Lifelong Friendships: Why Meeting Microbes Is Good For Your Baby’s Gut Health

Birth is often described as a magical new beginning, a special moment charged with love and hope for the future. I write this while looking at my toddler’s photo in my office. But, I am not going to tell you how cute and funny he is or how much sleep I’m missing since he came to this world. I want to tell you another story, the story of how babies get acquainted with tiny invisible friends that will be with them for life. I am talking about the multitude of microorganisms, that make our bodies their home as soon as we see the light, mostly in the gastrointestinal tract, but also the skin, airways and genitals. Baby’s body is like an empty house ready to be occupied by a myriad of microorganisms. Some studies suggest that the placenta is not sterile, and colonisation starts in utero, but it is during and after birth when baby is massively exposed to microorganisms.

During vaginal delivery, colonisation starts immediately with the main source of microorganisms being the mother, but also the surrounding environment and other humans or pets that meet baby. Within 24 hours of birth the microbiome may look a bit random and very diverse, without a clear pattern of maternal and other environmental sources. However, diversity goes down during the first week of life showing that babies are exposed to many different species but only few pioneers can survive and colonise. Mainly those of maternal origin end up colonising baby’s gut in the longer term, with those originating from mum’s gut dominating and being more persistent. As expected, colonisation from the different maternal sources continues to contribute to baby’s microbiota well after birth (Ferretti). To me, this gives an extra meaning to all the kisses and cuddles.

During caesarean birth, baby’s is mainly exposed to mum’s skin microbiota and from the surrounding environment, as the contact with vaginal and gut microbiota goes missing.

Baby’s intestine is first colonised by pioneering species belonging to Staphylococcus, Streptococcus, Enterococcus and Enterobacter genera. These species create an anaerobic environment for obligate anaerobes (microbes killed by the concentration of oxygen in normal air) to survive and thrive. Anaerobic bacteria are then observed within the first few weeks of life and belong to Bifidobacterium, Bacteroides, Clostridium and Eubacterium genera (Wopereis).

The first year of life is dominated by Bifidobacterium species, which are particularly relevant in the microbiota of breastfed babies for their ability to specifically degrade human milk oligosaccharides (HMOs). This means that some Bifidobacterium have evolved with us. How cool is that? Bifidobacterium species are there when we need them, but when breast milk is not available anymore, the condition for their growth (HMOs) goes missing. At this point, some Bifidobacterium are replaced by strains able to degrade oligosaccharides of other origins, such as plants (B. longum) or switch to other substrates, such as mucin (B. bifidum) (Stewart).

Babies that are not breastfed, because of cessation of breastfeeding or because formula fed, show a microbiota that is more mature, i.e., more similar to the adult microbiota, which is more diverse and dominated by other species, such as Bacteroides. This happens because the reduction in Bifidobacterium spp. makes room for others. Significant changes in the microbiota are observed when breastfeeding stops, rather than when solid food is introduced (Stewart). These changes reflect on the metabolic capabilities of the microbiota that starts acquiring the ability to degrade more complex molecules such as starch.

Once breastmilk is completely replaced by solid food the microbiota goes through a transitional phase, with an increase in diversity, which is followed by a stable phase from the age of 3. During this latter phase, the microbiota does not undergo major changes, it is characterised by increased bacterial diversity and a dominance of Firmicutes (Stewart).

After three years of age, the microbiota still develops, and with age, it gets more and more similar to that of adults. Bifidobacterium is increased in children up to 12 years of age, compared to adults. Moreover, children’s microbiota shows similar functionalities across the age group, with an increase in functions involved in development (e.g. vitamins biosynthesis). Meanwhile adults’ microbiota is increased in genes involved in inflammation, which is considered a sign of aging (we are getting old, sigh!) (Hollister).

It comes naturally to think that the increase in Bifidobacterium in children is a heritage of breastfeeding. However, it is more complicated than that. Bifidobacterium was found to be increased in children that were formula fed and had a diet poor in plant-based food during pre-school age. Their Bifidobacterium belongs mainly to a species (B. adolescentis) often found in adults rather than in breastfeeding children. Children that were breastfed and had a diet rich in plants, had an increase in Prevotella or Bacteroides. Their microbiota had a richer pool of genes in general, and specifically of those involved in the fermentation of complex carbohydrates and in the production of beneficial molecules such as butyrate and succinate, compared to children with a microbiota dominated by Bifidobacterium (Zhong).

Other factors influence the gut microbiota development in children, the environment where they grow up is one of them. Children that grow up in farms have a signature microbiota that gives them protection in developing asthma. This signature microbiota was strongly influenced by their contact with farm animals and pets (and their microbiota), and likely influenced by a diet richer in cereals, meat, bread, yogurt, cake and vegetables or fruits (Depner).

There are many variables contributing to our microbiota configuration, from delivery mode to the environment, passing by diet. Our microbiota goes through incredible changes in a relatively short time just as babies and toddlers do. It then slows down a bit just as older kids do but keeps developing over time to reach maturity with us. Its contribution to our health is undeniable and if we can’t change the past, we can always thank them by feeding them (and us) some delicious dietary fibre.

…and if your toddler, just like mine, decides that greens are not for them, you can always blend them and tempt them with some beetroot and oat cookies, they are not going to refuse, guaranteed!

References and further readings

Ferretti, Pamela, et al. "Mother-to-infant microbial transmission from different body sites shapes the developing infant gut microbiome." Cell host & microbe 24.1 (2018): 133-145.
Wopereis, Harm, et al. "The first thousand days–intestinal microbiology of early life: establishing a symbiosis." Pediatric Allergy and Immunology 25.5 (2014): 428-438.
Stewart, Christopher J., et al. "Temporal development of the gut microbiome in early childhood from the TEDDY study." Nature 562.7728 (2018): 583-588.
Hollister, Emily B., et al. "Structure and function of the healthy pre-adolescent pediatric gut microbiome." Microbiome 3.1 (2015): 1-13.
Zhong, Huanzi, et al. "Impact of early events and lifestyle on the gut microbiota and metabolic phenotypes in young school-age children." Microbiome 7.1 (2019): 1-14.
Derrien, Muriel, Anne-Sophie Alvarez, and Willem M. de Vos. "The gut microbiota in the first decade of life." Trends in microbiology 27.12 (2019): 997-1010.