I bake bread using a sourdough starter. The starter is a culture of lactobacillus and some kind of yeast. They apparently eat the sugars or carbohydrates in the dough during fermentation but when I look at the nutritional info for fully baked sourdough bread I see 56gm of carbohydrates per 100gm and my question is, why do these organisms stop eating and what is it exactly that they leave behind? They seem to consume something in the dough then they stop as if they have run out of food at which point you need to bake the bread else it becomes "over-proved". Why do they stop eating and what is actually left over when the fully fermented dough goes in the oven?
Flours contain a diverse array of carbohydrates which vary depending on the specific type of flour (wheat, rye, teff, etc). There will usually be a lot of starch (itself having variable amounts of different types of branching), some small mono and oligosaccharides (again of varying types) and "fiber", which is a broad term for polysaccharides that are more resistant to digestion.
To add to the variables, the specific types of bacteria and yeast in a sourdough fermentation can vary in their ability to digest the different types of carbohydrates.
So one part of the answer to your question is that yes, there are carbohydrates that cannot be digested, but the specific molecules that are not digested will depend on the flour and the microbes. The cause of the undigestibility is either 1) the monosaccharides are linked in a way that they cannot be cut apart or 2) the microbes lack the metabolic capability to digest the monosaccharide.
But generally in a bread dough, the digestible carbohydrates have not been completely consumed, so some of the remaining carbohydrate is digestible. The reason it is not used up is that the baker stops the fermentation before it reaches that point so that the dough still has a good consistency.
It is also true that the fermentation activity slows down considerably before this point, even though it does not stop. There are two reasons for this. 1) the pH drops, which slows the metabolism of the bacteria and 2) the easily digestible carbs get used up first, so the later fermentation rate can be affected by the slow rate of breakdown of the more difficult to use carbohydrates. Ultimately, the dynamics of the fermentation are determined by the choice of flour, the microbial population and the conditions (temp, water content, whether and how often the baker works the dough, etc).
From the introduction in a paper on the different lactic acid bacteria (LAB) cultures in sourdough:
Sourdough LAB give rise to the characteristic qualities of several kinds of foods (flavor, texture, taste, and shelf life) by producing metabolites such as lactic acid, acetic acid, and ethanol. However, it is not easy to control sourdough LAB fermentation, due to the spontaneous occurrence of complex phase successions of LAB communities during subculture. Previous studies have characterized three phases, each dominated by the genera Weissella, Pediococcus, and Lactobacillus, whose succession determines the balance of metabolites in sourdough.
Over time, the pH of the dough changes (hence sourdough).
One of the major characteristics of sourdough fermentation is a drop in pH proportional to the maturation of the LAB community that produces lactic and acetic acid, eventually reaching a pH of approximately 4.0. Since pH changes must induce stress on the LAB community, assessment of pH conditions is necessary to understand and control the evolution of the LAB community in sourdough.
[OP, in comments] but there comes a point where they don't eat any more and you need to either feed them more flour or they will die apparently, that is why you keep a starter in the fridge to slow the consumption speed but I am still unclear on what is left over? if they eat carbs why don't they eat the rest of the 56gm of carbs left over per 100gm?
The purpose of "feeding" is to dilute the acids and replenish the carbs. It also dilutes the concentration of bacteria. The combined effects result in better conditions for cell life and reproduction. Every time they metabolize ("eat") some carbs, they also produce some acid and ethanol. It is the waste products that keep them from reproducing more as the sourdough matures.
Your question is based on a false premise. They don't stop when they run out of food. When you overproof the dough, there is still tons of edible carbohydrates left in the dough, mostly starch.
If you wait for the fermentation to stop on its own, this will happen not due to running out of food, but due to the accumulation of too much waste material. The usual story taught is that it is the ethanol - this is why we didn't have strong alcohol before destillation was discovered, you can only ferment up to 15-ish percent alcohol before your fermenting organisms die (and you usually get this percentage in wine, beers are below that, even with tricks for producing strong beer). I could imagine that other stuff combines with the ethanol to kill them off, the whole ammonia, thioles etc. produced by vigorous fermentation are not very friendly to microorganisms.
But you are not even waiting for the fermentation to stop. Overproofed dough is still very actively fermenting. It just goes into a state where its gluten can no longer trap gases - I don't know if this is because you have too much gas, or because the microstructure of the gluten mesh changes, probably both. Anyway, at that point, you cannot bake good bread, but this has nothing to do with stopped fermentation.
To answer literally your question of "why do they stop eating"
- if you leave them alone until they stop on their own, they stop because they die out due to pollution (poisoned by their own waste)
- if you throw your dough because it overproofed, they don't stop eating
- if you use your dough for baking before it is overproofed, they stop eating because they die from the heat in the oven
To sum it up, fermentation processes in the kitchen (not only dough, but also yogurt or sauerkraut) do not mean that the microorganisms use up their food. On the contrary, they use up a tiny fraction of the food available, and most of it is left unchanged in the finished product.
What yeast does:
glucose => etanol + carbon dioxide.
What lactobacilus does:
glucose => lactic acid
They usually don't find glucose around them, so they break down the starch first (starch is abundant in the dough).
They both also do other things, like making new cells from the ingredients they find around them, but these other things are of less importance in bakery.
Why they stop at some point? Well, in the usual bread-making, they stop only when you bake the bread and the temperature kills them.
They can be significantly slowed down (like any other organism that cannot control its own temperature) by cooling down the dough. That's how ready-made dough is sold.
If you leave the dough alone, they will live and reproduce up to the point where etanol, carbon dioxide and lactic acid are too much for them. Depending on the water content of the dough, the availability of oxygen, the ability of the carbon dioxide to escape and the initial mixture of bacteria and yeast, you may get some kind of beer. In general, no more fermentation happens in the beer, as long as there is neither oxygen nor dilution. The microorganisms will just slowly die off because they don't tolerate that much of their own products around.
Or you may get something less pleasant than beer, because the dough is usually not air-tight and because other microorganisms are always present. Given time, air and if the mass is not too dry, the end result will be carbon dioxide, nitrogen and some inorganic salts.