There are some basic rules that should be followed no matter what you ferment. People who ignore these basic principals risk turning their ferments into something that looks more like a high school science project than something you’d want to eat.
Try to embrace any ounce of OCD nature that you may have. You need to keep everything you use for fermentation as clean as possible to avoid contamination (ie boiling your jars and utensils). If you’re planing on keeping your ferments for long-term storage then this is even more important. Aim for sterile and you won’t fail.
I’m the first to admit that I am far from sterile; so I’ve had to throw away sauerkraut, sourdough, and kefir. And I once accidentally grew a mother on top of my yogurt (something that was not expected, I assure you). Learn from my mistakes, and keep it clean.
Fermenting at the right temperature is one of the main ways to keep the good bacteria in, and the bad bacteria out.
I generally specify somewhere warm, or somewhere cool. Somewhere warm means that the culture is happiest around 21 C (70 F). Think of near your hot water heater or above the fridge. Grain generally likes to be cultured warm. Somewhere cool means that the culture is happiest around 18 C (65 F). This is primarily required for fermenting vegetables.
Take into consideration seasonal variations in temperature. In the winter you might need to culture your sourdough a wee bit longer, and in the summer you might need to only ferment your sauerkraut for a few days rather than weeks.
Once you’re done fermenting, store your ferments somewhere cool. Traditionally this was a cellar or cold room, but the refrigerator also would work. Rule #1 cleanliness still applies during storage. So don’t double dip your pickle fork or you might end up growing something strange.
If your ferment looks funny, smells funny or tastes off, then don’t eat it. Every ferment walks the line between the yummy yeasts and bacteria that we want to grow, and those that cause food poisoning.
The goal of fermentation is to create an environment that favours a good culture. If a culture is thriving, then any invaders won’t be able to take hold. This generally involves keeping your fermentation at a particular temperature, keeping it anaerobic, and/or balancing the salinity and pH.
It also involves having a happy and vigorous starter. Many cultures start with a “mother”, a scoby, grains, etc. If you treat your culture like a pet (because, really, it is a pet) and take good care of your culture (regular feeding, exercise and attention) then your culture will do a good job of keeping unwanted bugs out of your fermentation. You should even consider naming your culture, because if you do a good job of taking care of it, it can become a family heirloom.
Cultures can cross contaminate each other. So if you plan on keeping several different types of similar cultures (ie, yeast cultures, or lactic cultures), then either don’t have them out of the fridge at the same time, or if you do, ferment them in separate rooms.
The reason why my yogurt grew a mother is because I had kefir sitting out on my counter at the same time. The lactic bacteria in the kefir decided to colonize my pots of yogurt. The result, though edible, wasn’t exactly what I was looking for.
All of this leads to my disclaimer: if you choose to eat something weird like pink kefir or molding sauerkraut and it makes you sick… then that’s YOUR fault… not mine. I am in NO WAY condoning you to eat disgusting food. Fermented food is delicious. If it’s not delicious then it’s probably not fermented… it’s just gone bad.
What should you do with bad food? Well, start with a sigh. Think about how you could keep things cleaner the next time. And then throw it away.