Beans cause gas because intermediate-sized carbohydrates are digested by gut microbes, producing CO2 and hydrogen gas.

“It turns out that the answer was discovered by scientists working for NASA. If you think about NASA and their missions - Mm-hmm. - back in the '70s, you can understand - Mm-hmm. - why they would want to control something like this. - Mm-hmm. - It turns out that beans contain, in addition to starch and sugars, a kind of intermediate-sized carbohydrate that our bodies do not have the enzymes to break down into sugars. So we can take care of starch, but not these intermediate-sized molecules. They pass into our gut unchanged, and then we have plenty of microbes that are happy to see those and digest them. In the process, they produce CO2 and hydrogen gas, and that's what we end up experiencing.”