Microbiome development and probiotics in children

Microbiome formation begins during the birth of a child. Over the next three years, the microbiome develops dynamically, expands and matures into a state of “adulthood”. This process is very important for the proper development of the nervous system and brain. That is why everything must be done for its proper development.

The importance of the intestinal microbiome was described at the beginning of the 20th century by Nobel Prize winner Élie Metchnikoff. He claimed that a lot of diseases were related to the activity of the intestinal microflora. At the same time he assumed that drinking fermented milk containing lactic-acid bacteria could prevent the development of pathogens and support the overall health of the human body.

Nowadays, the importance of a healthy intestinal microbiome is well known. Microorganisms that inhabit the human digestive tract are involved in the development and functioning of a great number of basic physiological processes (digestion, immunity, maintenance of homeostasis). They can also play an important role in several diseases from inflammation to obesity.

Recently, there have been studies demonstrating the fundamental influence of the intestinal microflora on the development and function of the central nervous system. Microorganisms affect it through metabolic, neuroendocrine and immune pathways. It is these studies that describe in more detail the two-way communication between the brain and the intestinal microbiota, so-called intestinal-brain axis.

These facts show that the intestinal microbiome plays an important role not only in the DEVELOPMENT of the body but also in health maintaining and promotion. However, everyone must take care of the intestinal microbiome whether through proper diet, physical activity or through PROBIOTICS, as well.

How does a microbiome develop?

Until recently, it has been generally accepted that fetuses in the womb are sterile and that microbial colonization of the body begins at birth. Currently, there is evidence of microorganisms occurrence in the placenta and other tissues surrounding the fetus in the uterus (such as umbilical cord blood). However, the numbers of microorganisms that are present are very low and the fact remains that intestinal colonization takes place mainly after the birth of a child.

As already mentioned, microorganisms begin to colonize the body during childbirth, i.e., before the baby’s first breath. The initial composition of the microflora is influenced by many external factors, specifically the mother’s microflora, the method of delivery, contact with fecal material, skin, doctors, midwives/assistants and the room in which the baby is born.

“The transmission of commensal bacteria from mother to child affects the development of its immune system.”

The method of delivery is an important factor in terms of the initial composition of the microbiome and the further development of the baby. Children born by caesarean section come into contact with the surrounding microflora at the first moment. Children born by caesarean section are more prone to diseases such as asthma, allergies or obesity. During vaginal delivery, babies are initially exposed to the mother’s vaginal microflora.

After birth, i.e., during the first days of a newborn’s life, the microflora begins to develop dynamically. In this way, the microbiome develops approximately during the first three years of life and then reaches “maturity” thus a state similar to that of adults. The development of the microbiome is constantly influenced by various external factors. One of the most important of them is the method of feeding.

Studies show that breastfeeding has a beneficial effect on the baby’s neuropsychological development. Breast milk is the source of all the nutrients a baby needs for healthy development. At the same time it is a source of good bacteria which are transmitted to the baby from the mother’s skin and mammary glands. Breasted infants usually have a more uniform population of intestinal microbes dominated by the genera Bifidobacterium and Lactobacillus. Bifidobacterium bacteria are the primary colonizers of newborns. They have a positive effect on the development of immunity, they reduce inflammation development, improve intestinal permeability and acetate production.

What is the role of probiotics and how do they affect the microbiome?

Probiotics are non-pathogenic live microorganisms which, when taken in sufficient quantities, have a positive effect on the health of the host. Probiotics must be of human origin, resistant to gastric acid and bile, able to adhere to the intestinal mucosa and able to colonize the intestine (albeit only for a short time).

Probiotics have a positive effect on the host through several mechanisms. In the first place, they have a fundamental effect on digestion, metabolism and balance in the intestines. 

The antimicrobial effect is mediated by their ability to modify the intestinal microflora, produce antibacterial substances, compete with pathogens for nutrients and place on the intestinal mucosa. Associated with this is their antitoxin effect and their ability to avert some of the effects of infections on the intestinal epithelium.

Probiotics are also able to modulate the immune system, regulate the allergic response of immune cells and the formation of cancer cells.

The effects of probiotics do not necessarily concern only the digestive tract. They can also have a positive effect on the urogenital, respiratory or oral mucosa and even on the skin.

It is generally believed that probiotics may play an important role in combatting various diseases. In particular, they are associated with non-alcoholic liver diseases, allergic reactions, asthma, atopic diseases, inflammatory bowel diseases, antibiotic diarrhea. They are also thought to improve the course of the symptoms of celiac disease, lactose intolerance, metabolic syndrome or diabetes.

Research in the field of psychobiotics, i.e., probiotic microorganisms that have a positive effect on the human psyche, has also expanded in recent years.

What about probiotics in children?

Currently, there exist a lot of guidelines and studies on how to use probiotics in various diseases but also in general healthy population. Unfortunately, there is only a limited number of research studies that focus on specific groups of population such as newborns and children.

Newborns and children belong to the most vulnerable groups. For this reason, the administration of probiotics to these groups should be much more strictly controlled. At the same time their administration in clinical practice should be governed by precise rules based on the available relevant evidence.

The European Pediatric Association and the Union of National European Pediatric Societies and Associations conducted a survey of scientific studies with a purpose to summarize guidelines and recommendations regarding the use of probiotics in pediatric medical practice and clinical practice.

Based on current guidelines and high-quality evidence, they have issued guidelines for the use of probiotics in pediatric practice, i.e., in children.

The use of strictly defined strains is recommended for use in children in the following cases:

  1. In upper respiratory tract infections in children attending day care centers (nurseries, kindergartens, schools).
  2. In nosocomial diarrhea (so-called hospital-acquired diarrhea).
  3. In antibiotic diarrhea.
  4. In acute gastroenteritis.
  5. In infantile colic in breastfed infants.

It should be stated that the use of probiotics is generally considered safe for healthy children. Premature babies, immunocompromised patients, critically ill patients, patients with central venous catheter, valvular heart disease and short bowel syndrome require special care when using probiotics.

It is necessary to pay attention to the quality of the used probiotic product and also to the representation of individual probiotic strains. In this case, the pediatrician should always evaluate the suitability of a particular nutritional supplement. The recommended daily dose should be in the range of 5 to 10 billion probiotics depending on the strains used and the composition of the particular nutritional supplement.

In summary, it can be said that the intestinal microbiome plays an important role in the proper development of immunity and digestion. Probiotics are safe for healthy children, especially if products with the proper probiotics and in appropriate doses are used. If a parent wants to give probiotics to his/her child, it is necessary to consult a pediatrician who will evaluate the available options and suitability of their use for a child.


MICHAIL, Sonia, et al. Clinical efficacy of probiotics: review of the evidence with focus on children. Journal of pediatric gastroenterology and nutrition, 2006, 43.4: 550-557.

HOJSAK, Iva, et al. Guidance on paediatric use of probiotics states that benefits are limited to several conditions and urges caution with specific vulnerable groups. 2018.

KLIGLER, Benjamin; HANAWAY, Patrick; COHRSSEN, Andreas. Probiotics in children. Pediatric Clinics of North America, 2007, 54.6: 949-967.

LENFESTEY, Mary W.; NEU, Josef. Probiotics in newborns and children. Pediatric Clinics, 2017, 64.6: 1271-1289.

CERDÓ, Tomás, et al. Probiotic, prebiotic, and brain development. Nutrients, 2017, 9.11: 1247.