A Novel Frontier in Gut–Brain Axis Research: The Transplantation of Fecal Microbiota in Neurodegenerative Disorders

Gut dysbiosis plays a significant role in the development of neurodegenerative diseases, with FMT showing promise in reestablishing microbial equilibrium. A systematic review encompassing 42 studies identified Bacteroidetes, Firmicutes, and Proteobacteria as dominant phyla across both healthy and disease-affected groups. In PD, increased levels of Akkermansia, Verrucomicrobiaceae, Lachnospiraceae, and Bifidobacterium were observed, while AD was linked to Bacteroides and Acidobacteriota [61]. Another review corroborated the connection of Akkermansia, Bifidobacterium, and Faecalibacterium with PD, while Alistipes, Bacteroides, Bifidobacterium, and Blautia were associated with AD. Escherichia/Shigella emerged as the most consistently linked microbial group. In a study involving 307 MS patients, stable associations with 11 microbial genera were identified, whereas no consistent microbial links were found for amyotrophic lateral sclerosis (ALS) [62]. Certain microorganisms play a crucial role in disease progression by disrupting the balance of inflammation, modulating neurotransmitter levels, altering gut permeability, and influencing immune responses. Both preclinical and clinical studies underscore their therapeutic potential. In models of dextran sulfate sodium (DSS)-induced colitis, Akkermansia muciniphila (AKK) demonstrated protective effects by decreasing inflammatory cytokines (TNF-α, IL-1β, IL-6) and inhibiting NLRP3 inflammasome activation. It also helped restore tight junction proteins (ZO-1, occludin, claudin-1), thereby preserving gut barrier integrity. Another study associated higher AKK levels with enhanced antioxidant enzyme activity (CAT, T-AOC), the increased production of acetate and butyrate, and reduced plasma IL-8 levels, further emphasizing its anti-inflammatory properties [63,64].

Several species of Bifidobacterium have been shown to exert beneficial effects on inflammatory regulation, neurotransmitter production, immune modulation, and gut barrier integrity. These findings emphasize the potential therapeutic role of these microorganisms, particularly in the context of gut and systemic health. In an animal study, Bifidobacterium dentium was demonstrated to contribute to the production of gamma-aminobutyric acid (GABA) by decarboxylating glutamate through the action of glutamate decarboxylase (gadB) [65]. Similarly, in a study involving mice with DSS-induced colitis, Bifidobacterium pseudolongum was found to reduce the mRNA expression levels of pro-inflammatory cytokines (IL-1β, IL-6, IL-10, and TNF-α). Interestingly, the mRNA levels of Tph1, encoding tryptophan hydroxylase 1 (TPH1), were significantly lower in mice treated with this microorganism [66]. Contrasting findings were reported in another animal study, where Bifidobacterium dentium was shown to increase serotonin (5-HT) concentrations by inducing the expression of 5-HT receptor subtypes (2a and 4) and the serotonin transporter. Additionally, fecal acetate, an SCFA, was significantly elevated in these animals [67].

Bifidobacterium animalis, through its metabolite lactate, reduced the mRNA levels of inflammatory cytokines (IL-1β, IL-6, IL-10, and TNF-α) in an animal study. This species also decreased the M1/M2 macrophage ratio by interfering with M1 macrophage upregulation. The inhibition of macrophage-induced inflammation was linked to interaction with the TLR4-MyD88 signaling pathway. Moreover, Bifidobacterium animalis showed potential in suppressing inflammation associated with NLR family pyrin domain containing 3 (NLRP3) inflammasome signaling [68]. Bifidobacterium bifidum was observed to upregulate Foxp3+ regulatory T cells through the interaction of its surface cell polysaccharide, β-glucan/galactan (CSGG), with TLR2. This interaction induced regulatory dendritic cells, highlighting a mechanism for immune modulation [69]. In an in vitro study, Bifidobacterium infantis protected epithelial barrier integrity against IL-1β-induced damage by correcting the expression of tight junction proteins, occludin and claudin-1 [70]. A human study involving an infant population revealed key immunological differences based on bifidobacterial abundance in the gut microbiota. Infants with low bifidobacterial levels exhibited increased neutrophils, basophils, plasmablasts, and memory CD8+ T cells, alongside elevated levels of mucosal-associated invariant T cells. Conversely, infants with bifidobacteria-enriched microbiota showed higher numbers of non-classic monocytes, considered anti-inflammatory, and antigen-experienced regulatory T cells expressing the CD39 receptor. These infants also exhibited elevated levels of anti-inflammatory cytokines IL-27 and IL-10 compared to higher levels of pro-inflammatory cytokines IL-17A, IL-13, and IL-1α in the bifidobacterial-deficient group. These findings suggest a critical role for bifidobacteria in shaping immune responses and maintaining homeostasis [71]. The gut–brain axis (Figure 2) and key microorganisms modulated by FMT and their effects on the gut–brain axis are shown in Table 2.

FMT impacts the gut–brain axis by altering the microbial composition, with key players such as Akkermansia muciniphila, Bifidobacterium, and Faecalibacterium prausnitzii supporting gut health, immune function, and neuroprotection. While early findings suggest its potential in addressing neurodegenerative diseases, significant challenges persist, including variability in microbial responses, inconsistent clinical outcomes, and the complexities of selecting suitable donors. Despite these difficulties, FMT offers a promising opportunity for personalized therapeutic approaches. However, further studies are essential to establish standardized protocols, identify precise microbial targets, and ensure its long-term effectiveness in treating neurological disorders.

As previously mentioned, the diversity of the gut microbiome is remarkably high and influenced by a wide range of environmental and genetic factors. To design personalized interventions that yield better outcomes, it is essential to build upon prior research exploring microbiome diversity, functional profiles, microbial interactions, co-occurrence patterns, and the proportional balance of microbiota across different races and regions targeted for intervention. FMT continues to hold significant potential as a therapeutic approach. One promising avenue involves defining the core microbiome of each region, which can be approached in at least four distinct ways, each with its own advantages and limitations:

1. Community Composition: Identifying the most shared microbial taxa within a specific region, which provides a straightforward representation of commonly present species but may overlook functional or ecological dynamics.

2. Functional Profile: Defining the core microbiome based on shared functional capabilities across microbial communities. While this approach emphasizes functional consistency, it may disregard taxa-specific contributions.

3. Ecological Parameters: Incorporating metrics such as taxonomic abundance, interactions, co-occurrence patterns, and other community-level characteristics. Although this provides a holistic view, no standard methods are available.

4. Stability: Examining the factors that contribute to the stability and resilience of microbial communities under environmental and physiological fluctuations. This approach focuses on long-term ecosystem sustainability, but like previous approaches, there are no widely accepted methods for stability evaluation. Such an integrative approach could provide a deeper understanding of regional microbiome characteristics, paving the way for more effective and tailored microbiome-based interventions [85].

FMT is a procedure that alters the recipient’s intestinal tract microbiota by introducing a fecal solution derived from a healthy donor. There are three types of fecal matter preparation used in FMT: fresh, frozen, and lyophilized. Fresh FMT involves the immediate transfer of fecal matter from a healthy donor, demonstrating a 93% efficacy rate in treating Clostridium difficile infections. Frozen FMT allows for the storage of donor fecal material for later use, with an efficacy rate of 88% in treating Clostridium difficile. Lyophilized FMT involves the dehydration of fecal matter, enabling long-term storage without the need for freezing, and has shown an efficacy rate of 83% in treating Clostridium difficile infections [86]. Donors are carefully selected and screened to ensure safety; they must have no personal medical history of autoimmune disease or significant allergy, metabolic disease (like diabetes, metabolic syndrome), gastrointestinal malignancy (and family medical history of the previous three categories), exposure to antibiotics in the prior 3 months (or other drugs which could affect gut microbiota), or recent travel with exposure to epidemic diarrheal disease and they must undergo testing to rule out potential pathogens [87,88,89]. In this context, standardized blood and stool screening tests have been established for the safe application of FMT, though mild variations exist across protocols.

Stool Testing: (1) Bacteria: Screening typically includes Clostridium difficile, Campylobacter, Helicobacter pylori (for the oral administration of FMT), Salmonella, Shiga toxin-producing Escherichia coli, and Shigella. Additional considerations include testing for Aeromonas, Plesiomonas, Listeria monocytogenes, Yersinia, Vibrio cholerae, and Vibrio parahaemolyticus. (2) Viruses: Key pathogens screened include Rotavirus and Norovirus. (3) Parasites: Tests are performed for Cryptosporidium, Cyclospora, Isospora, and Giardia.

Blood Testing: (1) Bacteria: Treponema pallidum (syphilis) is screened to prevent transmission risks. (2) Viruses: Comprehensive testing includes Hepatitis A, B, C, and Human Immunodeficiency Virus (HIV). These screening protocols are essential to mitigate the risks of pathogen transmission and ensure donor safety, particularly given the experimental nature of FMT in emerging indications such as neurological disorders [88].

Also, the following social factors should be considered: high-risk sexual behaviors, drug use, incarceration or long-term care facility residence, and body piercing or tattoos in the prior 6 months [88]. According to two systematic review studies, there was no significant evidence to suggest that related donors are superior to unrelated donors in terms of clinical outcomes [90,91]. The fecal solution, prepared by mixing stool with sterile water or normal saline followed by filtration to remove solid particles, can be administered through various routes, including nasogastric or nasojejunal tubes, esophagogastroduodenoscopy, colonoscopy, or retention enema. These methods allow the precise delivery of the microbiota into the gastrointestinal tract, making FMT a promising therapeutic approach for a range of microbiome-associated conditions [87]. FMT is not without potential adverse effects, which can manifest in both the short and long term. The short-term adverse effects of FMT are generally mild to moderate but can occasionally become severe. Commonly reported symptoms include gastrointestinal disturbances such as bloating, abdominal spasms, gaseousness, diarrhea, irregular bowel habits, and abdominal pain or tenderness. Other complications may include constipation, nausea, and belching. In more severe cases, patients have reported fever, hematochezia, and the aggravation of pre-existing inflammatory bowel disease (IBD). Rare but serious adverse events include Gram-negative bacteremia, bowel perforation, and even death in isolated instances. Such severe complications highlight the importance of rigorous donor screening and careful procedural execution. While data on long-term effects are still emerging, there is growing concern about the potential for FMT to influence host metabolism and immune function. Notable long-term effects include an increased risk of obesity and immune-mediated disorders, such as immune thrombocytopenia, rheumatoid arthritis, IBD, and irritable bowel syndrome (IBS). These findings underscore the complex and poorly understood interactions between the transplanted microbiota and the host immune system, warranting further investigation [92]. Enteropathogenic Escherichia coli (EPEC) and Shiga toxin-producing Escherichia coli (STEC) are potential pathogens that may emerge following an FMT procedure [93].

The bottom-up approach in designing personalized microbiota is an emerging method that can be categorized into two distinct strategies: phenotypic and target-based discovery. The phenotypic approach involves initially testing specific organisms in in vitro settings, followed by evaluating their effects in ex vivo models and animal studies. This method examines various outcomes, including immune, neuronal, metabolic, or microbial responses to the intervention. A prominent example of this approach is Lactobacillus rhamnosus JB-1. Studies have demonstrated its ability to reduce corticosteroid release, modulate the central expression of GABA receptors, and improve stress-related social and exploratory behaviors in mice [94]. The target-based approach leverages in silico predictions to evaluate the probiotic capacity of microorganisms to produce molecular effectors with potential modulatory roles in host or microbial pathways. This method necessitates the integration of multi-omics technologies, including genomics, transcriptomics, metabolomics, and proteomics, to comprehensively analyze the relevant mechanisms. A notable example of this strategy is the characterization of the Hafnia alvei 4597 strain, selected for its α-melanocyte-stimulating hormone (α-MSH) mimicking effect. This mimicry underpins its anorexigenic potential, which has been demonstrated in both murine and human studies [94].

Synthetic microbial communities (SynComs) are carefully curated consortia of microorganisms, often isolated from human mucosa or feces, designed to achieve specific therapeutic effects. These communities typically consist of two or more microbial species working synergistically to modulate host–microbiota interactions [95]. For instance, an in vivo study compared two live biotherapeutic products: GUT-103, a consortium of 17 microbial strains that demonstrated protective effects in IBD by preventing chronic immune-mediated colitis, and GUT-108, which effectively reversed chronic T-cell colitis in a humanized mouse model. The study highlighted the potential of GUT-108 not only for IBD but also for other conditions characterized by disrupted intestinal permeability and dysbiosis. These findings underscore the promise of SynComs as next-generation microbiota-based therapies, though further research is needed to translate these preclinical successes into safe and effective clinical applications [96].

Numerous studies have explored the integration of FMT with complementary interventions, such as dietary modifications, exercise, and pharmacological treatments, to enhance its efficacy. A scoping review highlighted the supportive role of diet in influencing compositional, functional, and clinical FMT outcomes. However, the available data remain limited and heterogeneous, with inadequate details regarding dietary protocols and their mechanisms of action [97]. Zinc supplementation prior to FMT has shown promise in patients with recurrent Clostridioides difficile infection (rCDI), likely due to its ability to address the high prevalence of malnutrition in this population [98]. Additionally, a randomized controlled trial (RCT) demonstrated that adherence to a Mediterranean diet reduced homeostasis model assessment-estimated insulin resistance (HOMA-IR) and lipid levels. However, when combined with donor FMT, no substantial synergistic effects were observed [99]. Another study compared two groups receiving FMT, where the second group’s donors were placed on a pre-diet regimen prior to FMT intervention. Recipients in this group exhibited a significant microbiota shift toward the donor’s composition, particularly with an increase in Eubacterium_sp_AF228LB. Functionally, this shift was accompanied by an enrichment of branched-chain amino acids, suggesting a diet-mediated enhancement in microbial metabolic activity [100].

These findings underscore the potential of combining FMT with tailored dietary interventions to optimize therapeutic outcomes. However, the lack of standardized methodologies and detailed mechanistic studies highlights the need for further research to establish evidence-based guidelines for such integrative approaches. Exercise, as a non-invasive intervention, holds significant promise in modulating gut microbiota composition, functional capacity, and metabolic output. Evidence suggests that physical activity can elicit beneficial changes in gut microbiota, although its effects may vary based on individual factors such as body composition. In a human study, sedentary individuals underwent six weeks of endurance-based exercise training, followed by a six-week sedentary washout period. The findings revealed that exercise increased fecal SCFA concentrations, particularly butyrate, in lean participants. This was accompanied by an enrichment of butyrate-producing bacterial taxa, including Clostridiales spp., Lachnospira spp., Roseburia spp., f. Lachnospiraceae, and Faecalibacterium spp. However, these beneficial microbial shifts were not observed in obese participants, suggesting that individual physiological differences may mediate exercise-induced microbiota changes [101].

In a clinical study involving melanoma patients resistant to anti-PD-1 immunotherapy, FMT was employed as a complementary intervention. Post-FMT analyses revealed the increased activation of CD8+ T-cells, a key component of antitumor immunity, alongside a reduction in interleukin-8 expression from myeloid cells, which is often associated with an immunosuppressive tumor microenvironment. These results underscore the potential of FMT to overcome resistance to immune checkpoint inhibitors by reprogramming the gut–immune axis [102]. These findings highlight the promising role of integrating pharmacological treatments with microbiota-based strategies to optimize therapeutic responses. Further research is needed to elucidate the underlying mechanisms and to explore their clinical applicability across a broader spectrum of diseases. Artificial intelligence (AI) holds transformative potential in advancing FMT research and applications, offering capabilities far beyond traditional methods. However, significant challenges remain, including data limitations, a lack of algorithm transparency, and ethical considerations. Despite these hurdles, AI’s anticipated roles in FMT include response prediction and optimization through donor, recipient, and microbiome-specific approaches. In a noteworthy study, Shtossel et al. proposed an AI-driven algorithm designed to identify optimal FMT donors and predict recipient outcomes based on donor microbiota profiles. The algorithm also facilitates FMT optimization to achieve desired therapeutic effects. This innovation is particularly valuable in cases where there are substantial differences between the microbiota of the donor and the post-transplant recipient. Their findings demonstrated that FMT could be effectively performed using either an ideal donor phenotype or a cultured microbial consortia, with promising results in both human and murine models [103].

These advancements underline the ability of AI to bridge computational and clinical sciences, paving the way for personalized FMT strategies tailored to specific disease phenotypes. Despite challenges related to data availability, algorithm transparency, and ethical considerations, the integration of AI into FMT research marks a pivotal step toward precision medicine, promising improved therapeutic outcomes and a deeper understanding of the complex interplay between microbiota and health. Large-scale clinical trials are essential to validate the safety and efficacy of the various innovative approaches discussed. Future research should prioritize developing a comprehensive framework to define regional core microbiomes based on functional, ecological, and stability metrics. These metrics could inform the selection of optimal donors or the design of synthetic FMT interventions tailored to specific conditions, including neurodegenerative disorders like PD and AD disease. Additionally, advancing therapeutic precision through engineered probiotics, such as those designed to target specific neurotransmitter pathways or systemic inflammation, represents a promising avenue. Proposing SynComs engineered to produce neurotransmitter precursors (serotonin, GABA) or to modulate inflammatory responses further highlights the untapped potential of microbiota-based interventions. These directions not only offer significant prospects for enhancing FMT efficacy but also open new horizons for addressing complex, multifactorial diseases with precision medicine approaches (Figure 3). Alternative strategies for FMT for gut microbiota modulation are shown in Table 3.

FMT has gained attention as a promising therapy for neurodegenerative disorders by addressing gut dysbiosis and influencing the gut–brain axis. Both preclinical and clinical evidence indicate that FMT can help restore microbial equilibrium, reduce neuroinflammation, and enhance cognitive and motor functions in conditions like PD, AD, MS, and ALS. Despite these encouraging findings, several challenges need to be addressed, including variations in donor selection, inconsistent clinical results, and a limited understanding of the long-term consequences. For FMT to become a viable treatment option, future research should prioritize standardizing procedures, refining donor screening methods, and incorporating microbiome-based precision medicine. Combining FMT with complementary approaches such as dietary modifications, pharmacological therapies, and engineered probiotics could further enhance its effectiveness. Although FMT has yet to be established as a standard treatment for neurodegenerative diseases, its potential to target underlying pathological processes underscores the importance of further exploration through rigorously designed clinical trials.

Cancer Research Center, Semnan University of Medical Sciences, Semnan, Iran.

All authors contributed to the study’s conception and design. Material preparation, data collection, and analysis, R.N. and M.E.; the first draft of the manuscript, B.F.D. and S.Y.; writing—original draft preparation, R.N. and M.E.; software, F.M.T.; writing—review and editing, M.E., B.F.D. and Z.A.; supervision and project administration, V.O. and M.E.; All authors have read and agreed to the published version of the manuscript.

The authors declare no conflict of interest.

This research received no external funding.