Microbiology has gotten a lot wrong studying yeast and bacteria. We’ve assumed, until quite recently, that if a microbe doesn’t grow in a dish it’s not there. And that a microbe is either on/live/growing or off/dead. And that we can study microbes in isolation — “pure culture” — away from other species in little sterile dishes and expect them to behave normally. In all fairness, microbiologists have sometimes seen these as a problems, but have mostly just gone on this way, writing books about what we think we know.
DNA detection and sequencing technology is showing just how many bugs don’t grow in dishes — “high throughput” technology can document (theoretically) all of the species in a drop of [insert favorite liquid here]. That’s pretty routine these days. And we’re slowly beginning to study how mixtures of microbes — you know, the way they live in the wild — behave in the lab. Wine was a bit ahead of the curve here: microbial enologists have been studying the goings-on of spontaneous and mixed fermentations since the late 1980’s.*