The human gut microbiota, a complex ecosystem of trillions of microbes, plays a pivotal role in maintaining host health by regulating digestion, immunity, metabolism, and even neurological functions [1] [2] . Disruption of this microbial balance, known as dysbiosis, has been implicated in various diseases, from gastrointestinal disorders like inflammatory bowel disease (IBD) and Clostridioides difficile infection (CDI) to systemic conditions such as obesity, diabetes, and neurodegenerative disorders [3] [4] .

With the rising global burden of chronic diseases, there is increasing interest in therapeutic strategies that target the microbiome. Fecal microbiota transplantation (FMT)—the transfer of fecal matter from a healthy donor to a recipient has emerged as a promising intervention for restoring gut microbial homeostasis [5] - [7] . Initially established as a treatment for recurrent CDI, FMT is now being investigated for a broad range of conditions, including ulcerative colitis, obesity, diabetes, autoimmune diseases, and neurological disorders such as autism and epilepsy [8] - [12] . Advances such as washed microbiota transplantation (WMT), a refined FMT technique involving automated purification to enrich beneficial microbes and remove impurities like food residues, pathogens, and pro-inflammatory components, have improved the procedure’s safety and efficacy [13] [14] . Compared to conventional FMT, WMT offers greater consistency and lower risk of adverse events, making it especially suitable for immunocompromised patients and standardized clinical applications.

The growing threat of antibiotic resistance has also spurred interest in FMT as an alternative or adjunct therapy [6] . Nevertheless, safety remains a key concern. A global review (2000-2020) reported adverse events (AEs) in 19% of FMT cases, most commonly diarrhea and abdominal discomfort, with serious adverse events (SAEs), including infections and deaths, occurring in 1.4%, particularly in patients with compromised gut barriers . These findings underscore the need for standardized protocols in donor selection, recipient preparation, and FMT administration [5] [15] [16] . Technological advancements such as metagenomic sequencing and metabolomic profiling have deepened our understanding of FMT’s therapeutic effects, which may involve restoring microbial diversity, modulating immune responses, and promoting production of short-chain fatty acids (SCFAs) [2] [17] - [20] . Meanwhile, methodological innovations like WMT continue to improve its clinical utility [13] [14] .

This review presents a comprehensive examination of FMT, covering its historical background, clinical applications, methodological considerations, and emerging indications, including autoimmune and metabolic diseases, dermatological conditions, glaucoma, and neurodevelopmental disorders such as autism spectrum disorder (ASD). By synthesizing current evidence, we aim to clarify FMT’s therapeutic potential and identify avenues for future research to optimize its clinical implementation.

Fecal microbiota transplantation (FMT) is a therapeutic procedure that involves transferring beneficial microorganisms from a healthy donor’s feces into a recipient’s gastrointestinal (GI) tract to restore and rebalance their gut microbiome ( Figure 1 ). FMT has a long and fascinating history, with its origins tracing back to ancient China, where fecal suspensions referred to as “yellow soup” were used as early as AD 300 - 400 to treat severe diarrhea and food poisoning [6] [21] . These early practices align with modern criteria for FMT and highlight its enduring therapeutic potential [12] . The modern era of FMT began in 1958 when Eiseman and colleagues successfully treated patients with pseudomembranous enterocolitis, later identified as CDI, marking the first documented use of FMT in contemporary medicine [22] . Since then, FMT has gained widespread recognition, particularly for its remarkable efficacy in treating recurrent CDI with success rates exceeding 90% [23] .

Similarly, Indian scriptures from 3000 years ago describe the therapeutic use of cow dung for gastrointestinal ailments [24] . By the 16th century, during the Ming Dynasty, fermented fecal preparations were applied to manage conditions such as diarrhea, constipation, and abdominal pain [5] . The term “transfaunation”, coined by Italian surgeon Hieronymus Fabricius Aquapendente, later influenced veterinary practices involving gut microbiota transfer [21] . A landmark 2013 randomized trial demonstrated the superiority of FMT over antibiotics for recurrent Clostridioides difficile infection (rCDI), achieving symptom resolution in 90% of cases [25] . This pivotal study catalyzed the adoption of FMT for refractory CDI and spurred exploration into its use for non-infectious diseases. Borody et al. [26] first reported the efficacy of FMT in ulcerative colitis (UC), marking its transition toward treating autoimmune and metabolic disorders. Today, FMT is being studied for a wide range of conditions, including obesity, neuropsychiatric disorders, and metabolic diseases, reflecting the systemic influence of the gut microbiome [3] [14] [27] .

FMT aims to restore microbial diversity or suppress pathogenic species by transferring donor microbiota to a recipient [12] . Pre-FMT colonic lavage may enhance engraftment by reducing residual pathogens [28] . The gut microbiome, shaped by factors such as genetics, early-life exposures, antibiotic use, and diet, exhibits functional redundancy across individuals. FMT introduces not only bacteria but also viruses, fungi, and donor-derived metabolites, complicating mechanistic studies [29] . Autologous FMT involves the use of an individual’s own previously collected and stored stool, typically for microbiota restoration following medical treatments that disrupt gut flora. In contrast, allogeneic FMT uses stool from a healthy donor to treat another individual, aiming to correct dysbiosis or restore microbial diversity in the recipient. Autologous FMT involves re-transplanting a patient’s own pre-collected healthy stool after microbiome disruption, such as following antibiotic use [3] .

Autologous FMT involves re-transplanting a patient’s own pre-collected healthy stool after microbiome disruption, such as following antibiotic use. This approach avoids the risks associated with allogeneic donor FMT and is particularly studied in allogeneic hematopoietic stem cell transplantation (allo-HSCT) to mitigate infections [14] . Emerging evidence suggests that autologous FMT may counteract weight regain post-dieting and modulate autoimmunity in type 1 diabetes (T1D). While autologous FMT has demonstrated success in T1D patients, clinical trials remain limited, and further research is needed to establish guidelines for defining healthy autologous stool and determining optimal collection times. Allogeneic FMT uses donor stool to treat conditions such as CDI, inflammatory bowel disease (IBD), and metabolic disorders. Maternal FMT in caesarean-delivered infants has been shown to restore microbiome diversity akin to vaginal birth, potentially preventing autoimmune diseases [3] .

In addition to bacteria, FMT introduces non-bacterial components such as viruses (particularly bacteriophages) and fungi, collectively referred to as the virome and mycobiome. These components may play therapeutic roles by influencing microbial community structure, modulating host immunity, and enhancing bacterial colonization resistance [30] . For instance, bacteriophages can selectively target pathogenic bacteria, while certain fungi may contribute to gut-immune interactions [31] . However, their presence also introduces confounding variables in mechanistic studies, as their individual and synergistic effects on the host and microbiota remain poorly understood. This complexity highlights the need for integrated multi-omics approaches to fully elucidate FMT’s mode of action and optimize its composition for targeted therapies [32] .

Despite its potential, standardizing FMT into a regulated clinical practice that aligns with expert consensus guidelines remains an ongoing challenge. The complexity of the gut microbiome, which includes bacteria, viruses, fungi, and metabolites, complicates mechanistic studies and the development of standardized protocols [30] . Additionally, the long-term safety and efficacy of FMT, particularly for non-infectious conditions, require further investigation. The historical evolution of FMT, from ancient remedies to modern therapeutic applications, underscores its potential to address a wide range of diseases. However, continued research is essential to optimize protocols, ensure safety, and expand its clinical use [23] .

Fecal Microbiota Transplantation (FMT) efficacy heavily depends on rigorous donor selection and screening to minimize infection risks. Prospective donors undergo comprehensive health evaluations, including questionnaires, clinical assessments, and stool and blood testing, guided by expert consensus [5] [16] ( Table 1 ) ( Figure 2 ). These protocols are updated to address emerging threats like COVID-19 and monkeypox [16] . Advances in sequencing have identified microbiota signatures such as richness, abundance, stability, and evenness linked to FMT success. However, stringent criteria result in low donor eligibility rates, e.g., 1.7% in a Chinese cohort and 3.9% in a U.S. study [31] .

CRE: carbapenem-resistant Enterobacteriaceae; ESBL: extended-spectrum β-lactamase; MDR: multidrug resistant; MRSA: methicillin-resistant Staphylococcus aureus; VRE: vancomycin-resistant enterococci; HIV: human immunodeficiency virus; HBV: Hepatitis B; HCV: Hepatitis C; FPG: fasting plasma glucose; PG: 2-hour plasma glucose; RPR: rapid plasma regain; VDRL: venereal disease research laboratory test; ALT: alanine aminotransferase; ALP: alkaline phosphatase; AFP: alpha fetoprotein; HDL: high-density lipoprotein; LDL: low-density lipoprotein.

Strict screening protocols are essential to reduce adverse events. U.S. and European guidelines recommend structured questionnaires, clinical interviews, and blood/stool tests within four weeks before donation [5] . While relatives were historically preferred for shared microbial traits [11] , evidence shows no significant outcome differences between related and unrelated donors [5] . For conditions like inflammatory bowel disease (IBD), unrelated donors may be preferable due to genetic factors [31] . The FMT French Group advises a ≤21-day gap between screening and donation to minimize contamination risks [21] . Universal stool banks report < 3% donor eligibility after rigorous screening, excluding candidates with abnormal BMI, recent antibiotic use, or pathogens like Dientamoeba fragilis and Blastocystis hominis . Preferred donors are typically aged 18 - 60, with protocols tailored to regional infectious threats. Autologous FMT, using a patient’s pre-collected stool, avoids novel pathogen introduction [5] [15] [16] .

Comprehensive blood and stool testing within four weeks before donation is mandatory to assess infectious risks . Screening includes major pathogens, with additional tests based on geography, recipient condition, and donor history [3] . For example, donors in endemic regions are tested for human T-lymphotropic virus types I/II or Strongyloides stercoralis, while immunosuppressed recipients may require screening for cytomegalovirus (CMV) IgG and bacterial cultures for Vibrio cholerae and Listeria monocytogenes [5] [32] . Donor blood samples are archived per European guidelines [33] , and stool is frozen at −80˚C within 8 hours if results are pending [10] . Validated preparations are delivered or cryopreserved . Multi-donor approaches enhance microbial diversity and response rates in IBD [23] , but may reduce stability due to compositional fluctuations [21] . Innovations like germ-free animal colonization and gastrointestinal simulation devices aim to standardize production [31] [34] . Strain and spore-based therapies, such as MET-2 and SER-109, show >90% efficacy against recurrent Clostridioides difficile infection (rCDI), offering promising avenues for FMT standardization despite challenges like colonization antagonism [14] [23] .

Fecal microbiota transplantation (FMT) can be administered via multiple routes, including oral capsules, nasogastric/nasojejunal tubes, endoscopies, colonoscopies, and retention enemas ( Figure 3 ). The choice depends on factors like patient preference, invasiveness, target site, cost, and risks [5] . Upper GI delivery (e.g., nasoduodenal tubes) benefits patients with inflamed colons but carries risks like aspiration pneumonia [3] .

Mid-GI delivery via transendoscopic enteral tubes is minimally invasive and suitable for frail patients [23] . Lower GI methods, such as colonoscopy and retention enema, directly target the colon, with colonoscopy allowing mucosal assessment but requiring bowel preparation [28] . Retention enema is less invasive and effective for recurrent Clostridioides difficile infection (CDI) [6] .

Oral capsules offer a non-invasive, patient-friendly option, showing efficacy comparable to colonoscopy for CDI ( Figure 4 ) [3] . However, challenges include high production costs and the need for multiple capsules. Comparative studies show mixed results, with some suggesting lower GI routes may have higher efficacy for CDI [28] , while oral capsules are equally effective [35] . The optimal FMT delivery method remains patient-specific, with ongoing research needed to refine techniques, enhance microbial engraftment, and improve accessibility [12] . Both fresh and frozen FMT have demonstrated similar clinical efficacy in treating recurrent or refractory CDI [5] [36] . Frozen FMT is often preferred due to logistical advantages, such as ease of storage and transportation, which reduce donor dependency. Fresh FMT requires immediate administration within six hours after stool preparation, whereas frozen samples must be thawed in an ice bath for 2 - 4 hours before use [5] [35] .

The gut microbiome plays a critical role in the pathogenesis of autoimmune diseases, with dysbiosis characterized by an imbalance in microbial composition being a common feature across conditions such as inflammatory bowel disease (IBD), multiple sclerosis (MS), rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE) [31] . Dysbiosis is associated with distinct microbial signatures and functional changes, including impaired gut barrier integrity, molecular mimicry, altered microbial metabolites and aberrant immune activation, which collectively contribute to autoimmune pathogenesis.

Obesity and its associated metabolic syndrome represent a global health crisis, contributing to significant morbidity, including type 2 diabetes (T2D) [58] . Despite available treatments for T2D, its prevalence continues to rise, necessitating novel therapeutic approaches. Emerging evidence suggests that obesity is linked to alterations in the gut microbiome, positioning FMT as a potential intervention . The gut microbiome plays a critical role in host immunity, energy metabolism and nutrient processing. It facilitates the digestion of indigestible fibers, enhances energy harvest and produces essential metabolites such as short-chain fatty acids (SCFAs) [9] . Additionally, the microbiome modulates glucagon-like peptide-1 (GLP-1) release and bile acid metabolism, which are integral to lipid digestion and metabolic regulation . Dysregulation of bile acid pathways has also been implicated in atherosclerosis, with interventions targeting these pathways showing promise in reducing atherosclerotic risk [59] .

FMT may address obesity and metabolic syndrome by modulating these pathways, potentially reducing insulin resistance and improving lipid metabolism. For instance, FMT could counteract the heightened energy harvest observed in obese individuals, whose microbiomes are more efficient at extracting energy from food [60] . Conversely, FMT has been shown to promote weight gain in malnourished patients, as demonstrated in a case report of an anorexia nervosa patient [61] . Furthermore, animal studies indicate that certain microbiota can increase gut permeability, leading to systemic endotoxin exposure (e.g., lipopolysaccharide, LPS, which is associated with inflammation, hypertension, and metabolic dysfunction [62] . While gut permeability is typically assessed via biopsies, non-invasive methods like the 5-sugar absorption test offer a reproducible alternative [63] .

Animal studies have demonstrated that obesity can be transferred from obese to lean germ-free mice via microbiome transplantation, suggesting the potential for reversing this process [64] . Clinical studies have shown mixed results: FMT from lean donors reduced insulin resistance in metabolic syndrome patients [65] , while FMT from obese donors exacerbated insulin resistance in recipients [62] . Similarly, FMT has demonstrated potential in modulating the gut-brain axis and enhancing outcomes in metabolic syndrome, including non-alcoholic fatty liver disease (NAFLD) and non-alcoholic steatohepatitis (NASH) [66] [67] . However, other studies, including those using post-bariatric surgery donors, have not demonstrated significant weight loss or improved insulin sensitivity despite changes in microbiome composition [68] [69] . These contradictory results emphasize the necessity for additional research to better understand FMT’s role in managing obesity and metabolic syndrome.

Gut microbiota dysbiosis is increasingly linked to chronic inflammatory skin diseases, with fecal microbiota transplantation (FMT) emerging as a potential therapy to restore microbial balance and reduce inflammation [73] . However, challenges such as infection risks, adverse reactions, donor-recipient compatibility, and regulatory concerns hinder its widespread use. Standardization is complicated by donor variability, administration methods, and antibiotic preconditioning. Despite these issues, FMT’s immune-modulatory properties show promise for treating conditions like atopic dermatitis (AD) and melanoma [74] . The gut microbiota, dominated by Bacteroidetes and Firmicutes, plays a key role in immune regulation. Research is exploring links between microbiota composition, disease susceptibility, and microbial metabolites’ impact on health. FMT, successfully used for decades to treat recurrent Clostridioides difficile infections, is now being investigated for chronic inflammatory skin diseases [73] [74] .

The gut microbiome influences retinal diseases like glaucoma through microbial metabolites and immune modulation. While Lachnospiraceae, producers of short-chain fatty acids (SCFAs), are generally beneficial [94] , SCFAs may exacerbate glaucoma by activating retinal microglia, causing neuroinflammation and retinal cell loss [83] . Lachnospiraceae UCG010, a key SCFA producer, is a potential therapeutic target for preserving optic nerve function in glaucoma. Toll-like receptor 4 (TLR4), which recognizes bacterial lipopolysaccharide (LPS), plays a role in glaucoma pathogenesis by triggering inflammatory cytokine production and disrupting lipid metabolism [83] . In glaucoma patients, TLR4 expression is elevated in retinal microglia, and LPS administration in animal models induces axonal degeneration and neuronal loss through TLR4 activation and complement-mediated damage [94] .

Glaucoma patients exhibit a higher prevalence of Helicobacter pylori infection than healthy individuals [95] . Primary open-angle glaucoma (POAG) patients exhibit gut microbiota dysbiosis, with increased Prevotellaceae, Enterobacteriaceae, and Escherichia coli, and decreased Megamonas and Bacteroides plebeius, linked to distinct metabolic profiles and clinical phenotypes [96] . Mitochondrial DNA variants associated with glaucoma are enriched in patients with altered Firmicutes and Proteobacteria populations [83] [94] .

The ocular surface and intraocular microbiota are increasingly studied in glaucoma, with microbial alterations linked to disease progression, often associated with preserved anti-glaucoma eye drops. Glaucoma patients using these drops exhibit a more diverse microbiome, with increased gram-negative bacteria and reduced tear film stability compared to healthy controls [97] . In uveitis glaucoma, Paenibacillus and Dermacoccus levels are elevated, while Morganella and Lactococcus are reduced [98] . Rhodococcus is more abundant in uveitis glaucoma than in POAG [99] . Glaucoma patients show a predominance of Firmicutes (61.1%) and Verrucomicrobiota (11.8%), with reduced Actinobacteriota [97] . The predominant genera include Akkermansia, Corynebacterium, Faecalibacterium, Lachnospiraceae, and Blautia. In glaucoma patients, there is an increase in anaerobic, gram-negative bacteria associated with lipopolysaccharide production and anaerobic metabolism, whereas healthy individuals have a greater abundance of gram-positive bacteria linked to carbohydrate synthesis and oxidative phosphorylation [94] [97] .

Anti-glaucoma eye drops, particularly those with benzalkonium chloride (BAK), may alter the ocular surface microbiota, with BAK suppressing gram-positive organisms, though some studies suggest minimal impact [94] [97] . Bacterial presence in the intraocular environment, previously thought sterile, has been confirmed, with glaucoma patients showing increased Propionibacterium acnes and decreased Staphylococcus warneri [100] . H. pylori has been identified in trabecular meshwork and iris specimens, supporting its role in POAG pathogenesis [94] .

Oral and gastric microbiota dysbiosis contribute to glaucoma through systemic inflammation. Severe periodontal disease and H. pylori infection are linked to increased POAG risk, with eradication improving IOP and visual fields [83] [94] . Glaucoma patients exhibit higher oral bacterial loads, with increased Streptococci and reduced Lactococcus [101] . Recent tooth loss is associated with a 1.45-fold increased POAG risk [102] . H. pylori is histologically confirmed in 87.5% of chronic OAG and 88.9% of pseudoexfoliation glaucoma patients, with higher anti-H. pylori IgG in aqueous humor and serum [94] . Eradication slows POAG progression, reduces IOP, and improves visual fields [94] [103] .

FMT introduces beneficial microbes from healthy donors, restoring gut microbiome balance and promoting short-chain fatty acid (SCFA) production, which enhances gut barrier integrity and reduces inflammation [104] [105] . FMT also regulates systemic immune responses through immune-modulatory compounds [106] [107] . The gut-eye axis underscores the link between gut microbiota and ocular health, with dysbiosis contributing to systemic inflammation, gut barrier disruption, and retinal damage ( Figure 5 ) [108] . Preclinical studies show FMT may mitigate retinal inflammation and cell loss; mice receiving fecal samples from glaucoma patients exhibited increased retinal damage compared to those receiving healthy donor samples [94] . For example, mice receiving fecal samples from glaucoma patients exhibited increased retinal inflammation and cell loss compared to those receiving samples from healthy donors [109] . A clinical trial in Sjögren’s syndrome patients demonstrated FMT improved dry eye symptoms in 50% of cases, highlighting its therapeutic potential for ocular diseases [88] .

The gut-brain axis, a two-way communication network connecting the gut and brain, is essential for neurodevelopment and behavior ( Figure 6 ). This interaction begins in utero, with bacteria and their metabolites transported between mother and fetus via amniotic fluid. Postnatal factors such as delivery mode (vaginal or cesarean), maternal health, breastfeeding, diet and early antibiotic use significantly influence gut microbiota colonization [110] [111] . The gut microbiota is primarily composed of two major phyla: Bacteroidetes and Firmicutes. Maternal factors like obesity, high-fat diets, and gestational diabetes can alter neonatal gut microbiota, potentially contributing to autism spectrum disorder (ASD) [11] .

The gut-brain axis operates through neuroendocrine, neuroimmune, and autonomic pathways, involving the hypothalamic-pituitary-adrenal (HPA) axis, the enteric nervous system (ENS), and the vagus nerve [11] . Dysregulation of this axis has been implicated in various diseases, including ASD, obesity and Alzheimer’s disease . Research using germ-free (GF) animals, probiotics and antibiotics has demonstrated the gut microbiota role in brain function. GF mice exhibit altered sociability, locomotor activity and repetitive behaviors, highlighting the microbiota importance in stress response, cognition and CNS homeostasis [112] [113] . Probiotics like Bifidobacterium longum 1714 have been shown to reduce stress and improve neurocognitive function in mice [114] , while antibiotic-induced microbiota depletion in mice leads to anxiety, cognitive dysfunction and altered neuromodulator levels [115] .

FMT is a highly successful therapy for recurrent Clostridioides difficile infection (rCDI), achieving cure rates above 90% [23] . FMT is FDA-approved for rCDI and is being explored for conditions such as IBD, irritable bowel syndrome (IBS), obesity, multiple sclerosis, and melanoma immunotherapy [3] [47] [82] . While FMT is generally safe in immunocompetent individuals, short-term adverse effects such as diarrhea, constipation, bloating, and abdominal discomfort typically resolve within 48 hours [108] [131] . Reports of mortality are usually linked to pre-existing conditions rather than FMT itself [1] . Long-term risks remain unclear, emphasizing the need for rigorous patient screening and procedural adherence. Regulatory frameworks such as the European Union Tissues and Cells Directive (EUTCD) and FDA guidelines mandate stringent safety measures, including donor screening, adverse event reporting, and biobanking for retrospective analyses [5] .

Large-scale studies in China have identified additional indications, including extraintestinal diseases linked to gut microbiota imbalances [105] . Emerging research suggests potential benefits for neurological and metabolic disorders such as Parkinson’s disease, Alzheimer’s disease, epilepsy, autism spectrum disorder, depression, diabetes, and fatty liver disease [4] . However, contraindications include active sepsis, severe immunosuppression, massive gastrointestinal bleeding, and toxic megacolon [132] . A key challenge in FMT is colonization antagonism, where donor-derived microbes face resistance from the recipient’s native microbiota. Studies indicate that only 35% of post-FMT microbiota originates from the donor, with the rest deriving from the recipient or environmental sources [45] . Machine learning models, such as random forest and LASSO regression, have shown promise in predicting FMT success by considering donor-recipient compatibility and procedural factors [45] .

FMT is generally safe, though concerns remain regarding pathogen transmission, particularly multi-drug-resistant bacteria, due to the heterogeneous nature of donor fecal material [132] . Rigorous donor screening, including serological and hematological assessments, helps mitigate infection risks, but the process is costly, with only 10% of candidates qualifying [40] [133] [134] . Long-term effects, such as potential links to autoimmune diseases, remain an area of concern [31] . European guidelines recommend an eight-week follow-up period to monitor adverse effects [5] [132] . To enhance safety, washed microbiota transplantation (WMT) has been developed, which removes impurities and reduces adverse events, particularly in IBD patients [14] . Future developments in personalised FMT techniques that make use of metagenomic analysis and bacterial ecosystem modelling might improve the way it is used in metabolic disorders, autism spectrum disorder and autoimmune disease.

FMT expands beyond recurrent Clostridioides difficile infection (rCDI) into metabolic, autoimmune, and neurological disorders, both ethical and mechanistic considerations come to the forefront. Ethically, informed consent is vital, particularly in experimental indications where long-term risks and efficacy remain uncertain [135] [136] . Clear communication of benefits, limitations, and potential complications is essential. Donor compensation also raises concerns about undue inducement, potentially compromising disclosure of health risks; thus, regulatory frameworks must ensure voluntary, non-coercive participation and fair, transparent practices [137] . Furthermore, equity of access remains a pressing issue, as high costs associated with donor screening and microbiota processing may restrict availability to well-resourced populations. Scalable, cost-effective models are needed to ensure broader accessibility without sacrificing safety or efficacy [16] .

From a biological standpoint, FMT exerts its effects across diverse conditions through shared core mechanisms: restoration of short-chain fatty acid (SCFA) production, which supports epithelial health and metabolic balance; immune modulation via expansion of regulatory T cells (Tregs), contributing to immune tolerance; and reinforcement of gut barrier integrity, which limits microbial translocation and systemic inflammation [21] [138] . These converging pathways reflect the gut microbiota’s central role in maintaining homeostasis and support the rationale for FMT’s use in a broad spectrum of diseases. However, to optimize outcomes and address ethical complexities, future research must integrate multi-omics analysis, patient stratification, and standardized clinical protocols.

The 21st century marks a transformative period in intestinal microbiome research, emphasizing the critical role of gut microbiota dysbiosis in both intestinal and systemic diseases. FMT has emerged as a groundbreaking therapy, demonstrating the ability to restore microbial balance and revolutionize the treatment of recurrent Clostridioides difficile infection (CDI). Beyond CDI, ongoing studies are investigating its therapeutic potential in metabolic, autoimmune, skin diseases, glaucoma and autism spectrum disorder. However, widespread clinical adoption faces key challenges, including variability in donor selection, standardization of safety protocols, and uncertainties surrounding long-term efficacy. Innovations such as multi-donor FMT, synthetic microbiota formulations, and precision microbiome-based therapies offer promising avenues to enhance treatment consistency and scalability. Future research must prioritize patient-specific treatment strategies, deeper insights into host-microbiome interactions, and regulatory frameworks to ensure safety and efficacy. Through well-designed clinical trials and interdisciplinary collaboration, FMT could evolve into a cornerstone of personalized medicine, offering novel and targeted therapeutic options for a broad spectrum of diseases.