Tips to Restore Intestinal Flora in Children

The intestinal flora of children must also be cared for, as it's a barrier that strengthens the immune system and prevents diseases.
Tips to Restore Intestinal Flora in Children

Last update: 28 August, 2023

Don’t be alarmed, but our children’s intestines are inhabited by more than 400 species of microorganisms that colonize them from the time they’re in their mother’s womb. What’s more, to everyone’s surprise, the more varied the community of bacteria or intestinal flora, the healthier the baby will be. Therefore, we’ll share with you some tips to restore the intestinal flora of children when it is altered.

What’s intestinal flora?

The intestinal flora or microbiota can be described as an army of bacteria that live in the mucosa of the large intestine. There, they work together to achieve the health of the host. It’s made up of trillions of bacteria that together weigh between 300 and 600 grams. More than 95% of them live in the lumen of the colon, while the rest live in the stomach and small intestine.

Where do the bacteria come from?

Everything seems to indicate that the colonization of the microbial flora in the intestine begins in the mother’s womb and then continues at birth. As the child grows, environmental factors and nutrition also play a role in this process.

  • From the womb: In 2017, the journal Pediatric Obesity entitled one of its papers as Are we colonized with bacteria in utero? The evidence seems to indicate that there’s a direct transmission of bacteria from the mother’s womb to the child. This is why the overall mother’s good health during pregnancy is so important.
  • The mode of birth: The intestinal flora varies depending on whether the delivery is by cesarean section or vaginal delivery. When it’s by cesarean section, colonization appears later and is of low proportion and low diversity. On the other hand, in vaginal delivery, vaginal and fecal bacteria colonize the intestine and show high diversity.
  • Gestational age: In preterm babies, the flora is less diverse and there’s a low number of beneficial bacteria, known as probiotics. These include bifidobacteria and lactobacilli.
  • Feeding: Breast milk is the main factor that allows colonization of the newborn’s intestine. It facilitates the growth of 85% of probiotic bacteria. Later, others appear that grow with the changes in the diet during growth.
  • Genetic and environmental factors, physical activity, and lifestyle: The flora can change depending on environmental conditions or social status. The environment, geographic location, race, and even exposure to pets from a young age have a significant effect on the microbiome of children, as reported in Elife magazine.

What are its main functions?

The main functions of gut flora are outlined by Only About Children:

  • Strengthens the immune system: The gut houses 70% of the body’s immune system and establishes a protective barrier against pathogenic bacteria that prevent disease.
  • Maintain digestive health: Probiotics produce a small fat called butyric acid, which serves to energize cells in the colon. They also stimulate bowel movements to prevent constipation.
  • They produce vitamins: Bifidobacteria produce B vitamins to support host health.
  • They contribute to mental health: Intestinal flora produce chemicals between the gut and the brain that help activate neurotransmitters that promote mental health.
A doctor examining a child's abdomen.
In children, the intestinal flora is very unstable and undergoes changes during the first years. Then, it begins to balance until adulthood.

How can intestinal flora be altered in children?

Here are the causes that lead to the alteration of dysbiosis of the intestinal flora in children.

Uncontrolled use of antibiotics

Some antibiotics that destroy the pathogenic bacteria that cause disease can also undo the intestinal flora. In addition, as reported in the journal MicrobiologyOpen in 2022, the indiscriminate use of antibiotics can alter the microbial composition, modify its function, and increase the resistance of bacteria to these drugs.

Incorrect nutrition

The Journal of Translational Medicine in 2017 explains that some dietary components can modify the variety of intestinal bacteria. Among them are excess sugars, refined cereals, unhealthy fats, or low fiber content in the diet.


Some diseases such as diarrhea of infectious origin can alter the balance between the different forms of intestinal flora in children. Others, such as those mentioned in the PeerJ can also modify the bacterial ecosystem.

If any of these factors alter the intestinal flora, it should be balanced as soon as possible. The role of dysbiosis in the development of several metabolic disorders such as diabetes, obesity, and those related to the immune system is well documented.

You should immediately consult your pediatrician in the following cases: The child has frequent migraine, suffers from intolerance to certain foods, is very susceptible to infections, suffers from constipation and alternating diarrhea, colic, or presents excessive gas and abdominal pain.

Tips to restore the intestinal flora in children

When any of these factors affect the quantity and diversity of the intestinal flora in children, it’s crucial to rebuild it immediately. Some simple strategies that you can implement at home are used for this purpose.

Feeding properly

Some simple dietary changes can help to restore intestinal flora. The journal Cell Metabolism says that one way is to provide the bacteria with nutrients that allow their growth, which are called prebiotics.

Fiber as a prebiotic

Because it’s not digested, dietary fiber travels to the colon to be fermented by the bacterial flora. This is how they obtain energy and maintain the functions of their cells. Initially, vegetables that are a source of fructoligosaccharides (FOS) are recommended. This type of fiber has been shown to restore pre-existing intestinal flora. They can be found in asparagus, onions, banana, strawberries, apples, leeks, tomatoes, peaches, and chicory, among others.

Vegetables to include are those that provide digestible carbohydrates, such as fructose, glucose, and sucrose. These are found in fruits and non-starchy vegetables. Carrot juice or applesauce are good options to help restore intestinal flora. Other sources of fiber are found in whole grains, such as rice, corn, and wheat.

A toddler eating chickpeas.
Legumes, such as chickpeas, lentils, peas, and beans, enrich meals with resistant starch and support intestinal flora.


Another way to restore intestinal flora is through commercial probiotics. This involves increasing the consumption of foods made with fermenting and beneficial bacteria. Among this group, fermented dairy products such as yogurt are recommended, but those whose label says that it contains “live cultures”; and kefir, a less thick type of sour milk.

Perform anti-stress activities

The journal Brain, Behavior, and Immunity, in 2019, shared that stress in children and adolescents affects the microbial composition of the intestinal flora, regardless of diet. In addition, it indicates that positive emotions must be aroused in them so that they lower the level of stress and stabilize the intestinal microbiota. Therefore, it’s important to give children space through painting, sports, dancing, or crafts, among other tasks.

Chew food well

An Open Access article concluded that proper chewing can play a key role in providing a favorable intestinal environment. Therefore, a good tip is to encourage good eating habits in children to facilitate digestion and improve intestinal flora.

Reduce antibiotic intake

The indication of antibiotics should be left to the pediatrician. However, as parents, we must be aware of the effect of the excessive use of these drugs on intestinal health.

Follow a healthy diet and lifestyle

We must try to maintain or restore intestinal flora in our children, as it’s a barrier that strengthens the immune system and prevents diseases. In case of an alteration, we must go immediately to the health professional who can prescribe the appropriate treatment. In addition, we advise you to maintain a healthy diet, including the addition of more beneficial bacteria. Also, encourage good chewing habits and promote anti-stress activities.

All cited sources were thoroughly reviewed by our team to ensure their quality, reliability, currency, and validity. The bibliography of this article was considered reliable and of academic or scientific accuracy.

  • Hasan, N., & Yang, H. (2019). Factors affecting the composition of the gut microbiota, and its modulation. PeerJ7, e7502.
  • Kumbhare, S. V., Patangia, D. V. V., Patil, R. H., Shouche, Y. S., & Patil, N. P. (2019). Factors influencing the gut microbiome in children: from infancy to childhood. Journal of biosciences44(2), 49.
  •  Michels, N., Van de Wiele, T., Fouhy, F., O’Mahony, S., Clarke, G., & Keane, J. (2019). Gut microbiome patterns depending on children’s psychosocial stress: Reports versus biomarkers. Brain, behavior, and immunity80, 751–762.
  • Pandey, K. R., Naik, S. R., & Vakil, B. V. (2015). Probiotics, prebiotics and synbiotics- a review. Journal of food science and technology52(12), 7577–7587.
  • Patangia, D. V., Anthony Ryan, C., Dempsey, E., Paul Ross, R., & Stanton, C. (2022). Impact of antibiotics on the human microbiome and consequences for host health. MicrobiologyOpen11(1), e1260.
  • Patel, R., & DuPont, H. L. (2015). New approaches for bacteriotherapy: prebiotics, new-generation probiotics, and synbiotics. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America60 Suppl 2(Suppl 2), S108–S121.
  • Singh, R. K., Chang, H. W., Yan, D., Lee, K. M., Ucmak, D., Wong, K., Abrouk, M., Farahnik, B., Nakamura, M., Zhu, T. H., Bhutani, T., & Liao, W. (2017). Influence of diet on the gut microbiome and implications for human health. Journal of translational medicine15(1), 73.
  • Song, S. J., Lauber, C., Costello, E. K., Lozupone, C. A., Humphrey, G., Berg-Lyons, D., Caporaso, J. G., Knights, D., Clemente, J. C., Nakielny, S., Gordon, J. I., Fierer, N., & Knight, R. (2013). Cohabiting family members share microbiota with one another and with their dogs. eLife2, e00458.
  • Sonnenburg, E. D., & Sonnenburg, J. L. (2014). Starving our microbial self: the deleterious consequences of a diet deficient in microbiota-accessible carbohydrates. Cell metabolism20(5), 779–786.
  • Yaoita, Fukie & Watanabe, Keita & Kimura, Ikuo & Miyazawa, Masayuki & Tsuchiya, Shinobu & Kanzaki, Makoto & Tsuchiya, Masahiro & Tan-No, Koichi. (2022). Impact of habitual chewing on gut motility via microbiota transition. Scientific Reports. 12. 10.1038/s41598-022-18095-x.Por
  • Zaman, S. A., & Sarbini, S. R. (2016). The potential of resistant starch as a prebiotic. Critical reviews in biotechnology36(3), 578–584.

This text is provided for informational purposes only and does not replace consultation with a professional. If in doubt, consult your specialist.