Early exposure to antibiotics linked to changes in the gut microbiota and increased risk of autoimmune diseases in children

Antibiotic treatment administered to the mother during childbirth is associated with changes in the child’s gut microbiota as well as an increased risk of autoimmune diseases in childhood. The finding is reported in the doctoral dissertation of Licentiate of Medicine Sofia Ainonen, which will be examined at the University of Oulu on Friday 6 February.

In her dissertation, Ainonen investigated the association between early antibiotic exposure and the child’s gut microbiota, as well as later immune-mediated diseases and overweight.

The most common reason for antibiotic exposure during vaginal delivery is prophylactic antibiotic treatment given to the mother. This is administered to mothers who carry group B streptococcus (GBS). The aim of the treatment is to prevent the newborn from developing serious infections such as sepsis or meningitis. In Finland, almost one in four women who give birth vaginally receive antibiotics.

Previous studies have linked antibiotic exposure early in life to short-term changes in the child’s gut microbiota, and these changes have been suspected to be associated with an increased risk of autoimmune diseases, allergies, asthma and overweight.

The first part of the dissertation examined the effects of antibiotic exposure at birth and antibiotic courses administered during the first year of life on the child’s gut microbiota at one year of age. The prospective cohort study was based on data from one hundred children born vaginally.

The results showed that antibiotic exposure at birth was associated with changes in the gut microbiota that were still present at one year of age, and that the effect was more pronounced than that of antibiotic courses given to the child during the first year of life.

The second part of the dissertation was a register-based study examining the later health of approximately 40,000 children born vaginally at Oulu University Hospital and Oulaskangas Hospital. The study followed the occurrence of autoimmune and allergic diseases as well as the development of overweight and obesity.

According to the results, antibiotic exposure at birth was associated with an increased risk of autoimmune diseases in childhood and with increased use of medication for obstructive airway diseases. By contrast, routine antibiotic courses received by the child during the first two years of life were associated with overweight and obesity later in childhood.

The study is observational and does not demonstrate a causal relationship between antibiotic exposure and later health problems.

“It is possible that the observed associations are explained by factors other than antibiotics. However, the findings support the view that early antibiotic treatments and the gut microbiota may be important for a child’s later health,” Ainonen emphasises.

When used appropriately, antibiotics are life-saving, but the results of the study support avoiding unnecessary antibiotic courses, particularly in early childhood.

Read the dissertation

Further information about the public defence

Created 4.2.2026 | Updated 4.2.2026