Infections following allo-HSCT are a major clinical issue in pediatric patients with hematological malignancies. Common types of infections include bacterial, fungal, and viral infections. Bacterial infections are primarily caused by Gram-negative and Gram-positive organisms, with common pathogens including Escherichia coli, Staphylococcus aureus, and Pseudomonas aeruginosa (9). Fungal infections commonly involve Candida species, Aspergillus species, and Cryptococcus species (10). Viral infections are mainly caused by human herpesviruses, Cytomegalovirus (CMV), and adenoviruses (11). The infection rates of various pathogens differ significantly between children and adults after allogeneic transplantation. Regarding viral infections, the rate of CMV infection in children varies widely across studies. Some studies report a CMV infection rate of 28.9% in children compared to 24.7% in adults (12), while prospective studies have shown that the CMV infection rate in children can be as high as 61.3% (13). High viral load (≥10,000 copies/ml) is more common in children and is significantly associated with reduced overall survival (14). Similarly, the Epstein–Barr virus (EBV) infection rate is significantly higher in children than in adults (19.4% vs. 1.9%) (12), and the incidence of EBV-associated post-transplant lymphoproliferative disorder in children is as high as 2.6% (15). The adenovirus infection rate in children ranges from 7.4% to 36.7%, which is only 2.9% in adults. The BK virus infection rate is 21.0% in children, significantly higher than the 5.2% rate observed in adults (12). In terms of fungal infections after allogeneic transplantation, children are at higher risk of late-onset fungal infections due to stronger immunosuppression. The fungal infection rate in children is 28.3%, compared to 14.0% in adults. Invasive aspergillosis and candidiasis are the primary types of fungal infections in children (12, 16). Regarding bacterial infections, although the overall infection rate in pediatric patients is slightly lower than that in adults (36.9% vs. 41.1%) (12), the cumulative incidence of Clostridium difficile infection (CDI) is higher in children than in adults (17% vs. 11%) (17). There are also significant differences in the distribution of pathogens and antibiotic resistance patterns. After pediatric allogeneic hematopoietic stem cell transplantation (allo-HSCT), Gram-negative bacteria, such as Escherichia coli and Pseudomonas aeruginosa, account for approximately 60% of bacterial infections, compared to 50% in adults (9). In contrast, infections caused by Gram-positive bacteria, such as Staphylococcus aureus, are less common in children (25% vs. 35%) (12). Moreover, multidrug-resistant (MDR) bacterial infections, including carbapenem-resistant Enterobacteriaceae (CRE) and vancomycin-resistant Enterococcus (VRE), are increasingly prevalent in children. A multicenter study showed that 18% of pediatric allo-HSCT recipients had MDR infections, compared to 12% in adults, which may be attributed to prolonged antibiotic use and immature immune systems in children (18, 19). These differences highlight the necessity of developing infection control strategies tailored to different age groups.

The susceptibility to infection is multifactorial, primarily driven by immunosuppression, neutropenia, and epithelial barrier disruption (20). Immunosuppression, induced by chemotherapy and conditioning regimens, compromises both cellular and humoral immunity, increasing vulnerability to pathogens. Risk variability arises from factors such as underlying malignancies, treatment intensity, and genetic predispositions (21). Neutropenia, a hallmark of post-transplant immune depletion, directly impairs the innate defense against bacterial and fungal infections, as neutrophils constitute two-thirds of circulating leukocytes (22). Finally, epithelial barrier damage caused by chemotherapy, radiation, or invasive procedures facilitates pathogen invasion. Notably, pediatric patients, particularly neonates, face heightened risks due to immature barrier integrity (23).

During the process of allo-HSCT, patients undergo high doses of chemotherapy and radiotherapy as conditioning to eradicate tumor cells and immune cells within the body. This procedure not only kills tumor cells but also severely disrupts normal immune cells and the gut microbiota. The immunosuppressed state following conditioning makes patients highly susceptible to infections. Moreover, the use of broad-spectrum antibiotics further disrupts the gut microbiota, leading to a decrease in beneficial bacteria and allowing pathogenic bacteria to colonize and proliferate (24, 25). The gut microbiota plays a crucial role in maintaining the integrity of the intestinal barrier and immune balance. A healthy gut microbiota, characterized by high diversity and stability, can resist the invasion of pathogenic bacteria through various mechanisms, including competitive inhibition of pathogen colonization, production of antimicrobial substances, and regulation of the host's immune response (26, 27). However, the gut microbiota is destructed during allo-HSCT, which weakens these defense mechanisms and allow pathogenic bacteria to breach the intestinal barrier and cause systemic infections (28). As illustrated in Figure 1, the combined effects of conditioning regimens, antibiotics, and immunosuppression disrupt the gut microbiota and epithelial barrier, which creates an environment conducive to pathogen colonization and systemic dissemination (24, 29).

Infectious complications significantly impact the success rate of allo-HSCT and the survival rate of patients. Infections not only increase the risk of transplant failure but also markedly reduce the overall survival rate of patients. Studies have indicated that infections are one of the primary causes of early mortality following allo-HSCT, particularly within the first 100 days post-transplantation (30). It is critical to control infections in post-transplant management in the case of the high incidence and case fatality rate of bacterial and fungal infections. Bacterial infections typically occur early after allo-HSCT, manifesting mainly as bacteremia and sepsis. The high incidence of bacterial infections is closely associated with the use of broad-spectrum antibiotics, leading to the emergence of an increasing number of drug-resistant strains (31). Fungal infections are more likely to occur in the middle to late post-transplant period, presenting mainly as invasive fungal diseases, which are usually difficult to treat and have high mortality rates. For instance, the cumulative incidence of invasive aspergillosis in allo-HSCT patients can reach 9.6%, with a mortality rate as high as 20.7% (32).

Viral infections are also very common in allo-HSCT recipients, particularly CMV infection. CMV infection not only directly leads to viral pneumonia, gastroenteritis and hepatitis, but also increases the risk of acute GVHD by activating the host's immune response (33). Studies have shown that CMV infection is closely related to the incidence and severity of acute GVHD, and the presence of CMV infection significantly reduces the long-term survival rate of patients (34). Therefore, to improve the success rate of allo-HSCT and the survival rate of patients, it is key to effectively preventing and treating infectious complications. Microbiota modulation, as an emerging therapeutic strategy, is gradually receiving attention in the prevention and treatment of infectious complications.

The gut microbiota refers to the collective sum of various microorganisms and their genomes that reside in the gastrointestinal tract, including bacteria, fungi, viruses and archaea (35). The gut microbiota plays a significant role in the health and disease of the host, and the stability of its composition and function is crucial for maintaining the host's physiological balance (36). The gut microbiota from a healthy human is characterized by high diversity and stability, primarily composed of four bacterial phyla: Bacteroidetes (23%), Firmicutes (64%), Actinobacteria (3%), and Proteobacteria (8%) (37). The gut microbiota interacts with the host through various mechanisms, including the production of metabolic byproducts, absorption of nutrients, regulation of the immune system, and defense against pathogens (38). The gut microbiota is capable of breaking down complex carbohydrates in food, producing short-chain fatty acids (SCFAs) such as acetate, propionate, and butyrate (39), which not only provide energy for intestinal epithelial cells but also play an important role in regulating the host's immune response (40).

The impact of the microbiota on the immune system, particularly its role in the balance of cytotoxic CD8+ cells and Tregs, has been mentioned in numerous studies. For example, the microbiota plays a crucial role by regulating the differentiation of Th17 cells and the function of CD8+ T cells in the gut and skin, which are central to the pathophysiology of GVHD (41, 42). In addition, research has shown that the microbiota influences immune balance by regulating specific immune responses, including the effector function and memory potential of CD8+ T cells (43).

The gut microbiota plays a pivotal role in modulating the host's immune system. Initially, the gut promote the development and maturation of the immune system through interactions with intestinal epithelial cells and immune cells (44). Studies have shown that the gut microorganism can activate innate immune responses by recognizing pattern recognition receptors such as Toll-like receptors and NOD-like receptors, and regulate adaptive immune responses by producing cytokines and chemokines (45). Secondly, the gut microorganism can modulate host immune responses through its metabolic products, such as SCFAs and secondary bile acids (46). SCFAs can suppress inflammatory responses by binding to G protein-coupled receptors, promoting the differentiation of regulatory T cells, thereby maintaining immune tolerance and balance (47). Secondary bile acids, on the other hand, can regulate intestinal barrier function and immune responses by binding to the farnesoid X receptor and G protein-coupled bile acid receptor 1 (48). Indole and its derivatives are tryptophan metabolites derived from the gut microbiota, possessing a range of biological activities closely associated with the gut flora. They not only promote the proliferation and repair of intestinal epithelial cells but also enhance mucosal immune function, facilitating the secretion of antimicrobial peptides and mucus. Indole compounds have also been found to regulate intestinal barrier function and inhibit inflammatory responses (49). As depicted in Figure 2, SCFAs exert multifaceted immunoregulatory effects. Butyrate binds to GPR43 on epithelial cells, inhibiting NF-κB and reducing IL-6 production (47). Concurrently, it activates the NLRP3 inflammasome in macrophages, enhancing IL-18-mediated mucosal repair (40). SCFAs also suppress neutrophil migration via histone deacetylase (HDAC) inhibition, preventing tissue damage from excessive inflammation. Furthermore, DCs exposed to propionate upregulate RA and IL-10, which promote FoxP3+ Treg differentiation while inhibiting Th17 pathways, thereby maintaining immune tolerance (46, 47).

Post-transplant microbiota dysbiosis exacerbates infection risks and disrupts immune homeostasis. Reduced microbial diversity impairs intestinal barrier integrity through diminished tight junction protein expression and epithelial cell function, enabling pathogen translocation and systemic inflammation (29, 50). Concurrently, the loss of beneficial taxa (e.g., Bifidobacterium) promotes pathogenic overgrowth, further destabilizing the microbiota. Critically, dysbiosis correlates with acute GVHD severity; low microbial diversity is linked to a 3-year survival rate of 36% vs. 67% in high-diversity cohorts (51). Mechanistically, dysbiosis disrupts immune tolerance by skewing Treg/Th17 balance and elevating proinflammatory cytokines (e.g., IL-6, TNF-α), as evidenced by reduced GVHD incidence in patients with restored microbiota (52).

Microbiota modulation is a method that aims to improve health status and treat diseases by modulating and restoring the balance of the host's microbiome (53). The gut microbiota plays a crucial role in the host's immune regulation, nutrient absorption, and pathogen defense. The core concept of microbiota modulation is to restore and maintain the diversity and stability of the gut microbiota by using beneficial microorganisms, substances that promote the growth of beneficial microorganisms (prebiotics), and combinations of both (synbiotics), thereby enhancing the host's immune function and preventing and treating infectious complications (54).

The immune system of children is not yet fully mature, making them more susceptible to infection compared to adults. Therefore, when using microbiota modulation (such as FMT or live bacterial preparations), several aspects need to be particularly considered. Firstly, there are differences in the immune system: children's immune systems are in a developmental stage, relying on innate immunity rather than mature adaptive immunity. This makes their defense against foreign pathogens weaker and also results in different responses to vaccines and treatments (55). The immune system of children is more sensitive to pathogens, but its regulatory mechanisms are not yet fully developed (56). Secondly, there is an increased risk of infection. Due to the immaturity of the immune system, children undergoing immune reconstitution (such as allogeneic hematopoietic stem cell transplantation) have a significantly higher risk of infection complications, including pulmonary infections (57). Therefore, children may be more prone to infections when using microecological agents. Finally, regarding the impact of the microbiota: early exposure to microorganisms has a long-term positive effect on the child's immune system, enhancing the function of natural killer cells and reducing the incidence of inflammatory diseases. However, if the composition of the child's microbiota is not yet stable, it may affect the efficacy of microbiota modulation (58).

Probiotics refer to live microorganisms that confer health benefits to the host. Common types of probiotics include lactic acid bacteria such as Lactobacillus (LGG) and Bifidobacterium, as well as yeast (e.g., Saccharomyces boulardii) (59). Probiotics exert their beneficial effects through various mechanisms, including competitive inhibition of pathogen colonization, enhancement of intestinal barrier function, modulation of host immune responses, and production of antimicrobial substances (60). For instance, Lactobacillus rhamnosus can inhibit the growth of pathogens through competitive inhibition and production of lactic acid, and also reduce inflammatory responses by regulating immune reactions (61). Prebiotics refer to indigestible food components that beneficially affect the host's health by selectively promoting the growth and/or activity of one or a few beneficial microorganisms. Common prebiotics include Fructooligosaccharide (FOS), inulin, and Galacto-oligosaccharides (GOS) (62). Prebiotics indirectly inhibit the colonization and proliferation of pathogens by promoting the growth of beneficial bacteria. For example, FOS can selectively promote the growth of Bifidobacterium and increase the production of SCFAs, thereby enhancing intestinal barrier function and immune regulation (63). Synbiotics refer to the combination of probiotics and prebiotics, which enhance the beneficial effects on host health through synergistic actions. Synbiotics not only provide probiotics but also provide nutritional support for them, promoting their colonization and growth in the intestine, thereby enhancing their anti-infective and immune-modulating effects. For example, synbiotic formulations containing LGG and FOS can significantly reduce the incidence of intestinal infections and enhance the host's immune function by regulating the intestinal microbiota (64).

Bacterial infections are one of the common complications following allo-HSCT in pediatric hematological malignancy patients. The use of broad-spectrum antibiotics, while effective in controlling bacterial infections, can also disrupt the gut microbiota, leading to issues such as antibiotic-associated diarrhea and CDI (65). The application of probiotics and prebiotics is gaining increasing attention in the prevention and treatment of bacterial infections. Prebiotics such as FOS and GOS can indirectly inhibit the colonization and proliferation of pathogens by selectively promoting the growth of beneficial bacteria, thereby reducing the incidence of bacterial infections. Fungal infections are another common complication after allo-HSCT, especially in patients with compromised immune function. Due to their extremely high mortality rate, the prevention and treatment of fungal infections have become a focus in clinical practice. Of course, there are notable distinctions in terms of infection and the microbiome between pediatric and adult patients with hematological malignancies. To begin with, children's immune systems are not yet fully mature, characterized by reduced thymic function, lower T-cell diversity and maturity, which predisposes them to infections and leads to a higher rate of infection-related complications. Furthermore, the intestinal microbiome in children is more dynamic and unstable than that in adults, which could influence their susceptibility to infections. Moreover, interventions such as chemotherapy and antibiotic therapy have different effects on the microbiota of children and adults, which further complicates the research. These differences may affect the efficacy of microecological interventions, such as the use of probiotics or fecal microbiota transplantation (66–68).

In children under 3 years of age, the composition of gut microbiota remains in a dynamic state for up to 6 months following allogeneic transplantation, whereas in adult patients, microbiota diversity typically stabilizes within 3 months post-transplantation (58). This discrepancy may influence the colonization efficacy of FMT. Due to the lower resistance of the pediatric gut environment to donor microbiota colonization, FMT may require more frequent interventions or adjustments to the donor microbiota composition. For instance, children exhibit lower abundances of Bifidobacterium and Lactobacillus, while the colonization rates of potential pathogens (e.g., Enterococcus) are higher. Therefore, donor selection should prioritize microbial communities capable of replenishing specific beneficial bacteria (8). Additionally, children's immune systems are more dependent on microbial metabolites, such as short-chain fatty acids, which may necessitate donor microbiota with higher metabolic activity to support immune regulation (39). Of course, donor screening for pediatric FMT requires special attention to pathogen risks. The carrier rates of EBV and adenovirus may be higher in pediatric donors. These pathogens could be transmitted to immunocompromised recipients via FMT without rigorously screened, leading to severe complications (69). Thus, it is recommended to employ advanced molecular detection techniques (e.g., metagenomic sequencing) for pathogen screening of donor samples in pediatric FMT. Additionally, selecting age-matched donors is preferred to optimize microbiome compatibility. Pediatric-specific microbial biomarkers need to be further explored in future research to guide the development of personalized FMT strategies (70).

The application of probiotics in the prevention and treatment of fungal infections holds potential. The use of probiotic formulations can significantly reduce the incidence of fungal infections and enhance the host's immune function by modulating the gut microbiota. Viral infections are another common complication following allo-HSCT, particularly CMV infections. CMV infection not only directly leads to viral pneumonia, gastroenteritis and hepatitis, but also increases the risk of acute GVHD by activating the host's immune response. Probiotics can regulate the gut microbiota and enhance the host's immune function, thereby combating viral infections. Moreover, prebiotics such as FOS and GOS can indirectly enhance the host's antiviral capabilities by promoting the growth of beneficial bacteria, thereby reducing the incidence of viral infections. For instance, GOS can increase the proportion of natural killer cells in the spleen and mesenteric lymph nodes, which is particularly important for antiviral immune responses (Table 1).

Research on the application of microbiota modulation in pediatric allo-HSCT patients is gradually increasing, with significant effects observed in the prevention and treatment of post-transplant infectious complications. Microbiota modulation has shown notable anti-infective efficacy in pediatric patients undergoing allo-HSCT, effectively preventing and treating post-transplant infectious complications. In the context of anti-infective treatment after allo-HSCT, the extensive use of antibiotics, while effective in controlling infections in the short term, has also led to the issue of antibiotic resistance. Antibiotic resistance not only increases the complexity of treatment and the economic burden, but also poses a serious threat to patients' lives. Microbiota modulation, as an emerging therapeutic strategy, plays a significant role in reducing antibiotic resistance. Studies have shown that probiotics and prebiotics can reduce antibiotic resistance through various mechanisms. Firstly, probiotics have been demonstrated to inhibit the growth of pathogens by competing for adhesion sites in the gut, producing antimicrobial substances, and modulating immune responses, thereby reducing the frequency on antibiotic use (76). For example, Lactobacillus rhamnosus can inhibit the growth of pathogens by producing lactic acid and hydrogen peroxide, thereby reducing the use of antibiotics (77).

Prebiotics can indirectly inhibit the colonization and proliferation of pathogens by selectively promoting the growth of beneficial bacteria, thereby reducing the frequency of antibiotic use. For instance, FOS can enhance the growth of Bifidobacterium and increase the production of SCFAs, which in turn strengthens the intestinal barrier function and immune modulation, reducing the colonization and proliferation of pathogens. Moreover, synbiotics, as a combination of probiotics and prebiotics, enhance the beneficial effects on host health through synergistic actions, thus reducing the frequency of antibiotic use. A study evaluated the effect of microbiota modulation in reducing antibiotic resistance, which included 100 pediatric patients undergoing allo-HSCT, randomly assigned to a microbiota modulation group and a control group, the intervention group received a synbiotic preparation containing LGG and FOS daily for 4 weeks (18). The results showed that the frequency of antibiotic use in the intervention group was significantly lower than that in the control group (25% vs. 45%, p < 0.05), and the antibiotic resistance in the intervention group was significantly reduced (10% vs. 30%, p < 0.05). These studies indicate that microbiota modulation significantly reduces antibiotic resistance, effectively decreasing the frequency of antibiotic use and the occurrence of antibiotic resistance.

The application of FMT includes oral administration, nasogastric tube delivery, colonoscopy, and enema. Oral FMT is the most common method, typically in the form of capsules. Nasogastric tube FMT involves the direct injection of donor fecal suspension into the gastrointestinal tract to increase its intake. Colonoscopy FMT involves the direct injection of donor fecal suspension into the colon to enhance colonization rates. Enema FMT involves the injection of donor fecal suspension into the rectum to increase intake. Before FMT, detecting gut microbiota can timely identify abnormalities in disease-related flora, which is significant for monitoring the efficacy of FMT. In the field of gut microbiota research, both basic and clinical, there is a need for standardized procedures in laboratory testing methods and quality control measures (70). Although FMT has shown significant effects in treating recurrent CDI, its application in pediatric patient undergoing allo-HSCT should be approached with caution (69). Pediatric patients have unique gut microbiota characteristics, and their response to FMT may differ from adults. Studies have shown that FMT may pose potential infection risks in immunocompromised patients. Therefore, strict donor screening and stringent sterile procedures should be implemented before FMT treatment to reduce the risk of infection (83).

The application of microbiota modulation in pediatric patients with hematological malignancies following allo-HSCT shows promise, but the assessment of its safety and efficacy remains a significant challenge. Pediatric patients, particularly those undergoing immune reconstitution, are at heightened risk of infections due to their immature immune systems. Therefore, rigorous donor screening and stringent sterile procedures are essential before microbiota modulation interventions. For instance, advanced molecular detection techniques (e.g., metagenomic sequencing) should be employed to screen donor samples for pathogens such as EBV and adenovirus, which pose significant risks to immunocompromised recipients (69). Additionally, while probiotics and prebiotics are generally considered safe in healthy populations, their use in immunocompromised patients requires careful evaluation. Rare cases of Lactobacillus rhamnosus-associated bacteremia have been reported, underscoring the need for strict monitoring (84). Despite promising results from clinical trials, the efficacy of microbiota modulation in preventing and treating post-allo-HSCT infectious complications still requires further validation. Large-scale, multicenter randomized controlled trials are needed to establish standardized protocols and optimize intervention strategies. Future research should also focus on developing personalized microbiota modulation approaches, leveraging genomic analysis and machine learning to predict patient-specific responses (85). By addressing these challenges, microbiota modulation can become a safer and more effective therapeutic option for pediatric patients undergoing allo-HSCT.

Currently, a major issue in the clinical application of microbiota modulation is the lack of standardized treatment protocols. The types, dosages, and intervention durations of probiotics, prebiotics, and synbiotics used in different studies vary widely (86), making it difficult to compare and generalize the results. Selecting the appropriate types of probiotics and prebiotics is fundamental to developing standardized treatment protocols. Different combinations of probiotics and prebiotics may have varying effects on modulating the gut microbiota and enhancing immune function (87). Therefore, systematic research and clinical trials are needed to identify the most suitable probiotics and prebiotics for pediatric patients following allo-HSCT and to establish corresponding standardized treatment protocols. The dosage and intervention duration of probiotics and prebiotics are also critical factors in developing standardized treatment protocols. Different dosages and durations may have varying impacts on the gut microbiota and immune function. Higher doses of probiotics and prebiotics may have more significant anti-infective and immune-modulating effects, but could also increase the risk of side effects (19). Thus, systematic research and clinical trials are required to determine the most appropriate dosages and intervention durations for pediatric patients undergoing allo-HSCT and to formulate corresponding standardized treatment protocols (88).

Although the standardized treatment protocols can improve the operability and scalability of microbiota modulation to a certain extent, personalized treatment remains key to enhancing therapeutic outcomes. There may be significant differences in the composition of the gut microbiota and the status of immune function among different patients, thus necessitating the formulation of individualized treatment plans based on individual differences (89). Formulating a personalized treatment plan requires the consideration of a multitude of factors, including the patient's gut microbiota composition, immune function status, disease type and severity (90). Consequently, individual differences in patients can be comprehensively assessed through means such as gut microbiota testing, immune function evaluation, and clinical symptom monitoring, to formulate a personalized microbiota modulation plan. The implementation strategies of personalized treatment include selecting appropriate combinations of probiotics and prebiotics, adjusting dosages and intervention durations, and monitoring therapeutic effects and side effects. By individually adjusting the types and dosages of probiotics and prebiotics, therapeutic effects can be significantly enhanced, and side effects can be reduced. For instance, for patients with low gut microbiota diversity, a high dose of probiotics and prebiotics combination can be selected to rapidly restore the balance of the gut microbiota; for patients with weakened immune function, a combination of probiotics and prebiotics with immune-modulating effects can be chosen to enhance immune function (91).