This subject keeps coming up, and it seems to me that people are freaking out unnecessarily. So I thought I’d start a thread on the subject. As far as I can see, there are three potential situations that people might worry about:
A strong flavor from a previous batch carrying over to the next batch.
A non-yeast organism present that carries over (could be from intentionally soured beer or from infection)
One strain of yeast carrying over and creating non-desired flavors in the new beer.
Is there anything I missed?
Taking the third point first (a brewer recently posted a question about this with regards to saison yeast), I think that is a total non-issue. With proper cleaning and sanitation, the chance of some small remnant population of yeast surviving to the next brew is very slim. And if any does, it will be so out-competed by the healthy, abundant population of pitched yeast that it won’t be an issue. This is one reason you never hear about pitching more than one yeast strain to increase the complexity of the fermentation esters: it doesn’t work. One strain will dominate and not let the other strain contribute at a detectable level.
The second situation (non-yeast organism) is more of a concern, but still not very much of one. Proper cleaning and sanitation will be quite effective in metal, plastic or ceramic (including glass) equipment, unless there are crevices that the sanitizer can’t get to, such as occurs on hose and valve fittings. I’ve personally had zero contamination issues when using scratched plastic fermentation buckets after infections (which were directly traceable to fresh fruit additions). The sanitizer is pretty good at killing those organisms. However, if some do survive, and they eat something different than the pitched yeast, they will have the potential to thrive and not be checked by the healthy yeast.
The first situation is a very real concern, and you just have to make a batch of root beer in your beer equipment to know how bad it could be. It depends on the specific flavor compounds and equipment characteristics, but especially with plastic and rubber parts you should keep this in mind.