This is an interesting study about gut bacteria, intestinal gas and obesity – but I don’t exactly agree with conclusions.
The authors conclude that people become obese because they have higher amounts of hydrogen and methane (if we could only stop the hydrogen and methane!). But to me the opposite seems more likely. People struggling with obesity eat more (especially the carb types we talk about on this site), suffer more malabsorption and produce more of these gasses because they have small intestinal bacterial overgrowth (SIBO). That’s why obesity is linked to GERD which is linked to SIBO.
Amazing how often this happens in science. There is no thought given by the authors of the study to which direction flows cause and affect or even other confounders as you pointed out, such as presence of the specific starches as percentage of the diet, that produce those gases.