How to support your baby’s intestine – or the microbiota in the first days of life

Probably most of us have heard about the intestinal microflora, i.e. the world of bacteria and other microorganisms living in our intestines. We have addressed this topic many times on the blog because it is very important! Gut bacteria are our true friends, they populate our digestive tract at the time of birth and stay in it throughout our lives. And they are work hard during this time! An increasing amount of scientific research indicates the important role that these tiny creatures play in stimulating our immunity, producing B and K vitamins, and even regulating mood – remember that the intestine is the “second brain”, connected to the nervous system by vagus nerve.

Proper intestinal microbiota has advantages only so it’s worth knowing what to do to make the process of shaping it run harmoniously and correctly. Due to the fact that the formation of the microbiome is most intensive during the first thousand days of a baby’s life, this post is dedicated especially to new moms 🙂 


Microbial programming

In order to take care of our baby’s health in the best possible way, from the very first days of their life, we have to get understand what microbial programming is. Scientists have found that the shape of the intestinal microflora of a newborn baby affects to a large extent the risk of a number of diseases, such as allergies, autoimmune diseases, obesity and other diseases of civilization. In other words, the bacteria that dominate the intestines of our baby at the beginning decide on our baby’s health later in life! Therefore, it is worth making a special effort to ensure that only the desired microbes enter our baby’s digestive tract 🙂

How to achieve it? Let me share a few pieces of advice with you!


The first feed

An important moment for shaping the microflora is childbirth and the first feeding. If a baby is born naturally, he or she takes over the first bacterial “tenants” from his mother’s genital tract. And that’s perfect as these bacteria will become the pioneers in the baby’s intestines and prepare the digestive tract for further colonization. Unfortunately, babies born by c-section do not have this ideal start: the first bacteria that their body comes into contact with come from the hospital environment and it is not the optimal start for a healthy microflora.

However, all is not lost! The perfect support for the baby’s developing microbiota is breastfeeding. This food is not only perfectly suited to the needs of the baby – it is also a probiotic bomb! Mother’s milk contains particularly desirable bacteria of the genus Bifidobacterium, which should constitute about 90% of the intestinal microflora of a newborn and infant in the first weeks of life. In mother’s milk we also find a natural prebiotic (bifidogenic factor), which is food for good bacteria, that inhibits the growth of unwanted microbes in the intestine. Therefore, it is worth fighting for each month of natural breastfeeding, because this is what our baby’s microflora needs the most. And in the future it will pay off with a beneficial effect on health.



Unfortunately, natural childbirth is not always possible, and many mothers, despite their will to do so, also can’t breastfeed, or do it for a very short time. What can we do for the microflora if we already know how important the bacterial environment of the gut is for our baby’s health? The best solution will be to reach for probiotics, i.e. live strains of bacteria capable of supporting the intestinal microflora. Remember, however, that the intestinal microflora dynamically changes over the years and probiotics recommended for a few-year-old child will not necessarily be the best choice for a baby that’s several weeks old. For the youngest children, the optimal solution will be probiotics based on bacteria of the genus Bifidobacterium – these creatures  should constitute almost 100% of the entire microbiota which in the digestive tract of a newborn. These bacteria are the most needed and the safest in the first days of a baby’s life hence the natural choice should be to use probiotics based on bifidobacteria. 

It is a good idea to reach for a probiotic which contains 2 pro-health bacterial strains: Bifidobacterium breve BR0O3, Bifidobacterium breve B632, which can be used from the first days of life. We should also remember that the type of probiotic is one thing, but the time of supplementation is equally important. We should give the baby’s microbiota time to develop properly and instead of using a probiotic for a few days, it’s better to focus on this type of supplementation for a few weeks. This is especially important in the first days and months of life.

Probiotic should also be implemented when it is necessary to use an antibiotic – it has been known for a long time that antibiotics destroy not only the bacteria that cause the infection, but also the desired microbiota. In small children, the negative effect of an antibiotic on the microflora is even stronger than in adults, as the intestinal ecosystem is still forming. Remember to use the probiotic not only during antibiotic treatment, but also a few weeks afterwards for safety reasons. 



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Patrycja Szachta

PhD in Biological Sciences

She obtained a doctorate in biological sciences during her doctoral studies at the Department of Child Gastroenterology and Metabolic Diseases of the Medical University of Poznan. Author of numerous medical publications in Polish and foreign magazines and chapters in scientific monographs. Scientific Director at the VitaImmun Medical Center. Her tasks include designing and coordination of scientific projects conducted within the framework of the VitaImmun Medical Center. She has had a long practical and theoretical experience in the field of latent food hypersensitivity and intestinal microflora disorders. She specializes in the field of probiotics and prebiotics and the functioning of the gastrointestinal tract.

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