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Page 6 of 20 Manrique et al. Microbiome Res Rep 2024;3:23 https://dx.doi.org/10.20517/mrr.2023.80

effectiveness of cancer treatments such as immunotherapy and chemotherapy [75,76] [Figure 1].

[77]
[79]
Several diets, including Mediterranean , high fruits-vegetables-whole grains , low-FODMAPs ,
[78]
[80]
ketogenic , and gluten-free diets, have been associated with specific gut microbiome compositions.
Consequently, these diets have shown beneficial effects such as low inflammation, high insulin sensitivity,
weight loss, improved cognitive function, and better immunological activity, among others. However, it is
important to note that dietary interventions have to be chosen carefully based on each person’s baseline
physiological state and gut microbiome composition and functional profile to exert the desired
effect [73,75,80-82] .

Although many studies have shown that dietary interventions can specifically modulate gut microbiome
composition, it remains unclear whether there are universal baseline features associated with microbiome
[83]
responses to these interventions . Future studies should identify and stratify subjects with a diet-
responsive gut microbiota within study cohorts to maximize the success of these interventions . It is also
[84]
important to control for recent dietary patterns in observational studies, as interindividual differences in
microbiota response to dietary interventions are known to exist .
[85]
Prebiotics
The most accepted definition of prebiotics describes them as substrates that are selectively utilized by host
microorganisms, thereby conferring health benefits. The concept includes a substance, a physiologically
beneficial effect, and a microbiota-mediated mechanism [Figure 1]. Prebiotics could be present in
[86]
naturally or synthesized forms, including inulin, oligosaccharides, lactulose, pyrodextrins, dietary fibers, and
resistant starches, among other candidates .
[87]

Prebiotics play an important role in human health and are naturally included in low concentrations in
different dietary food products. Prebiotic fibers are a direct energy source for some members of the
microbiota, which will metabolize them, generating byproducts that can be used by other microbial species.
This phenomenon is known as the substrate cross-feeding effect, and it can deeply impact the composition
of the gut microbial ecosystem. An important example of the cross-feeding effect is the butyrogenic effect,
which consists of the modification of the environment by acids produced during fermentation of
prebiotics [88,89] .

Overall, prebiotics have shown potential for the treatment of various diseases by modulating the gut
microbiome. This holds true for IBD, where prebiotics can serve as a complementary therapy, aiding in
enhancing the composition of the gut microbiome and reducing inflammation in the gut . In the gut-brain
[90]
axis, a study conducted at Rush University found that prebiotics from plant origin, consisting mainly of
fibers (inulin, resistant starch, resistant maltodextrin, and rice bran), can help treat Parkinson’s disease by
promoting the growth of beneficial bacteria in the gut. The SCFAs produced by prebiotic metabolism can
help reduce inflammation in the brain and improve motor function . Beneficial effects have also been
[91]
[92]
described in the treatment and prevention of diabetes and obesity .
Probiotics
In 2013, ISAPP defined probiotics as “live microorganisms that, when administered in adequate amounts,
confer a health benefit to the host” . Before commercialization, the specific microorganisms used as
[93]
probiotics must be granted qualified presumption of safety (QPS) status. QPS status was developed by the
European Food Safety Authority (EFSA)’s scientific panel as an approach to provide pre-evaluations on the
safety of microorganisms intended for use in the food or feed chains [Figures 1 and 2].
[94]