Since the beneficial bacteria that colonize the intestines have a major role in the developing immune system of infants and children, and considering that asthma (and eczema, which is related to asthma) are considered immune-related conditions, it would make sense that destroying the good guys in the gut would predispose children to a host of immune-related health conditions later in life.
Well, this is exactly what the results of this study showed. Antibiotic exposure in the first year of life increased the risk of asthma for 3 to 18-year olds by up to 52%.
What I would suggest for any kid exposed to antibiotics -- at any point in their lives -- is to take probiotics during and after the treatment. This will help counter the negative effects of antibiotics, which is necessary at times, but definitely WAY over-prescribed.
Source: Prenatal or Early-Life Exposure to Antibiotics and Risk of Childhood Asthma: A Systematic Review
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