Enzymes are kind of like a chemical compound. Enzymes are proteins that work on molecules, they either build the molecules together, or some of them break the molecules apart. They are not a germ. But it would be impossible to create an enzyme by only chemical reactions, because it is a living biological material. So they take a simple harmless bacteria, something like lacto-bacillus, and they change it's DNA, they insert a code that tells the bacteria how to build this enzyme. So now they have a new race of bacteria that is really great at building this enzyme, or chemical, or whatever they want to make, and they grow a big colony of this bacteria, and each one of them has some of this chemical in them because they all make it.
Then the last step, there is probably a lot of ways that they can do this, but I think they spin the container of bacteria in a centrifuge so all the chemicals come apart and organize themselves by weight since they are all different density, then they suck out the layer that is the chemical or enzyme that they want. Or maybe they don't need to do that, maybe the bacteria just spits it out like how yeast spits out alcohol. Then they just put the liquid through a small filter and take out the chemical they wanted, and the bacteria doesn't get through the filter because it's bigger.
Simple bacterias are basically little factories, they take in ingredients and build them together into another object. Similar to enzymes in that way, but they can do more jobs than an enzyme. Every kind of enzyme basically has one job it is good at, maybe a couple jobs. Like some of them do the same process in both forward and reverse, both building and destroying the same object and the same components that the object comes from. But a bacteria can be coded to do multiple different jobs, it can build many different kinds of things, and it always increases more copies of itself to do even more work all the time and always producing larger amounts. So an engineered bacteria is really the greatest kind of tool for making any kind of biological chemicals or materials.