Scientists who compared groups of children aged one to six in Italy and rural Africa found striking differences in the composition of bug populations inhabiting their digestive systems.
They say the reason is their different diets and argue this could explain why western children are so prone to problems such as obesity and allergies.
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African children from Burkina Faso had a lower proportion of microbes associated with obesity in adults and higher numbers of bugs linked to leanness.
Other types of bacteria found in the guts of African but not Italian children assisted the digestion of plant foods and generated fatty acids known to protect against inflammation.
Researchers say this may help to prevent the over-active immune reactions that lead to allergies.
African children also had fewer of the bacteria that cause common stomach upsets and diarrhoea.
While the African children ate a diet consisting mainly of cereals, pulses and vegetables, their Italian counterparts ate diets high in animal protein, sugar, starch and fat, and low in fibre.
