Often termed the ‘lost organ’ the human gut contains trillions of microbes. A rich, diverse gut microbiota is considered to promote health, whereas a microbiota with reduced diversity is associated with gut inflammation and disease. Many factors affect gut microbes including host genetics, injury, diet, infection and antibiotics; the use of the latter being associated with the increased risk of obesity, cancer, asthma and diabetes in children.

The development of gut microbiota begins before the infant is born with maternal factors such as infection and birth-mode. Then at birth microbial gut colonization begins, continually developing for about 3 years, until the microbiota becomes more stable and adult-like. The gut microbiota in children under 3 years of age fluctuates and is more impressionable to environmental factors than the adult microbiota. During this time children experience significant developmental changes that influence their health status and gut microbiome. Children also suffer more infectious diseases and associated antibiotic usage, than adults. Studies indicate that most, but not all, bacterial species recover during the 6 months post-antibiotic treatment and that specific early-life exposures to antibiotics, caesarean section and formula feeding disrupts gut microbiome establishment.

It has been suggested there is an early-life ‘critical window’ of development during which the microbiota is disrupted beyond repair favouring susceptibility to future health issues. A major concern is permanent loss of beneficial bacteria after repeated early life infections and associated antibiotics, with cumulative effects increasing susceptibility to emerging health issues and infections.