Let's say you had such an organism.

Naturally, all the yeast individuals in your population have slight genetic variations. Maybe millions of them. Most have your plasmid to make X.

Due to natural selection, the competing priority—let's call it the "Y" product—is reproducing * surviving as much as possible. The yeast genes that make the yeast reproduce as much as possible and survive as well as possible will eventually be the largest population in your reactor.

So if X doesn't also achieve Y, the only thing that will be left in your reactor is a population that achieves Y.

The worst thing (which is true most of the time) is that achieving X is opposed to Y. Processing some chemical in the media that doesn't translate to food for the organism is wasted metabolic resources. So for most applications you can think of, your X population will die or reproduce away its X genes.

There's nothing you can parameterize to fix this! Like Y will happen regardless of what temperatures you use, or what media you use, or how much oxygen you give the reactor. By virtue of growing something, you're optimizing for Y. Either design X to also achieve Y, or fail. Evolution is opposed to you, not on your side!

In practice today, we don't understand the biological systems design well enough to make X also achieve Y. So what happens is you grow the yeast until you have a population with maximum metabolic efficiency (i.e., maximally achieves Y), and THEN modify the yeast to do X. It dies quickly, and your left with a little bit of product. This works, but it's not viable.

So from my understanding,

bacteria is competing to reproduce the fastest, and the chemical that we want is simply a byproduct of its metabolism or pathway for reproduction

issue is, however, the byproduct has to either be the most efficient factor for reproduction, or else by natural selection it will be removed

my question is, can we use the same techniques found in tree grafting to prevent or delay natural selection, and grow our byproduct?

question - so why does agriculture work? why are we able to grow tomatoes year after year.

is the entropy at the cellular level versus at a plant level so different that the processes are "locked" in place.

does it make more sense to try and grow plants that produce malic-acid tomatoes? sure it might be harder to geow one... but once grown, you can scale it infinitely.

I suspect that it's that you can manually select which tomatoes you want. It's a bit harder to select individual microbes.

So essentially, the difference between the trait you want, X, and the trait that survives, Y, doesn't exist. Every Y is an X, since generations of farmers are the ones manually doing the selection.

that makes a lot of sense. so in case of tomatoes, the survivability of the plant has no correlation with actual survival. it is being engineered by the farmers.

what we really need is a way to select and ensure survival of the yeast that we want.

Alot of companies do exactly that. Using systems like: http://www.tapbiosystems.com/

But it's not cost effective when producing millions of liters.

TAP Biosystems is the manufacturer of what is now called the Sartorius.

Also, if you look carefully at the Lygos website photos, you'll see the Sartorius.

@doctorpangloss's comment is 100% right. I'd add the small problem that behavior in small reactor != behavior in large reactor. Reactor scale-up is somewhat unpredictable and often ends in tears.