The first microbiome: birth, breastfeeding, antibiotics and what remains

Healthy state

In the womb, according to current knowledge, the child’s gut is practically germ-free. At birth and in the days after, bacteria move in: from the mother, from the surroundings and from everyone who holds the child. A study that followed 25 mothers and their babies for four months showed that bacteria from the mother’s skin and vagina settle only temporarily. Mainly strains from the mother’s gut, passed on during a vaginal birth, stay for good.

Breast milk contains something special: well over a hundred different sugar chains, the so-called human milk oligosaccharides (HMO), which the baby itself cannot digest at all. They are food for certain bifidobacteria, especially Bifidobacterium infantis. These bacteria ferment the sugars into substances that make the gut slightly acidic, keep pathogens away and calm the immune system. Breast milk thus specifically feeds the bacteria the baby needs.

The gut microbiota Microbiome, gut microbiota The community of all microbes in the gut, mainly bacteria, plus viruses, fungi and archaea. Most live in the colon. More in the chapter “Building microbial diversity” matures in stages. A large study of 903 children from Europe and the USA with over 12,000 stool samples found three phases: development up to about month 14, transition up to about month 30, and then a stable phase that resembles adult microbiota. The strongest influence was whether the child received breast milk. With weaning and solid food, the microbiota matured faster. Siblings and pets in the household also left traces.

During this time the immune system learns to tell friend from foe. It learns to tolerate harmless bacteria, food and pollen and to fight real pathogens. Studies suggest that this early learning phase helps determine how susceptible someone later is to allergies, asthma and other inflammatory diseases.

Disrupted state: causes and effects

In a caesarean section, contact with the mother’s gut microbiota during birth is missing. In a British study of 596 babies, the mother’s Bacteroides strains were often missing after caesarean section. Instead, hospital germs such as Enterococcus, Enterobacter and Klebsiella settled more often, some with antibiotic resistance. To a lesser extent the same was seen in vaginally born babies whose mothers received antibiotics during birth, and in babies who were not breastfed in the first weeks.

The good news: these differences largely even out. In the large study of 903 children, birth mode was clearly visible only in the first phase up to about month 14, and barely afterwards. Whether a caesarean section increases the later risk of allergies, asthma or overweight via the gut microbiota, as observational studies suggest, is not proven. Children born by caesarean section also differ in other ways, for example in the reason for the caesarean.

Bifidobacterium infantis has become rare in industrialised countries, even in breastfed children. One study found that when bifidobacteria, and above all their genes for using human milk sugars, were missing, babies had more signs of inflammation in the blood. Breastfed babies who received B. infantis as a supplement showed fewer messengers in the gut that are linked to allergies.

Antibiotics in the first two years of life are linked to a higher risk of several diseases. In a US study of more than 14,500 children, 70 percent had received at least one antibiotic in their first two years. They later developed asthma, hay fever, eczema, coeliac disease Coeliac disease An autoimmune disease in which gluten damages the lining of the small intestine. It is diagnosed with a blood test and usually a biopsy while you are still eating gluten. More in the chapter “Lactose, fructose, gluten: making sense of intolerances”, overweight and ADHD more often, by 1.2 to 2.9 times depending on the condition. Here too, it is unclear how much of this is due to the antibiotics and how much to the infections that made them necessary.

The environment also counts. Amish and Hutterite children in the USA have similar ancestry and lifestyles, but the Amish practise traditional farming with animals in the yard, the Hutterites industrial farming. Asthma and allergies were four to six times rarer in the Amish children, and house dust contained almost seven times as much bacterial material. In mice, dust from Amish homes protected against allergic asthma; dust from Hutterite homes did not.

In very premature babies, the gut is still immature, and the gut microbiota develops in intensive care under antibiotics. Here there is a risk of necrotising enterocolitis, a severe inflammation of the bowel that can be fatal. A Cochrane review of 60 studies with over 11,000 preterm infants found that probiotics Probiotics Live microorganisms that are meant to provide a benefit in sufficient amounts. The effect depends on the individual strain. More in the chapter “Using fermented foods well” roughly halved this risk and slightly reduced mortality.