Metabolized food does not yield the exact caloric energy measured by bomb calorimetry because biological digestion and gut microbiome fermentation result in incomplete absorption and variable net metabolizable energy.
Bomb calorimetry measures the gross heat of combustion of food, but physiological studies (such as those measuring human metabolizable energy and net energy content of dietary fibers) consistently show that humans do not extract 100% of this energy due to incomplete digestion, fecal losses, and microbial fermentation in the gut.