Using Sourdough Breads to reduce Fructans

There isn't really any scientific information available about the fermentation of fructans in sourdough. I did find this page which says that there are some lactobacilli that are effective at breaking down fructans, but the effectiveness varies by strain of bacteria and type of fructans. (There are also many lactobacilli that don't break down fructans: of 712, only 16 were effective.)

While a longer fermentation time will mean more of the sugars in your dough are digested, since you are aiming to ferment a specific type of sugar, the establishment of your starter may be more important. According to this study, a couple of the strains of lactobacilli shown to be effective at breaking down fructans are found in well-established starters.

In short, rather than giving your dough a long fermentation time, it may be more effective to make dough with a high proportion of a well-established starter instead. The starter will have had a longer cumulative fermentation period to break down fructans, and if your starter has the appropriate culture, it will be more effective at breaking down the fructans in the added flour of your final dough. There is little research on this specifically, so this is largely conjecture and entirely dependent on the culture of your starter.

You cannot ferment sourdough indefinitely.

The safest way to minimize the different sugar contents in the dough is just ferment as much of it as possible (though I never ferment more than 50% of the flour). While retarding exposes the dough to longer fermentation times it also exposes the microbes to lower temperatures (which slows fermentation). So unless by retarding you mean to let the dough "ferment to death" and just use it to improve the taste of a yeast bread, retarding will make no big difference in terms of sugar contents.

However, I'd like to tell you that starch is essentially a long chain of sugar molecules which get broken down in your intestines in any case (even by the same mechanism microbes in sourdough do it: using enzymes). So by ingesting starch you will - always - also get non-trivial amounts of fructose as well.

The big advantage to sourdough is that it can break down some sugars (or rather carbohydrates) that we (humans) cannot break down that well. If that's your goal: ferment 50% of the flour, knowing that it will also give the bread a strong taste.

Regarding your starter: As soon as your starter is strong enough to rise the dough on it's own again, the microbe composition and therefore the metabolism is not much different from your original starter. So in your case, it doesn't make a difference.

Personal experience: longer fermentation times allows me to eat sourdough without problems. Too short: 7–12 hours, and I feel the effects pretty quickly. About right: ~24 hour range, and I can eat and feel good. Just beginning to test the limit of what I can eat in a sitting before I feel the effects, or even if there is a (reasonable) limit.

Monash University's take: they concur with my experience. They say their tests indicate that longer fermentation of wheat bread, which in my understanding would always require a retarding step (correct?), is/can be okay for a low-FODMAP diet. They say a 2 slice max in a sitting. (Source.)

In reading about the process described by some of the baker's Monash has certified, it looks like what might be needed is a fermentation time in the 22-30 hour range. For example: Morpeth Sourdough Bakery says they have a 22 hour ferment time. You can find a link to their site by clicking here for a list of Monash Certified Bakeries.

Differences in process/ingredients should affect the needed time. Perhaps even a much shorter time could be achieved (?) if doing things a different way, such as a higher percentage of levain to begin with.

Just a thought: there are enzymes at work too, so while a cold rise slows down yeast/bacterial activity, enzymes may be the key factor in the longer time reducing the fructans.