human gut microbiome. Nature, 505(7484): 559-563. PMID: 24336217. DOI: 10.1038/nature12820 (section 8.1)
18. Sonnenburg E.D. et al. (2016). Diet-induced extinctions in the gut microbiota compound over generations. Nature, 529(7585): 212-215. PMID: 26762459. DOI: 10.1038/nature16504 (section 8.1)
19. Almonacid D.E. et al. (2017). 16S rRNA gene sequencing and healthy reference ranges for 28 clinically relevant microbial taxa from the human gut microbiome. PLOS ONE, 12(5): e0176555. PMID: 28463997. DOI: 10.1371/journal.pone.0176555 – along with a subsequent Expression of Concern (2022), DOI: 10.1371/journal.pone.0276752 (section 9.1)
20. Azad M.B. et al. (2013). Impact of cesarean section delivery and breastfeeding on infant gut microbiota at one year of age. CMAJ, 185(5): 385-394. PMID: 23422288. DOI: 10.1503/cmaj.121189 (FAQ 10.2)