There are multiple ways with different levels of accuracy.
I don’t think anyone really uses bomb calorimetry directly, b/c that has nothing to do with food calories and how human metabolism works. Eating a charcoal briquette won’t give the energy contained in that charcoal.
Instead, the calorific content can be estimated based on protein, fat, carb & fiber content (see: Atwater factors) of the food in question, since we know roughly how many calories human metabolism can extract from each gram of these types of macronutrients.
For more details, see: https://skeptics.stackexchange.com/questions/10070/can-a-bomb-calorimeter-meaningfully-measure-food-calories
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