Gut bacteria are a big confounder among a bunch of other things. Different types can do a lot of things differently, like extract more calories from the same food.

http://www.eurekalert.org/pub_releases/2012-09/ci-gbi091012....

They can even mess with your mind to make you crave junk food.

http://www.ucsf.edu/news/2014/08/116526/do-gut-bacteria-rule...

Transplanting them from a thin human to an obese mice slimmed the mice down.

http://www.nytimes.com/2013/09/06/health/gut-bacteria-from-t...

Jet lagged gut bacteria can contribute to obesity.

http://www.popsci.com/article/science/jet-lagged-gut-bacteri...

Diet soda can alter gut bacteria to make one gain weight.

http://www.prevention.com/health/diabetes/artificial-sweeten...

There are more gut bacteria than human cells in our body, and they actually release chemicals that affect the brain and have evolved to do that and there are a lot of other factors that influence gut bacteria, including what got passed on from your mother, what foods you ate during your life, what antibiotics you took etc. etc.

And gut bacteria is just one variable among things like activity levels, pollution levels, sleep amount and quality(not sleeping well can make you eat about 600 calories more the next day), peers(hanging out with obese people is likely to make you obese, obese people tend to have obese pets!), poverty, car ownership, smoking, tastebud sensitivity, commute time(people with longer commutes tend to be obese),genetics,water intake, muscle mass,stress levels, food additives, pregnancy, childbirth, menopause, time of the month for women, free time in a day(try cooking at home and exercise working 2 grueling jobs to make ends meet), drug side effects, emotional eating, type of exercise, micronutrients in food,portion sizes in restaurant, food advertising, food subsidies, vitamn level, thyroid function, insulin sensitivity, liver health, distribution of fat around body parts and inside organs,will power, processed foods, food availability and cost etc. etc. Some of these variables affect the others in a chaotic state machine kind of way.

It's no wonder that all these low carb, low fat, paleo, etc. diets are not one-size-fits-all solutions and that such discussions descend into WORKED-FOR-ME!!! Y U NO DO IT?!! platitudes. A calorie = a calorie is as true and as useless as answering the question "Why are there so many people inside the Super Bowl stadium during the game?" by saying "Because more people entered it than who left, if only people didn't get in, it wouldn't be so crowded."