Not necessarily GMO. In fact, as complex as it is, GMO is pretty out of the question for the time being. Types of bacteria *naturally* have many strains, and some of them are better for some things. So what you have to do is find a strain that is particularly good at what you want, and patent it.
For example, Dannon found a type of bacteria that was particularly good for yogurt, in that it generated bulk in the intestines, almost like Metamucil. But at the time, they thought it was two different species of bacteria.
In any event, Dannon found a bunch of previously unidentified strains of this bacteria, which though they did exactly the same thing as the parent strain, were unique enough to be patented. And this gave Dannon *naming* rights of those strains. So they were able to give these strains good *marketing* names in different countries, even though they were basically the same bacteria.
For their part, other companies found different strains that they patented with their own marketing names. Same bacteria though.
Nothing really nefarious about it.
This is where I'm confused. How can they patent what occurs in nature, whether rare or not?