There are natural microbes in flour, grains like rye, fruits...anything that has a sugar content. Its a natural function. Yeast is a naturally occurring living organism.They didn't know "yeast", but as far back as ancient Egypt, they knew leaven. It was what we would call a charlie today. It was what they used to rise each batch of dough they made for bread. No one knows for sure when the process was first used. Scientists believe that man knew how to leaven bread long before he knew how to write.
The yeast we use today is a pure culture. You can thank Louis Pasteur for that. He was the one who discovered that yeast was a living thing, and he is the one who isolated it as a pure culture. <shrug> I guess you could say he is responsible for the rise of the manufacture and marketing of yeast.