The authors of this current study explain that altered gut flora is the leading theory of why a history of c-section delivery increases the risk of childhood obesity. It's been shown that children delivered vaginally have different types of intestinal flora compared to children delivered via c-section--and this may not only explain a propensity toward obesity among children born via c-section, but may also explain higher rates of asthma, eczema, and allergies.
Each method of delivery introduces different bacterial species to the newborn, which eventually colonizes the child's intestines (and the rest of their body). This difference in gut bacteria affects the efficiency of energy extraction from food and nutrients, and may influence insulin resistance, inflammation, and fat deposits.
Specifically, higher numbers of Firmicutes and lower numbers of Bacteroides colonize the guts of children born by c-section. Other studies have shown this pattern in the gut microbiomes of obese individuals (see links to other posts below).
Considering that 1 in 3 deliveries in the United States is surgical (whether elective or emergency), the authors conclude, "a mother who chooses caesarean delivery...should be aware of potential health risks to her and her baby, including childhood obesity."
Source: Delivery by caesarean section and risk of obesity in preschool age children: a prospective cohort study
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