Many people are sceptical about taking probiotics, arguing that the bacteria will not even reach the gut where they should exert their effects because they will be digested, or at least destroyed, in the stomach. It is very easy to refute this argument, because the gut flora of newborn babies is poor compared to that of an adult – practically a few species of bacteria compared to the hundreds of species in an adult – and this gut flora could only have been formed over time through nutrition; and in any case, almost exclusively through oral intake. In the gut flora of babies, bacteria living in breast milk can be detected, but there have also been a number of other experiments monitoring specific, less common bacteria. Evidence was found that the presence of a bacterium can be detected in faeces already from the day after its ingestion.

But how long do the bacteria remain present? Once they have colonised, do they stay forever? Researchers have found answers to these questions. If the presence of a new bacterial species is linked to a particular food, it can be detected as long as the consumption of that food persists. However, a change in diet can cause the level of the bacterial species to drop almost immediately, and it may even disappear after a few weeks. This demonstrates how the composition of the microbiome depends on diet, and how quickly it can respond to a change in diet. Every species can survive in the gut as long as it is given enough food on which to grow. The gut flora of a person on a high-fat diet is completely different from that of a person eating a mainly plant-based diet. If the composition of the gut flora changes significantly due to some major external disturbance, we speak of dysbiosis.

The composition of the gut microbiome is influenced by several external and internal environmental factors: genetics, age, gender, etc. Of all the external factors studied so far, dietary habits have the greatest impact on gut microbiome composition. Faecal microbiome studies have shown that the composition of the gut flora responds dynamically to the introduction of a new diet, but if this new diet is only short-lived, it is not sufficient to permanently restore the dysbiosis observed in, for example, diabetic individuals. Overweight/obese individuals also show an imbalance of the gut flora. Microbiome studies in people with a Western lifestyle have found that diets high in fibre and carbohydrates increase the proportion of Segatella (formerly Prevotella) bacteria, while diets rich in fat and protein tend to favour the Bacteriodes group.

In overweight individuals who have been on a low-fat or low-carbohydrate, low-calorie diet for at least a year, the ratio of Bacteriodota/Bacillota (formerly Bacteroidetes/Firmicutes) increased. This change was greater the more weight the subjects managed to lose. Also, it was found that after a 6+6 weeks of a low calorie, protein-rich diet, the metabolism of obese/overweight individuals improved, and the species richness of the gut flora increased. However, the same change was negligible in individuals who already had a more species-rich gut flora to begin with.

Although microbiome testing has greatly advanced in the last decade, the exact role of the gut microbiome in the development and maintenance of obesity, diabetes, or other pathological conditions remains unanswered. Are changes in the composition of the gut flora in a cause or effect relationship with these diseases? Once we can answer these questions, it will be possible to develop therapies that can cure these diseases by correcting dysbiosis through a specific diet and/or faecal transplantation.

We have already seen that one of the most significant impacts on the composition of the microbiome is exerted by nutrition. It is perfectly logical that if we change our diet, the composition of our microbiome will change as a result. How fast is this change? How permanent is it?
Throughout evolution, humans have experienced periods of food shortage. Before preservation and even conscious food storage, there were many times when diets had to be changed abruptly. Our ancestors mainly hunted in winter, while they had access to plant food in summer and autumn. Our digestion, and with it our gut flora, had to follow the periodic changes in diet. But how fast is this change?
In fact, the effect of a minimal change in diet is almost immediate. Members of our microbiome are forced to live on the food we eat. If we eat more of one type of food, the bacteria that feed on it can multiply very quickly. Although the alpha diversity of the gut flora, i.e., the number of species, does not change significantly, the beta diversity, i.e., the ratio of the members of the gut flora to each other, does. That is why we also ask about the diet of the last 24 hours in our stool genomics test questionnaire. Researchers have shown that while a complete change in diet causes a rapid shift in the composition of the microbiome, the same change occurs very quickly in reverse as well. If the change in diet does not prove to be permanent, the original gut flora composition will be restored at the end of the change. It is therefore very important that if we are forced to make changes to our lifestyle, including our diet, in the interests of our health, we do not do so on a campaign basis, but permanently.

In ecology, diversity, or species richness, essentially shows how many species live in a given area. The higher the number of different species, the greater the diversity. We distinguish between alpha diversity, which tells us how many species can be counted, and beta diversity, which also looks at the ratio of the species relative to each other. The gut flora and our digestive system can be studied in a similar way. For example, if you look at two people, and 100 bacterial species can be described in both, then their alpha diversity is the same because 100 species can be identified in each. However, if one person is dominated by only 10 species and in the other the 100 species are evenly distributed, then the beta diversity of the first person is lower because he has fewer species in greater proportion, whereas the second person has all species equally distributed, and therefore has a higher beta diversity.

What metrics can be used to describe diversity? One of the most commonly used metrics in ecology is the Shannon index. This index measures both the alpha and beta diversity of species, and the higher the index, the greater the degree of diversity.

From the Shannon index, it is easy to calculate the value of evenness, which also measures both alpha and beta diversity. Evenness can take a value between 0 and 1 and is therefore informative in itself.

Prebiotics are natural food components that are not affected by digestive enzymes in the upper gastrointestinal tract and reach the large intestine unaltered, where they stimulate the growth of beneficial bacteria called probiotics. The most important prebiotics in food are inulin and lactose.

Beneficial bacterial flora in the gut is essential for proper gut function. Prebiotics help to restore and maintain the balance of the normal, healthy gut flora – the probiotics – by feeding the bacteria it is composed of. Important sources of prebiotics include Jerusalem artichokes, onions, bananas, garlic, beans, wheat, peas, artichokes, oatmeal, and milk.

The pH of the colon changes when the breakdown of water-soluble fibres begins. Acidic by-products are formed, which shift the pH of the colon in an acidic direction. It is known that an acidic pH is more conducive to the growth of beneficial bacteria in the gut. Therefore, adequate fibre intake is an essential part of a healthy diet.

Prebiotics and probiotics can also be consumed in the form of various dietary supplements (for example, as an adjunct to antibiotic treatment). Symbiotics are a combination of probiotics and prebiotics, i.e., preparations that combine the beneficial effects of both components.

Short-chain fatty acids are organic compounds that play an important role as food for the epithelial cells lining the colon. The best known of these are butyrates, which stimulate intestinal epithelial cells to divide and may also play a role in the prevention of colon cancer by inhibiting inflammatory processes in the colon. In the absence of butyrates, the cells of the intestinal epithelium do not function properly and commit "suicide" by autophagy. Butyrates also play a key role in maintaining immune homeostasis, both locally in the alimentary tract and at the level of the whole body, through the butyrate circulating in the blood.

Butyrates are produced by beneficial gut bacteria (probiotics) that feed on prebiotics (plant nutrients containing adequate amounts of dietary fibre). A decrease in butyrate-producing bacteria leads to microbial dysbiosis, which is reflected in low overall biodiversity and low numbers of key butyrate-producing bacteria. One way to restore healthy butyrate levels in the gut is through faecal transplantation from donors with an adequate butyrate-producing gut flora. Also, butyrate can be replenished to adequate levels from external sources by taking oral butyrate supplements.

Despite their apparent simplicity, bacteria can interact with other organisms in complex ways:

Symbiosis is the close coexistence of individuals (usually depending on each other) of two or more different species. In symbiosis, both parties benefit.

Commensalism refers to a relationship between two populations that benefits one party and is indifferent to the other.

Most of the bacteria are harmless or beneficial, but there are some species that cause infectious diseases; these are called pathogenic bacteria.

Opportunistic pathogens are microorganisms that do not cause disease in healthy organisms, only in those that are susceptible to a predisposing factor. Such predisposing factors include diabetes, alcoholism, HIV infection, etc.

Dysbiosis is an imbalance in the gut flora caused by low levels of beneficial bacteria and an overgrowth of harmful bacteria, fungi, or parasites. Abnormal shifts in the gut flora can be caused by antibiotic use, illness, stress, the ageing process, poor dietary habits (eating sugar, processed foods, or foods to which you are sensitive or allergic), and other lifestyle factors. Over the past decade, there has been a dramatic increase in the incidence of intestinal dysbiosis, with both environmental and lifestyle factors playing significant roles.

The symptoms of dysbiosis are often not recognised because the complaints do not clearly indicate a problem, and many cases go undiagnosed, even though the condition is a common cause of certain diseases. We have put together a list of the most common questions about gut flora imbalance.

The most common symptoms of dysbiosis include:

1. Increased bowel gas production or bloating, which persists most days of the week
2. Crampy, urgent bowel movements or mucus in the stool at least once a week
3. Dullness, anxiety, or depression
4. Food intolerance
5. Lack of micronutrients
6. Chronic bad breath
7. Loose stools, diarrhoea, constipation, or a combination of both

Certain conditions can further increase the chance of dysbiosis:

1. Diagnosed irritable bowel syndrome (IBS)
2. If you have a history of gastritis or food poisoning
3. Prolonged antibiotic treatment
4. Carbohydrate intolerance
5. Fatigue, low energy
6. Use of antacids to treat heartburn, reflux, or hiatus hernia
7. Autoimmune diseases such as Hashimoto's disease, psoriasis, multiple sclerosis

The most effective method of diagnosing dysbiosis is stool microbiome testing. This can provide accurate information on the species composition of the gut flora. Furthermore, stool microbiome testing also enables the monitoring of the effectiveness of dysbiosis treatment by repeated sampling.

Many of the hundreds of bacterial species that live in our intestinal tract are taxonomically well described, and we are already familiar with the specific effects of most of them on the human body. Taxonomy classifies different species with nearly identical characteristics into genera, genera into orders, orders into classes, and classes into phyla. All the bacteria in the gut flora belong to a few bacterial phyla. Each has its own function, but two bacterial phyla, Bacteriodota (formerly Bacteroidetes) and Bacillota (formerly Firmicutes), are of particular importance. Both strains include hundreds of individual bacterial species, yet even the ratio of these strains to each other is a key determinant of our health.

The relative proportion of Bacillota (formerly Firmicutes) and Bacteriodota (formerly Bacteroidetes) shows strong correlation with the body mass index (BMI) and various inflammatory diseases of the digestive tract. If Bacillota (formerly Firmicutes) are present in significantly higher proportions, the risk of obesity and inflammatory bowel disease is higher, and vice versa: those with a high BMI or with inflammatory bowel disease also have significantly higher Bacillota/Bacteriodota (formerly Firmicutes/Bacteroidetes) ratios. This can be interesting because the cause-and-effect relationship is not always clear. Is it the effect of high BMI that increases the Bacillota/Bacteriodota (formerly Firmicutes/Bacteroidetes) ratio, or is it the altered gut flora composition that causes the higher BMI? Interestingly, the answer to both questions is yes.

Following a Western-style diet, high intakes of sugar, fat, and protein increases the proportion of Bacillota (formerly Firmicutes) bacteria, while high fibre and low fat intake decreases it, to the benefit of the Bacteriodota (formerly Bacteroidetes) strain. However, transplantation of the gut flora of people with a higher BMI into others led to increased weight gain in the recipients. It is evident that gut flora status and nutrition go hand in hand, interacting closely.

Yet, what can we do to keep this ratio in check? There is no need to resort to drastic methods; the best way to influence the composition of the gut flora is through our diet.

The composition of the gut flora is determined by our diet, lifestyle, and diseases. However, this community of hundreds of species is not only influenced by external factors, but also by the members of the community themselves.

Different species composition is observed in different parts of the intestinal tract. The initial segment of the intestinal tract is dominated by bacteria that can utilize easily digestible nutrients, while the more distant parts are dominated by bacteria that live on more difficult-to-digest nutrients. Bacteria secrete hundreds of thousands of different metabolites. Many of these can be used by the human body, but they can also be used as nutrients for other bacteria to help them grow. However, what is nutritious for one species may have a negative effect on another. Certain fermentation products, such as the lactic acid, can shift the pH of surrounding areas to such an extent that they inhibit the growth of other bacteria that are sensitive to pH.

Some bacteria produce natural antibiotics, called bacteriocins, which selectively inhibit the growth of certain bacterial species.

But there are also members of this community that have not been discussed yet. The normal flora of our digestive tract includes certain bacteriophage viruses as well as fungi. These form a tight community with bacteria, and their populations are closely interdependent.

The intestinal tract is home to a dense network of neurons that act as a 'second brain', significantly influencing the way the body works. The 'second brain', or gut nervous system, is made up of roughly 400 million neurons arranged in a network that travels along the gastrointestinal tract, carrying impulses. This makes it the second largest cluster of neurons in the body after the brain, and it can function almost completely independently of the central nervous system. Although it communicates with the brain (e.g., via the spinal nerve), it can continue to function even if the connection between them is broken. The gut nervous system does not affect decision-making or consciousness, but it still plays a key role in our lives by regulating digestion. Some theories even suggest that the system can affect our emotions by producing different hormones.

Parkinson's disease is a slowly progressing neurodegenerative disease. According to current medicine, it is incurable. The disease starts with the formation of protein aggregates that are deposited in the brain, leading to the destruction of nerve cells over time.

Researchers have been able to prove that the cause of Parkinson's disease lies in the gastrointestinal tract. They have found that the defective protein aggregates are also present in the gut nervous system (the "second brain") and are transported from there to the brain via the so-called vagus nerve. This is supported by the observation that patients with Parkinson's disease often develop gastrointestinal symptoms before the movement disorders characteristic of the disease. Data from almost 15,000 patients who had their vagus nerves cut to treat gastric ulcers have been reviewed. It was found that the surgery gave patients a natural defence against Parkinson's disease. In their case, the pathway through which the disease-causing substances from the gut could have reached the brain was interrupted.

Researchers hypothesise that the development and severity of Parkinson's disease may be due to changes in the composition of the normal gut flora. In an experiment, the gut flora of Parkinson's patients were transplanted into laboratory mice, and they developed more severe movement disorders and neuroinflammatory symptoms than controls. To date, the mechanisms and pathways through which the gut flora exerts its effects on the development of neurodegenerative diseases, including Parkinson's, are poorly understood. One of these possible pathways involves the role of short-chain fatty acids produced by gut bacteria in mediating the activation and maintenance of inflammatory processes in the brain. The constant state of activation and the release of inflammatory cytokines inhibit neuronal function and increase cell death, which also contributes to the maintenance of the disease.