(Rolls eyes) You're determined to add complexity, aren't you?
The hypothesis would be: "this phenomenon was the result of an intentional action by an intelligent agent."
Simple as that.
Now, verifying the hypothesis may very well be difficult to do -- but the hypothesis itself is much easier than you apparently wish it to be.
For example, when confronted with our insulin-producing bacterium, we can state the following ID hypothesis: "this insulin-producing bacteria does what it does as a result of deliberate genetic modification."
One source of evidence to support the hypothesis would be to sequence the bacterial genome. It will reveal the "extra" human insulin gene among what otherwise appears to be "regular" bacterial DNA -- about what one would expect from the recombination process.
As a "scientist" who rejects the possibility of a valid ID hypothesis, you'd be stuck trying to show how that human insulin gene got into the bacterium by natural means. You could probably even come up with a mechanism -- albeit one that requires a whole lot more, and more tenuous, assumptions than the ID hypothesis does in that case.
So what intentional act and what intelligent agent led to the development of citrate plus e.coli?
If one can tell that a gene modified organism was the result of the intentional act of an intelligent agent couldn't this only be detected against the background of an organism that the majority of the genome was not the intentional act of an intelligent agent but the accumulation of millions of rounds of mutation and selective pressure?