Not all calories are equal.
Source: Why the calorie is broken — Quartz
Differences in height, body fat, liver size, levels of the stress hormone cortisol, and other factors influence the energy required to maintain the body’s basic functions. Between two people of the same sex, weight and age, this number may differ by up to 600 calories a day
The microbes in our intestines digest some of the tough or fibrous matter that our stomachs cannot break down, releasing a flow of additional calories in the process. But different species and strains of microbes vary in how effective they are at releasing those extra calories, as well as how generously they share them with their host human.
None of this means that the calorie is a useless concept. Inaccurate as they are, calorie counts remain a helpful guide to relative energy values: standing burns more calories than sitting; cookies contain more calories than spinach. … This is a new challenge, and it is likely to require a new metric. One option is to focus on something other than energy intake. Like satiety, for instance. … Adam Drewnowski, an epidemiologist at the University of Washington, has his own calorie upgrade: a nutrient density score. This system ranks food in terms of nutrition per calorie, rather than simply overall caloric value.