Good bacteria: what are they and why are they important for the body?

Digestion does not always run as smoothly as one would like. Bloating, altered bowel movements, or other unpleasant sensations can arise for a multitude of reasons. Inside our intestines lives a vast community of microorganisms, known as the gut microbiota, and a significant part of it consists of beneficial bacteria that perform various functions useful to the body.

Although much is said about the gut microbiota today, it is not always clear what role beneficial bacteria truly play, whether they can be obtained through food, and when probiotics might be beneficial. In this article, you will learn what beneficial bacteria are, what functions they perform in the body, in which foods they can be found, and what scientific research indicates about the benefits of probiotics for bloating, constipation, or diarrhea.

The human gut is home not only to bacteria but also to many other microorganisms – fungi, viruses, and other microscopic organisms. This entire "community" is called the gut microbiota. Each person's microbiota is unique and can be influenced by diet, age, lifestyle, medications, and environmental and other individual factors.

Beneficial bacteria – this is a simple, everyday term used for bacteria that, by living in the gut, perform functions beneficial to the body. They help break down some of the substances obtained from food, produce various metabolites, interact with the intestinal lining and other microorganisms, which is why bacteria should not be automatically associated with diseases. Many different microorganisms coexist in the gut, and a healthy microbiota relies not on a single "good" bacterium, but on the balance of the entire community of microorganisms and the functions they perform.

In everyday language, beneficial bacteria and probiotics are often used synonymously. And this is understandable, as many probiotics indeed contain beneficial bacteria. However, from a scientific perspective, there is a small but important difference between these terms.

The concept of probiotics is more specific: they are live microorganisms that, when administered in adequate amounts, confer a health benefit on the host. Furthermore, probiotics are not necessarily bacteria – they can also be certain yeasts. So, calling probiotics beneficial bacteria in everyday language is not uncommon, but strictly speaking, these terms are not entirely the same.

A simple comparison:

Beneficial bacteria are not just passive "residents" of the gut – they constantly interact with our bodies. One important function is related to the intestinal barrier, which helps separate the gut contents from the internal environment of the body. The gut microbiota and the substances it produces play a role in maintaining the integrity and protective functions of this barrier.

No less important is the connection with the immune system. Research shows that the gut microbiota interacts with immune cells and contributes to the normal functioning of the immune system. In other words, there is a constant mutual "dialogue" between our microorganisms and immunity.

Some gut bacteria can also synthesize B vitamins and vitamin K. However, this function should not be understood to mean that gut bacteria can replace vitamins obtained from food – how much of the vitamins produced by the microbiota actually become available to the human body depends on the specific vitamin and other factors. And one of the most important functions of beneficial bacteria for the gut is related to what they do with the food we eat. More on that in the next section.

Human digestive enzymes cannot break down all substances obtained from food. Some fiber reaches the large intestine unchanged or only partially digested, where it becomes a food source for gut microorganisms. This is where fermentation begins – a process during which gut bacteria break down fiber and produce various substances, including short-chain fatty acids (SCFAs).

The main SCFAs are acetate, propionate, and butyrate. They are not merely by-products of bacterial activity. Scientific reviews show that SCFAs participate in maintaining the functions of the intestinal lining and barrier, and butyrate is an important energy source for colon epithelial cells.

This is one example demonstrating why good bacteria are important for the gut, not just because of the presence of microorganisms themselves. Their functions and the substances they produce when interacting with our diet are also significant.

The connection can be imagined as a simple chain:

Food → Fiber → Gut Bacterial Fermentation → SCFAs → Gut Cells and Barrier

The role of bacteria does not end there. Gut microbiota also participates in nutrient metabolism, and SCFAs may be involved in regulating gut motility. All of this shows that normal digestive system function depends on a complex community of microorganisms, their functions, and their interaction with our diet.

The balance of good bacteria is not maintained by one specific habit, but by a combination of many dietary, lifestyle, and environmental factors. The following are most commonly associated with changes in the gut microbiota:

• Low-fiber diet. Fiber is an important substrate for gut bacteria, which ferment it to produce short-chain fatty acids.

• High consumption of ultra-processed foods. Studies link this dietary pattern to changes in gut microbiota composition and diversity, although causal relationships are not yet fully understood.

• Lack of sleep and chronic stress. The gut and brain communicate in both directions, so changes in sleep and stress can also be related to changes in microbiota. These associations are still being actively investigated.

• Low physical activity. Data from systematic reviews and meta-analyses show that physical activity may be associated with changes in gut microbiota composition and diversity.

• Certain medications. Various medications can affect the gut microbiota, with antibiotics being one of the most prominent examples.

Read more about the use of good bacteria after antibiotics in our detailed article.

Live microorganisms can be obtained through food. Some of the best-known sources are fermented products: natural yogurt with live cultures, kefir, fermented vegetables, kimchi, or miso. However, it is important to know that not every fermented product still contains live bacteria in its final form.

During fermentation, microorganisms act in food, but subsequent heating or pasteurization can destroy them. For example, sauerkraut or kimchi may contain live microorganisms if not pasteurized after fermentation, so when choosing a product, it is worth checking its label for information about live or active bacterial cultures.

Prebiotics are also important – food components utilized by gut microorganisms that can promote the activity of health-beneficial microorganisms. They are naturally found, for example, in onions, garlic, leeks, legumes, whole grains, and some fruits.

The benefits of probiotics are not uniform in all cases. Certain probiotics can be beneficial for specific digestive disorders, but their effect depends on the situation and is not universal.

Bloating is one of the common symptoms of irritable bowel syndrome (IBS), so the effect of probiotics on this condition has been extensively studied. According to a systematic review and meta-analysis, probiotic use was associated with a small reduction in bloating, but the results should be interpreted with caution due to different probiotic strains and other study differences. This means that probiotics for bloating may be beneficial for some people, but a uniform effect from all probiotics should not be expected.

Probiotics for diarrhea can be beneficial in certain cases, but their effect depends on the cause of the diarrhea and the chosen probiotic. Their benefits have been studied in acute infectious diarrhea, as well as for the prevention of traveler's diarrhea.

For example, a systematic review and network meta-analysis of 17 RCTs showed that probiotic use was associated with an approximately 15% lower risk of traveler's diarrhea compared to placebo. The results for different probiotics vary, so this effect cannot be attributed to all products.

Important: If diarrhea is severe or prolonged, if blood appears in the stool, if there is a high fever or signs of dehydration, you should consult a doctor.

The effect of probiotics has also been studied in functional constipation. According to a systematic review and meta-analysis, probiotic use was associated with more frequent bowel movements, better stool consistency, and reduced constipation symptoms. However, different probiotics were used in different studies, so a uniform effect cannot be expected from all of them.

There can be many causes of constipation, so not only good bacteria are important, but also diet, fiber and fluid intake, physical activity, and other factors. Read more about the causes of constipation and what to do in our detailed article.

The short answer is no. For most healthy people, the basis for maintaining gut microbiota is a varied, fiber-rich diet and healthy lifestyle habits. Probiotic supplements may be beneficial in certain situations, but they do not replace a balanced diet.

To take care of your gut microbiota, you don't need to look for one special product or supplement. Much more important is to create the right conditions in your daily diet for various gut bacteria to get the nutrients they need.

Quick reminder

Good bacteria are a natural part of the gut microbiota, important not only for digestion but also for other bodily functions. Probiotics can sometimes help resolve specific digestive issues, but their effect is not uniform, and supplements are not necessary for everyone. The foundation of maintaining gut microbiota is a diverse, fiber-rich diet and long-term healthy lifestyle habits.