Probiotics (sometimes referred to as psychobiotics in this context) can modulate communication between the microbiota, gut and brain through multiple pathways. They influence neuronal signaling (e.g., via the vagus nerve and the enteric nervous system), hormonal responses (such as modulation of cortisol and the HPA axis) and immune activity (including cytokine regulation and inflammation; Mörkl et al., 2020). Certain probiotic bacteria, particularly Lactobacillus and Bifidobacterium species, produce neuroactive compounds - for instance, neurotransmitters such as GABA and serotonin, as well as short-chain fatty acids - that can affect brain function (Rahmannia et al., 2024). In addition, probiotics strengthen the gut barrier by reducing intestinal permeability and systemic inflammation, thereby protecting the brain from inflammatory stress (Rahmannia et al., 2024). Through these mechanisms—such as reducing neuroinflammation, modulating neurotransmitter levels, and influencing neuronal circuitry via the vagus nerve—probiotics contribute to a more favorable biochemical environment for brain health and emotional regulation.

A review by Dronkers et al. (2020) reported that probiotics (the most studied strains were Lacticaseibacillus rhamnosus GG (LGG) and Bifidobacterium animalis subsp. lactis BB12) were administered in over 1,000 clinical trials with an average sample size of 74 participants. These clinical studies addressed 700 different diseases and conditions and were registered at ClinicalTrials.gov run by the United States National Library of Medicine and/or the World Health Organization’s International Clinical Trials Registry Platform (Dronkers et al., 2020). In addition to strain and dosage activity, the potential benefits of probiotics are often limited by interactions with the host microbiome (Suez et al., 2019). In the last 5 years, there have been more than 500 case studies/year, systematic reviews and meta-analyses covering a wide range of conditions, confirming that probiotic interventions have beneficial effects in various gastrointestinal, metabolic, immunological, neuropsychiatric and various other conditions (Bagdadi et al., 2025). In particular, probiotics have been shown to exert condition-specific benefits through multiple mechanisms. In psychiatric disorders (excluding schizophrenia), clinical studies reported improvements in mood regulation, anxiety reduction, and cognitive performance, possibly mediated by modulation of the gut-brain axis and reduction of systemic inflammation (Hong et al., 2022; de Lima et al., 2025). In allergic diseases, probiotics were associated with decreased symptom severity and improved immunological tolerance, potentially via restoration of gut microbial balance and enhancement of regulatory T-cell responses (Xi et al., 2025). For patients with type 2 diabetes mellitus, probiotic supplementation improved glycemic control, insulin sensitivity, and inflammatory markers, highlighting their role in metabolic regulation (Wang et al., 2024). In gastrointestinal disorders such as irritable bowel syndrome, probiotics alleviated abdominal pain, bloating, and irregular bowel habits, likely through normalization of gut motility and modulation of the gut microbiota (Ceccherini et al., 2022; Li et al., 2020). Similarly, in inflammatory bowel diseases, osteoarthritis, and chronic kidney disease, clinical evidence supports their role in reducing disease activity, inflammatory biomarkers, and oxidative stress, thereby contributing to improved quality of life (Karim, 2025; Liu C, et al., 2024). However, for diseases such as COVID-19, systemic sclerosis, Crohn’s disease and scleroderma, the results of the studies are inadequate. Clinical efficacy remains limited, and interpretation of results is compromised by the lack of standardization when using different strains (even within the same species), the inability to determine individual contributions in multi-strain formulations and the lack of consistency in dosage and duration of probiotic use. Furthermore, reproducibility of clinical trials is limited as they differ in design (small numbers of participants and heterogeneous groups, short duration), do not capture participants’ health status, age, diet and baseline microbiota, focus on short-term symptom improvement and report symptom relief without investigating mechanisms, e.g., metabolomics and immunomodulation. Common probiotic strains have been extensively studied and are well known for their health benefits (Table 1).

Recent innovations in the use of probiotics include the development of multi-strain and customized psychobiotic formulations aimed at influencing anxiety and depression, cognition and neuroinflammation (Kamal et al., 2025; Messaoudi et al., 2011); the combination of probiotics with prebiotics (fiber-based substrates that promote the growth of probiotics), resulting in synbiotic therapies for enhanced effects on the gut and brain; next-generation encapsulation and delivery technologies (e.g., microbiotics); and the development of new products (e.g., microencapsulation, enteric coatings, phage-probiotic combinations) to improve strain viability and targeted release in the gut (D’Amico et al., 2025; Ranadheera et al., 2017); precision approaches using specific strains such as Limosilactobacillus reuteri (L. reuteri) for behavioral modulation in autism or B. longum for stress resistance; and ongoing research on genetically engineered probiotics that produce neuroactive compounds (e.g., GABA, serotonin) or immunomodulatory molecules directly in the gut (Charbonneau et al., 2020). Taken together, these innovations are moving probiotics from general gut health agents to targeted therapeutics for gut- and brain-related conditions such as anxiety, depression, Alzheimer’s, Parkinson’s, and autism spectrum disorders. They are increasingly recognized as modulators of gut and systemic health, including the gut-brain axis (GBA; Ali et al., 2025). Future studies should conduct longer-term studies considering the standardized strain-specific design and protocols, and personalized approaches based on patients’ microbiome profiles.

Several innovative microbial approaches have been extensively explored for the production of galacto-oligosaccharides (GOS), offering sustainable and efficient alternatives to conventional synthesis methods. One remarkable process includes the β-galactosidase immobilized on different substrates (Hackenhaar et al., 2021; Carević et al., 2018). Geiger et al. (2016) stated that a simple recombinant β-galactosidase from Streptococcus thermophilus DSM 20259 could convert 80% of whey lactose to GOS in 5 h. They also reported that ≈ 1 kg of GOS was produced from 3 kg of whey permeate powder. From Greek yogurt, the β-galactosidase synthesized by Cryptococcus laurentii whole-cells produced the GOS whey at 36% (w/w), and 50% of the initial lactose was converted at a specific productivity equal to 2.3 mg/U·h (Fischer and Kleinschmidt, 2021). Based on an expression system developed on the T7 RNA polymerase promoter in E. coli, Kittibunchakul et al. (2019) noted a high recombinant β-galactosidase activity (26,000 U/L). This value was 28-fold and 1,000-fold higher than the production of native β-galactosidase from L. helveticus DSM 20075 when grown on lactose and glucose, respectively. To improve their catalytic activity and GOS production, seven β-glucosidase mutants were obtained from Thermotoga naphthophila RKU-10. Interestingly, the F414S mutant showed efficient properties since the GOS production was improved from 140 mM to 207 Mm using 0.2 mM lactose (Yang et al., 2018). On free or immobilized forms, commercial enzymes have been employed in GOS production. The primary commercial enzymes used in GOS synthesis process are bacterial β-galactosidases (e.g., Kluyveromyces lactis) and fungal (e.g., Aspergillus oryzae) sources (Maráz et al., 2022). From different microbial sources, Mano et al. (2019) confirmed that Kluyveromyces lactis commercial enzyme named Lactozyme™ 2,600 L could display an optimal performance for lactose conversion, yield and specific productivity (50 g GOS/g enzyme×h).

Due to their superior properties compared to other prebiotics, xylo-oligosaccharides (XOS) have gained more attention. XOS are stable across a broad pH range (2.5–8.0) and at temperatures up to 100 °C. Moreover, xylobiose has 0.3–0.4 times the sweetness of sucrose, and the approved daily dietary intake of XOS (2.1 g) is lower than that of most other oligosaccharides (Amorim et al., 2019). Notwithstanding these merits, XOS is more costly than the other prebiotics (Yegin, 2023). Because of the diverse enzyme systems they possess, each microorganism has a distinct XOS utilization pattern. For instance, XOS containing uronic acid are utilized by only a few bifidobacteria of human origin. Bifidobacterium adolescentis can metabolize both arabino-XOS and linear XOS (Falck et al., 2013), whereas Levilactobacillus brevis grows preferentially on linear XOS (Precup et al., 2022).

To date, most commercial xylanases are produced by bacteria (e.g., Bacillus and Streptomyces) and fungi (e.g., Thermomyces, Trichoderma, and Aspergillus). As a result, xylanases from these sources became dominant in the enzyme market. To categorize the extracellular enzymes including xylanases synthesized by Bacillus sp. AR03, Hero et al. (2021) exploited a proteomic approach. By LC–MS/MS identification, these authors reported a glucuronoxylanase GH30-8 and an endoglucanase GH5-2. From Bacillus sp. strain BP-7. Gallardo et al. (2010) reported that GH5 xylanase (Xyn5B) was able to act on linear XOS, and xylooligomers with methylglucuronic groups were generated. A novel xylanase produced by Streptomyces spp. (B6) was able to generate two xylanases attributed to GH10 and GH11 families (Liu et al., 2022a). In another study conducted by Boonchuay et al. (2014), Streptomyces thermovulgaris TISTR1948 used xylanase for XOS production. The enzyme production was conducted at 50 °C and 250 rpm for 96 h utilizing the rice straw as a carbon source, and the principal oligomer was xylobiose with 85.15 mg/g. Adsul et al. (2009) described an efficient process for the hydrolysis of xylan by using Streptomyces matensis xylanase, yielding mainly xylotriose and xylobiose as the predominant XOS products. Enzymes from Aspergillus have also been employed for XOS production using lignocellulosic biomass. For example, Akpinar et al. (2007) applied a two-stage approach to produce XOS from cotton stalk, first extracting xylan with KOH and then hydrolyzing it with commercial Aspergillus niger xylanase. Maximum XOS production was observed at 40 °C and pH 5.4 with 2% xylan (10 mL) and 4.4 U/mL enzyme (1 mL). To produce XOS by a packed bed reactor in continuous mode, Aragon et al. (2013) employed xylanase immobilization of Aspergillus versicolor by using several support materials. The glyoxyl agarose constitutes the most effective support for xylanase immobilization and maintained till 85% of its catalytic activity. After incubation at 60 °C, the immobilized enzyme was nearly 700 times more stable than the free fraction, and retained full activity after 10 cycles of 1-h process. In addition, the immobilized xylanase delivered 2.5-fold higher xylobiose production as compared to free fraction.

The xylan bioconversion from agricultural residues into XOS without prior pre-treatment has been revealed to be possibly economical alternate for industrial application. Crude xylanase from Aspergillus fumigatus R1 was qualified to yield 1.08% (w/w) of XOS from raw wheat husk xylan. XOS with a DP up to 5 were detected in the final hydrolysate, being xylobiose the greatest principal oligosaccharide during the entire reaction time (Chavan et al., 2023). This enzymatic process avoids the formation of unwanted by-products typical of chemical extraction.

Fructo-oligosaccharides (FOS) are enzymatically produced from sucrose through a transfructosylating reaction catalyzed by β-fructofuranosidase (FFase) or fructosyltransferase (FTase) enzymes. Aspergillus flavus NFCCI 2364 FTase was explored to produce FOS from 16 agro-wastes (Ganaie et al., 2017). Smaali et al. (2012) used β- Ffase from Aspergillus awamori NBRC4033, demonstrating high yields and indicating the efficiency of agro-residue biomasses as substrates. Silva et al. (2013) stated that inulinase from Aspergillus niger (A. niger) and Kluyveromyces marxianus (K. marxianus) NRRL Y 7571 was able to generate FOS from inulin, with specific yields of kestose, nystose, and fructosyl nystose. Diez-Municio et al. (2013) showed that the inulosucrase from Lactobacillus gasseri DSM 20604 could generate FOS and maltosylfructosides (MFOS) from sucrose and sucrose/maltose mixtures. For short-chain FOS (scFOS) and oligolevans production, an inventive two-phase system of levansucrase (from Bacillus amyloliquefaciens)/endo-inulinase (from A. niger) used the sucrose. This system permitted levansucrase to create levans, while endoinulinase monitored molecule size, with 6-kestose being the primary scFOS (Ni et al., 2021). In addition, the immobilization of levansucrase improved the levan production over scFOS (Ni et al., 2021). To produce FOS from sucrose, Soliman et al. (2017) studied the immobilization of inulinase isolated from A. niger. The used material was on polyurethane foam, attaining a 30% total FOS yield, including GF2, GF3, and GF4. Bersaneti et al. (2018) revealed that levansucrase from B. subtilis could generate FOS and levan concurrently at 41 g/L of FOS and 87 g/L, respectively. Huang et al. (2016) stated that Aspergillus aculeatus M105 produced extracellular FTase, achieving FOS yields of 68 and 66% (w/w), respectively. By using the inulosucrase (IslA4), issued from Leuconostoc citreum, and sucrose, Peña-Cardeña et al. (2015) produced FOS containing compounds f-nystose, nystose, neokestose, 1-kestose and 6-kestose.

Many additional produced prebiotics can be isolated or produced from several microbial sources. Manno-oligosaccharides (MOS) production emphasizes a substantial progress in the utilization of renewable resources for producing appreciated prebiotic. A genetically engineered endo-β-(1,4)-mannanase, isolated from B. subtilis and expressed in Escherichia coli, could generate mannans to MOS with a degree of polymerization arraying from 4 to 7 (Sathitkowitchai et al., 2022). The β-mannanase from Penicillium aculeatum APS1 can degrade glucomannan (from konjac) and galactomannan (from locust guar and bean gums). The enzyme produces low molecular weight at DP ≤ 4 (Bangoria et al., 2021). From Streptomyces cyaenus, a mannanase hydrolyzed palm cake kernel with oligo-mannans (DP ≤ 7). In addition, the mannotriose and mannobiose were detected throughout the reaction period (up to 8 h; Purnawan et al., 2017).

To improve the production of isomalto-oligosaccharides (IMOs), recombinant enzymes engineering showed an important progression. In this line, Kaulpiboon et al. (2015) used pullulanase, a modified amylomaltase Y101S, and transglucosidase from A. niger. This enzyme blend enabled the production of long-chain IMOs at pH 7.0 and 40 °C.

Table 2 summarizes some examples of major microbial enzymatic producing prebiotic (GOS, XOS and FOS). Besides the biochemical and production aspects described above, the physiological and clinical effects of prebiotics have also been investigated extensively. Several studies have shown that the intake of prebiotics such as GOS, FOS, and XOS can positively alter the composition of the gut microbiota, increase short-chain fatty acid production, and improve intestinal barrier function. In clinical trials, prebiotics have been associated with positive results in gastrointestinal health, including relief from constipation and irritable bowel syndrome, with beneficial effects on metabolic disorders such as obesity and type 2 diabetes (Sanders et al., 2019; Markowiak and Śliżewska, 2017; Davani-Davari et al., 2019; Gibson et al., 2017). These evidences highlight the importance of prebiotics not only as industrially significant compounds but also as key regulators of human health.

The gut microbiota play a crucial role in systemic immunity by modulating cytokine production, regulating immune cell activity, and strengthening the intestinal barrier (Sivan et al., 2015). Certain probiotics further enhance immune defenses by stimulating phagocytosis, activating natural killer cells, and interacting with dendritic cells (Piccioni et al., 2023). They also boost antibody production, improve vaccine responses, and promote anti-inflammatory cytokine release, potentially reducing the risk of colon cancer and colitis. Additionally, gut microbes contribute to pathogen defense through competitive exclusion, antimicrobial compound production, and nutrient metabolism, impacting overall immunity and health (Cano et al., 2024).

While the exact mechanisms by which probiotics exert their immunomodulatory effects are not yet fully understood, several potential pathways have been proposed. Probiotics are believed to influence immune function through the inhibition of Toll-Like Receptors (TLRs), which play a central role in the recognition of microbial components and the activation of inflammatory responses. By downregulating TLR expression, probiotics can reduce the activation of inflammatory pathways such as NF-κB, which is involved in the transcription of pro-inflammatory cytokines (Plaza-Diaz et al., 2019). Additionally, probiotics may modulate the activity of innate immune cells, such as Natural Killer cells, enhancing their cytotoxic potential and improving immune surveillance (Kwok et al., 2022). Probiotic supplementation has also been shown to impact oxidative stress markers, reducing oxidative damage and improving the balance between antioxidants and oxidants. By modulating factors such as nitric oxide and C-reactive protein, probiotics help mitigate the risk of inflammatory diseases, cardiovascular dysfunction, and metabolic disorders. These mechanisms highlight the potential of probiotics to regulate immune responses, although further research is needed to clarify strain-specific effects and optimal intervention strategies (Kwok et al., 2022).

While many studies report the general immunomodulatory benefits of probiotics, it is important to emphasize the significant strain specificity in their effects on immunity. Variability in host response due to genetic, environmental, and lifestyle factors further complicates the translation of findings. Moreover, there is a notable lack of long-term human clinical trials assessing safety, efficacy, and optimal dosing regimens of specific probiotic strains in diverse populations. Addressing these research gaps is crucial for advancing the clinical application of probiotics in immune-related conditions and for developing personalized probiotic therapies tailored to individual immune profiles (Kim et al., 2014; Sempach et al., 2024). Application-based studies have demonstrated the immune-enhancing potential of specific probiotic strains. For instance, L. plantarum supplementation in mice enhanced immune organ activity, modulated immune cell populations, and increased antimicrobial substances and immunoglobulin levels (Sivan et al., 2015). Additionally, this strain strengthens mucosal immunity while maintaining immune homeostasis, making it a promising antigen delivery carrier. It enhances antigen immunogenicity, boosts defense against harmful antigens, and has been recognized for its potential as a mucosal vaccine carrier due to its ability to modulate immune tolerance (Zare et al., 2024). Similarly, Kang et al. (2021) observed that heat-killed Lactococcus lactis MG5125 and various Lactobacillus strains suppressed nitric oxide production by up to 86.2% and reduced the expression of nitric oxide synthase and cyclooxygenase-2 induced by lipopolysaccharides. This suggests that heat-killed probiotics may offer a stable alternative to live probiotics in functional foods, while still modulating immune responses effectively.

Early-life gut microbiota composition influences allergy development. Intestinal dendritic cells regulate Treg cells, which are linked to immune tolerance. Additionally, oligosaccharide supplementation has alleviated atopic dermatitis symptoms in children, with improvements associated with changes in peripheral eosinophil levels, highlighting the immunomodulatory role of prebiotics (Kim et al., 2024). Similarly, probiotics play a crucial role in immune regulation beyond early childhood, including in physically active individuals. In athletes, probiotic supplementation has been shown to influence immune regulation in several ways. Tavakoly et al. (2021) demonstrated that probiotics modulate key immune cell populations, including reductions in T cytotoxic lymphocytes and monocytes, while multi-strain formulations increase leukocyte counts. Complementing these findings, Guo et al. (2022) reported that probiotics enhance immune defense by increasing IFN-γ and salivary IgA levels while reducing TNF-α and IL-10, particularly in short interventions. The absence of significant effects on other inflammatory markers suggests that probiotics selectively regulate immune responses, highlighting their potential role in optimizing immune function in athletes. These findings underscore the importance of selecting appropriate strains and tailoring interventions based on the target population and desired immune outcomes.

A series of microbial metabolites have been implicated in the regulation of brain function, including branched-chain amino acids, trimethylamine-N-oxide, short-chain fatty acids, tryptophan metabolites, gamma-aminobutyric acid, bile acid metabolites and choline (Meher et al., 2024). Their mode of action is principally indirect, for example by improving intestinal health, exerting anti-inflammatory effects and modulating the production of metabolites such as serotonin, leptin and insulin that affect brain function. However, they may also have a direct effect, for example through the activation of aryl hydrocarbon receptor that takes place through the production of indoles (Aoki et al., 2018; Pappolla et al., 2021). Research has mainly focused on short-chain fatty acids, tryptophan metabolites, and ghrelin as well as the impact of probiotic, prebiotic and symbiotic supplementation on their production. These compounds are important due to their protective effects against obesity, depression, anxiety, colitis, atopic dermatitis and cancer. Table 4 presents recent studies demonstrating these protective effects. These compounds also mediate gut-brain axis communication via neuronal, endocrine, and immune pathways, engaging diverse microbial, neural, hormonal, and immune mediators (Table 5). These mechanisms enable bidirectional signaling between the gut microbiota and the brain, influencing mood, cognition, behavior, and neurological health.

Short-chain fatty acids (SCFA) are microbial metabolites with fewer than six carbon atoms, produced in the colon. The most represented ones are acetate, propionate and butyrate; formate and lactate are also produced, but at lower quantities. In the cecum and the proximal colon there is an increased availability of fermentable substrates compared to the distal colon. These substrates include resistant starch and components of plant cell walls, which have escaped digestion in the small intestine. Thus, the concentration of SCFA tends to be higher in the proximal colon and is depleted toward the distal colon (van der Beek et al., 2017). SCFA concentrations are estimated at 70 and 140 mM in the proximal colon and 20–70 mM in the distal colon (Wong et al., 2006). Their ratio along the colon is similar, namely 3:1:1 (acetate:propionate:butyrate), which reflects their efficient and concentration-dependent absorption (Topping and Clifton, 2001). The factors that affect qualitatively and quantitatively the production of SCFA are the ones that affect the composition of the microecosystem and the metabolic activity of the producer microorganisms, such as diet (Flint et al., 2015; Garcia-Mantrana et al., 2018; Selma-Royo et al., 2019; Fusco et al., 2023; Yi et al., 2025), gut transit time (Wong et al., 2006) pH value (Wong et al., 2006; Yi et al., 2025) and bile salt concentration (Flint et al., 2015).

The pathways for acetate production, namely acetogenesis and the Wood-Ljungdahl pathway, seem to be widely distributed among the phyla that comprise the human gut microbiome. On the contrary, production of butyrate and propionate is substrate specific, and the respective pathways seem to be restricted to a few species. Butyrate is mainly produced through the CoA-transferase pathway and only a few species use the butyrate kinase pathway (Flint et al., 2015). Butyrate production via the CoA-transferase pathway is mainly driven by Eubacterium hallii, Eubacterium rectale, Faecalibacterium prausnitzii, Roseburia faecis, and other Lachnospiraceae species (Louis et al., 2010; Reichardt et al., 2014). On the other hand, the occurrence of the butyrate kinase pathway has only been reported in Coprococcus eutactus and Coprococcus comes (Reichardt et al., 2014). Interestingly, the presence and metabolic activity of Ruminococcus bromii is particularly important when resistant starch is available (Ze et al., 2012). On the other hand, propionate can be produced by three pathways, the succinate pathway used by Bacteroidetes and some Firmicutes, the propanediol pathway that operates only when fucose and rhamnose serve as carbon sources and is used by some members of the Lachnospiraceae family, and the acrylate pathway that is restricted to only a few members of the Firmicutes and is used to convert lactate to propionate (Reichardt et al., 2014; Flint et al., 2015).

As far as formate and lactate are concerned, the first is mainly produced by bifidobacteria and Eubacterium hallii (Schwab et al., 2017) while the second mainly by bifidobacteria, lactobacilli, streptococci and staphylococci (Jost et al., 2012; Pham et al., 2016). The lactate is then catabolized by bacteria such as Eubacterium hallii and Anaerostipes caccae toward the production of propionate and butyrate (Reichardt et al., 2014).

SCFA are considered as possible mediators of the communication between gut microbiota and the brain (Dalile et al., 2019). SCFA produced in the colon are rapidly absorbed by the colonocytes and used for energy production (Schonfeld and Wojtczak, 2016). The ones that are not catabolized in the colonocytes are transported to the liver, where they are used for energy production by the hepatocytes, with the exception of propionate that can also be used for gluconeogenesis and acetate that can also be used to produce fatty acids and cholesterol (Boets et al., 2017). As a result, only a small percentage of the SCFA produced in the colon can reach peripheral organs through systemic circulation, which has been calculated at 2, 9 and 36% for butyrate, propionate and acetate, respectively (Boets et al., 2015). SCFA modulate brain function through immune, endocrine and vagal pathways (Dalile et al., 2019). The interactions of SCFA with a variety of immune cells may modulate brain activity. More specifically, SCFA directly affect neutrophils by regulating the production of inflammatory cytokines and by acting as neutrophil chemoattractants (Rodrigues et al., 2016), inhibit the maturation of monocytes, macrophages and dendritic cells (Correa-Oliveira et al., 2016; Chang et al., 2014) and affect the differentiation and proliferation of T cells (Kim et al., 2014). Although a variety of mechanisms have been proposed, the inhibition of histone deacetylases appears to play a key role. The endocrine pathway is activated by the secretion of gastrointestinal as well as other metabolic hormones, which is affected by colonic SCFA. The production of SCFA in the colon activates orphan G protein-coupled receptors which results in the production of peptide tyrosine tyrosine (PYY) and glucagon-like peptide 1 (GLP1) by enteroendocrine L cells (Tolhurst et al., 2012; Larraufie et al., 2018). On the other hand, there are indications that the production of hormones such as leptin, ghrelin and insulin is modulated by colonic SCFA (Xiong et al., 2004; Robertson et al., 2005; Rahat-Rozenbloom et al., 2017); however, the underlying mechanism is yet to be fully elucidated. The mechanisms by which these hormones affect brain function have been extensively assessed, and especially in the case of PYY and GLP1, have already been proposed (Koda et al., 2005; Katsurada and Yada, 2016). In the case οf ghrelin, SCFA have been reported to interfere with ghrelinergic signaling, most likely by antagonistic binding to its receptor GHSR-1a (Torres-Fuentes et al., 2019). Indications that SCFA stimulate the vagal afferents have been repeatedly reported (Bercik et al., 2011; Bravo et al., 2011; Goswami et al., 2018). This activation may be mediated by the free fatty acid receptor 3 (FFAR3; Bonaz et al., 2018) that is expressed in nodose ganglion neurons (Nohr et al., 2015).

The aforementioned interactions of SCFA are considered as the main mechanisms through which they contribute to the reduction of symptom severity or treatment of gastrointestinal, metabolic, cardiovascular, neurological and other disorders that have been associated with the gut-brain axis (Xiong et al., 2022; Zhang et al., 2023; Facchin et al., 2024).

Tryptophan is an essential amino acid; therefore, humans rely on dietary intake. Dietary tryptophan is mainly used for protein synthesis. Free tryptophan, i.e., the tryptophan that is not used for protein synthesis is mainly catabolized through the kynurenine pathway to produce a wide range of biologically active metabolites, collectively termed kynurenines. Over 95% of free tryptophan catabolism occurs via this pathway (Polyzos and Ketelhuth, 2015). The kynurenines have wide physiological and often opposing roles that are essential in immune responses, inflammation, oxidative stress and neurodegeneration, affecting, thus, brain function (Tanaka et al., 2024). Tryptophan may also be used for the biosynthesis of serotonin and melatonin, the modulation of the brain function by both has been well documented (Carhart-Harris and Nutt, 2017; Lee et al., 2019). Finally, the gut microbiota may use tryptophan for the production of indoles and their derivatives. Colonic microbiota may shift from saccharolytic to proteolytic metabolism-depending on protein intake, carbohydrate availability, transit time, and pH-leading to protein degradation and tryptophan catabolism. This catabolic shift has been reported as more intense toward the distal colon (Smith and Macfarlane, 1996; Geypens et al., 1997; Zelante et al., 2013; Roager et al., 2016; Vieira-Silva et al., 2016). The capacity of several Gram-positive and -negative species to catabolize tryptophan and produce indoles and their derivatives has been reported; most of them belong to the genera Anaerostipes, Bacteroides, Bifidobacterium, Butyrivibrio, Clostridium, Desulfovibrio, Enteroroccus, Escherichia, Eubacterium, Faecalibacterium, Fusobacterium, Haemophilus, Lactobacillus sensu lato, Megamonas, Parabacteroides, Peptostreptococcus and Ruminococcus (Roager and Licht, 2018).

The gut microbiota may affect directly or indirectly tryptophan metabolism by the host. The direct effect may result from the reduction of tryptophan availability for the host, which may lead to decreased serotonin and 5-hydroxyindoleacetic acid production, which, in turn, may lead to depressive-like behavior (Lukic et al., 2019). Interestingly, a causal link has been suggested, as depressive phenotypes can be transferred via gut microbiota transplantation (Kelly et al., 2016). Serotonin production may also be modulated, either toward stimulation that has been reported to occur by spore-forming bacteria including Clostridium ramosum (Yano et al., 2015; Mandic et al., 2019), or toward disruption (Golubeva et al., 2017). Similarly, modulation of the kynurenine pathway may also take place, as in the case of Lactobacillus johnsonii N6.2, which reduced the production of indoleamine-2,3-deoxygenase that catalyzes the oxidation of L-tryptophan to N-formylkynurenine, the first step of the kynurenine pathway (Valladares et al., 2013). The indirect effect has been reported to occur either through butyrate production, which has been reported to suppress kynurenine production (Martin-Gallausiaux et al., 2018), or through the maintenance of gut integrity that may prevent gastrointestinal disorders, such as inflammatory bowel disease and irritable bowel syndrome, which have been associated with disruption of the serotonergic signaling pathways (Gracie et al., 2019). Maintenance of gut integrity can be achieved through a number of mechanisms including the promotion of cytokine release, such as IL-6, IL-17 and IL-22, by indole derivatives through the activation of the aryl hydrocarbon receptor (Zelante et al., 2013; Schiering et al., 2017; Busbee et al., 2020; Zhang et al., 2024).

These direct and indirect effects of gut microbiota on tryptophan metabolism by the host regulate intestinal and systemic homeostasis in both health and disease (Zhao P, et al., 2025). More specifically, the development of many diseases including digestion, respiratory, blood, neoplastic and non-neoplastic ones has been associated with disruption of tryptophan metabolism. Therefore, the therapeutic potential of restoration of tryptophan metabolism has been indicated (Platten et al., 2019; Chen et al., 2024).

Ghrelin is a 28 amino acid hormone primarily produced in the stomach. The acylated form of ghrelin binds with high affinity to the growth hormone secretagogue receptor (GHSR), and more specifically GHSR-1a. This receptor is ubiquitously expressed in central and peripheral nervous system and has been implicated in the regulation of an extended array of functions related to feeding behavior, metabolism and energy storage. Therefore, it is considered as a key molecule that communicates nutrition-related information along the gut-brain axis (Leeuwendaal et al., 2021).

Studies report both positive and negative correlations between gut microbiota and ghrelin levels (Parnell and Reimer, 2012; Hooda et al., 2013; Gomez-Arango et al., 2016; Kang et al., 2016; Liu et al., 2017; Massot-Cladera et al., 2017; Yanagi et al., 2017; Yang et al., 2019; Bo et al., 2019) suggesting a regulatory relationship (Mahana et al., 2016; Ikenoya et al., 2018). More specifically, ghrelin levels seem to be affected by the lipopolysaccharides of Gram-negative bacteria, as well as by metabolites such as formylated peptides, amino acids, hydrogen sulfide and SCFA. The first has been adequately exhibited in the case of Helicobacter pylori, whose lipopolysaccharide seems to activate an inflammatory response through TRL-4 stimulation and ghrelin-mediated GHSR-1a activation (Slomiany and Slomiany, 2017). Similarly, formylated peptides may also have an indirect effect on ghrelin levels as they activate the epithelial GPCR formyl peptide receptor 1 (FPR1) stimulating ROS generation by epithelial cells, which in turns increases plasma ghrelin concentration (Suzuki et al., 2011; Alam et al., 2014). Microbial proteolysis of dietary proteins produces amino acids that affect plasma ghrelin levels in a residue-specific manner. More specifically, L-glutamine, L-glutamic acid, L-lysine, L-threonine and L-valine increase ghrelin plasma levels while L-cysteine, L-leucine and L-tryptophan reduces them (McGavigan et al., 2015; Steinert et al., 2017; Elsabagh et al., 2018; Yin et al., 2018a, 2018b). L-cysteine holds an additional role as its degradation is the major pathway for hydrogen sulfide production. The latter has been reported to negatively affect the ghrelin secretion (Slade et al., 2018). A negative correlation has also been reported between SCFAs and ghrelin levels (Rahat-Rozenbloom et al., 2017). Two mechanisms have been proposed, a direct that includes antagonism for the GHSR-1a receptor and an indirect that includes FFAR2-mediated regulation (Torres-Fuentes et al., 2019).