You're missing the point. This is about explaining why the same amount of food (or energy) intake affects people differently. Research into metabolic syndrome has shown that there is no simple relation: eat less -> lose weight -> get healthy. Once you know what influences weight gain or loss, given a certain amount of food intake you can adjust for other parameters.
Absolute nonsense. From the Sunday Morning Herald summary (I don't have a Nature subscription):
They found that the gut microbiomes of the mice who lost weight were altered, and that these changes remained in place for many months and contributed to rapid and excessive weight gain if the mice were given high-fat diets again.
So the mice gained weight when they were fed a crap diet. And, quelle surprise, when human porkers give up their short-lived attempts to stick to a Mediterranean diet and shove their noses back in the McDonald's trough, they pile back on the pounds.
Neither article says that the mice had a calorie-controlled diet. It seem far more likely that the gut microbiome changes have an impact on appetite.