I would be a bit wary of changing the diet too rapidly as GAPS is a radical shift from most diets, especially from what I recall about the induction phase. I can't really offer many comments about these two diets and their appropriateness because I don't remember too much about them. Just bear in mind that one's diet is still going to massively shape the composition of the gut, so changes need to be gradual.
From a general standpoint, I would look at this in the context that the more severe dysbiotic conditions are marked by a severely diminished capacity to degrade many of these carbohydrates and this is purposeful and functional, so in some cases people may need to work from less to more hydrolyzed carbohydrates. Basically more everyday plant fibers versus carbohydrates that one would rarely encounter in their diet as have been described in this thread. It's a fine line to walk though, in that some people are clearly doing better with some of these very selective prebiotics, and they are presumably filling a metabolic and immunomodulary niche. Unfortunately the dynamic is utterly complex and the side effects from these more specialized, uncommon components of "food" are going to be often poorly tolerated. This might mean at first eating more common whole plant materials and slowly increasing the diversity of plant fiber as the initial means of shaping the microbiome.
I would hate to abandon prebiotics altogether, but perhaps there should be avoidance of super concentrated plant extracts, and synthetically hydrolyzed carbohydrate products. Reducing the "dosage" should always diminsh the response, so why not cut back to miniscule quantities. The longer I have done this, the more I see the wisdom in not trying to rapidly force changes, binge, or overdo it. It generally results in set-backs of one sort or another.
There are going to be substances that provoke a much more potent immune response because the only way these carbohydrates become accessible to any significant degree is if you have certain organisms that can chemically sever the bonds that modify the structure of the parent compound. Some of these substances are rather innocuous to those with severe disease simply because the community of organisms to hydrolyze one polymer that is in turn further modified by another, organism is lacking. When we come in with artificially hydrolyzed prebiotics or extraordinary concentrations of these prebiotics, as compared to our usual diet, including some that I am guilty of indirectly advocating, there is more risk of "immune imbalance." There is obviously a reason some of these carbohydrate substances are not found in nature to any significant degree unless biosynthesized or converted by the contributions of microorganisms. The differences in what organisms can break down Beta 1-4 versus Beta 1-3 glycosidic linkages is purposeful. It might be prudent to avoid some of the manufactured products, as in when they use a microbe to hydrolyze a polymeric compound and provide access to something an ill person can't take advantage of and use without excessive immune activation. The degree to which this actually happens in your body is self-regulated and tied to microbial enrichment, so we should proceed cautiously when circumventing nature. The same holds true for vitamin supplementation.
In the future I think we could combine analytic tools with genomic data to analyze one's individual metabolic and microbial signatures to allow predictions about what metabolic pathways need to be supported and microbial fixes need to be made and a very individualized supplemental prebiotic program could be developed. I know my own tinkering has started to narrow down this process to certain kinds of prebiotics. As I have described, I am favoring highly acetylated and sulfated storage polysaccharides and mucopolysaccharides. One commonality is that these are integral to the rebuilding of the intestinal epithelium and the organisms that live there. I also find that he provision of sulfate to facilitate this process is enormously helpful, but I recognize that transdermal magnesium sulfate is not for everyone.
While we have the capacity to gather and analyze metabolic and microbial pathways and compare this to norms, obviously we would need to figure out how to fix this most expeditiously and with the least cost to the host. I believe that these costs can be mitigated first and foremost by not overstimulating the broken immune system. This is where all plant materials have to be considered for what they are.
Things like Berberine are very intriguing, but as I mentioned the whole plant may be better for a number of reasons. One of those reasons is there are myriad ways in which this compound can affect someones microbiome. It possesses properties that will serve to diminish the Toll-like receptor and signalling which triggers an immune response to lipopolysacchride, which is a good thing. It's also a quarternary ammonium so it has antibiotic properties, which can have positive and negative net consequences. The negative meaning that there will be a reactive oxygen consequence to killing off organisms. Accordingly, the plant should facilitate the enrichment of microbes that participate in the differentiation/replication of T-cells. I'm guessing plants containing Berberine are rich in those polysaccharides I discussed above.
Many of these anaerobes in the colon have drug resistance to QA substances, in fact it is often used as an antibacterial agent. For example, Bacillus subtilis is likely largely resistant to the effects of Berberine. The resistance of certain microbes and the susceptibility of others is in large part what shapes the gut. It's that ROS/NS a.k.a. free radical damage that implies that you need the whole plant and the prebiotic contribution it conveys.
There is ample data from studies of inflammatory disease that I believe is on point, and while different inflammatory diseases/conditions clearly have different microbial/metabolic patterns that I have observed, there are some overriding patterns including consistent perturbations in the purine-nitrogen metabolism and TCA-glycolosis-fatty acid metabolism. These have downstream impacts on those processes that have been popularly addressed here chiefly through over-ramping metabolic capacity.
These processes can be dramatically enhanced, at least in vitro, through the provision of some of the key metabolites, principally butyate. I think the same can be achieved via the stimulation of those organisms that produce these, but the metabolic corrections are not so readily achieved. Working backward from butyrate is a good starting point, I think. Looking at some other key metabolites involved in mitigating the effects of endotoxins and modulating the immune response, also seems to be fruitful. I see a place for other things like indole and microbial sphingolipid biosynthesis. I believe these compounds also enjoy very strong evidence for having the capacity to reverse auto-immune processes and cancer, and at the root of this is restoring the energy metabolism and immunocompetence. The fact that these prebiotics substances are perfectly suited to favor the expansion of the known t-regulatory enhancing microbes that are central to synthesis of these same metabolites, and cross-disease microbiomic data tells me these microbes are consistently lacking, suggests we are on the right track. Unfortunately, we have a long ways to go.
I guess my first question is, what is her current diet?
My second question is what prebiotics has she tried, and what effects did these produce? This might be helpful to know.