Formation of gut microbiota and application of microecological regulators in children

Introduction

Human microecology is a developmental, dynamic process throughout life. The gut microbiota is central to human health, but its establishment early in life has not been quantitatively and functionally tested (1). The application of metagenomic analysis techniques allows characterization of the gut microbiome during the first year of life and assessment of the impact of delivery mode and feeding method on its establishment (2-5). Nutrition has an important influence on the composition and function of early microbiota, and microbial community composition and ecological networks are clearly characterized at each sampling stage, consistent with the functional components of the microbial community (6). Wang et al. concluded that the gastrointestinal tract of infants is sterile before birth, and that bacterial colonization only begins within 48 hours after birth (7). Specifically, the establishment of gut microbiota in the newborn begins with the rupture of the amniotic membrane. However, some other evidence suggests that microbial colonization may begin in utero. One study reports detectable bacterial DNA in amniotic fluid, placenta, and meconium, implying prenatal microbial exposure (8). However, the functional role and viability of these microbes remain debated, and the primary colonization surge still occurs postnatally through maternal and environmental sources. With increasing age, after 3 years, the composition and function of the gut microbiota in infants and young children gradually tend to stabilize but are susceptible to external factors, such as those during weaning and adding complementary foods, making them prone to gut microbiota imbalance (9,10). In addition, infants and young children’s immune systems are still underdeveloped and prone to infections and allergies (11,12). Roswall et al. analyzed the development of the gut microbiota of 471 Swedish children from birth to the age of 5 years and showed that the microbial communities in the intestines of children follow similar developmental pathways to maturity, and that despite differences in their respective rates of development, even at the age of 5 years, the children’s gut microbiota has not yet reached the complexity of that of an adult (13). At the first month of life, the infant’s gut microbiota is dominated by initially colonized parthenogenetic anaerobes such as Enterobacteriaceae, followed by a gradual increase in Bifidobacteria, with Bacteroides being the main contributors after 6 months to 1 year of age (14). There was temporal asynchrony in the development of the microbiota, with Actinobacteria, Bacillus, and Clostridia retaining child-like abundance, while others transformed into adult-like abundance. The core of the microbiota increases with age, as in the case of butyric acid-producing bacteria, and progresses towards an adult-like composition.

At present, it is imperative to pay attention to the development of children’s gut microbiota and that antibiotics may destroy the development of neonatal gut microbiota in order to meet the challenges of children’s microbiota and nutrition. Specific probiotic strains may prevent acute gastroenteritis, antibiotic diarrhea, infantile colic, and necrotising enterocolitis (NEC). The prophylactic probiotics with the strongest current evidence are Lactobacillus and Bifidobacterium for acute gastroenteritis, Saccharomyces boulardii and Lactobacillus rhamnosus GG for antibiotic-induced diarrhea, and Limosilactobacillus reuteri DSM 17938 for colic, acid reflux, and constipation in infants (15-17). Early supplementation of infants and young children with high quality probiotics to promote the formation of a healthy micro-ecology can enhance children’s immunity, promote digestion, improve appetite, alleviate lactose intolerance, and have far-reaching positive effects on health during infancy and childhood as well as in adulthood. Subsequently, we will develop the review of this paper in the following four sections, such as ‘general changes in gut microbiota in children’, ‘factors affecting the early establishment of gut microbiota in infants’, ‘microecological regulators and their mechanisms of action’ and ‘clinical application of microecological regulators in childhood diseases’.

General changes in gut microbiota in children

Human microorganisms can live on body surfaces that are exposed to the external environment, such as the skin, respiratory tract, genitourinary tract, and gastrointestinal tract. Among these different body parts, the gastrointestinal tract is the most complex micro-ecosystem and is closely related to human health. The initial bacteria in a newborn’s gastrointestinal tract come from the mother’s birth canal, the environment, and breast milk. The initial gut microbiota of breastfed children differs from that of artificially fed children (18). Gut microbial diversity increases further as infants reach weaning, with the addition of complementary foods and increased food diversity (19). It may be influenced by dietary changes. Lactobacillus is dominant in the intestines of breast-fed babies, but it is significantly reduced during weaning (20,21). Specifically, in one study, researchers found that Lactobacillus dropped 1.5 times during weaning (19). Akkermansia, which plays a key role in maintaining intestinal barrier integrity and modulating immune responses, has been associated with a variety of beneficial health outcomes in adults, including improved metabolic health and anti-inflammatory effects (22,23). The increase in Akkermansia spp. species during weaning indicates their importance in early infant health and development (19). Upon reaching adulthood, the composition of the microbiota is relatively stable, with Firmicutes, Bacteroides and Actinomycetes as the main microbiota. Figure 1 shows the changes in common bacteria during different stages of their life. From the perspective of infancy, due to environmental influences, the earliest established gut microbiota are Escherichia coli and Streptococcus. Two very important beneficial bacteria, Bifidobacterium and Lactobacillus, were subsequently colonized, and the number of Bifidobacterium rose rapidly to become the dominant gut microbiota in infants and young children. These beneficial intestinal bacteria play an important role in the development and maturation of the immune system of the gastrointestinal tract in early infancy, nutritional functions such as alleviation of lactose intolerance, enhancement of lipid and protein metabolism, and vitamin synthesis (24,25). The earlier the beneficial gut microbiota are established in infants, the more they are protected from infectious diseases, allergies and various digestive problems (26). Over time, common bacterial taxa in adults, such as Bacteroidetes, Eubacterium, and Anaerococcus, gradually colonize the intestinal tract and become predominant, with the gut microbiota composition closely resembling that of adults (27).

Figure 1 Changes in some common bacteria at different times of life.

Factors affecting the early establishment of gut microbiota in children

Mode of delivery

Numerous studies have shown that the mode of delivery has a significant effect on the establishment of infant gut microbiota. Ferretti and others showed that the top four sources of gut microbiota abundance in infants were the mother’s feces (22.1%), vagina (16.3%), mouth (7.2%) and skin (5.0%) (28). The microorganisms that initially colonize infants delivered vaginally are similar to the maternal vaginal microbiota, whereas the microorganisms that initially colonize infants delivered by cesarean section (C-section) are predominantly derived from the maternal skin microbiota (29). Thus, infants delivered vaginally receive a richer microbiota from their mothers than infants delivered by C-section. This is corroborated by the study of Bäckhed et al., which demonstrates that cesarean delivery may reduce diversity and cause microbial imbalance in the infant gut microbiota (30). The mode of delivery can significantly affect the colonization of Bifidobacteria in the infant’s gut, with the proportion of children with normal Bifidobacteria colonization being significantly higher in the first 3 months in infants delivered by normal delivery than in those delivered by C-section (31). Bifidobacteria play an important role in promoting the maturation of the infant’s immune system, resisting the invasion of pathogens, and promoting nutrient absorption (32).

Feeding methods

Diet is a key element in the symbiotic relationship between gut microbiota and animal hosts. The host provides habitat and nutrients for gut microbiota, while the microbiota contributes to human health. Food delivers many substrates for microbial metabolism and at the same time can influence the structure and composition of microcosm in different ways. Stewart et al. concluded that feeding practices can significantly influence the composition of infant gut microbiota early in life (33). There are significant differences in the composition of the gut microbiota between breast-fed and formula-fed neonates. Breastfed infants have mainly Bifidobacteria as the dominant strain, while formula-fed infants have a richer composition of gut microbiota, dominated by Escherichia coli and Bacteroides, with a higher number of other gut microbiota, such as Clostridium and Bifidobacteria (34). Hesla et al. analyzed the abundance of Bifidobacteria in the intestines of 6-month-old infants and the highest was found in exclusively breastfed infants, followed by partially breastfed infants and the lowest was found in the intestines of non-breastfed infants (35). Among them, high abundance of Bifidobacterium longum in breastfed infants is mainly provided by B. longum infantis, which is able to efficiently utilize mammalian-derived oligosaccharides, especially human milk oligosaccharides (HMOs) (36). These oligosaccharides are not easily digested. They are polysaccharides that are left intact as they pass through the upper digestive tract and nourish specific microbiota in the colon, primarily by selectively promoting the growth of Bifidobacterium spp. Similarly, Bacteroides possess enzymes that break down the oligosaccharides in breast milk, which they are able to convert into energy, thereby promoting their own growth and development (37).

The impact of breastfeeding on gut microbiota is not only due to the selective promotion of bifidobacterial reproduction by HMOs in breast milk, but more and more studies have shown that beneficial bacteria contained in breast milk itself are also an important source of beneficial bacteria in infants’ intestines. Recent studies have shown that breast milk contains a large number of lactic acid-producing bacteria (LAB), including Streptococcus, Lactobacillus, Lactococcus, Enterococcus, and Bifidobacterium. These LAB have various functions such as inhibiting the growth of pathogenic microorganisms, immunomodulation, and regulating intestinal health (38). Among these, Bifidobacterium longum, B. breve, Lactobacillus griseus, and Streptococcus salivarius had the highest percentages. It has also been noted that infants born by C-section have lower abundance of Bifidobacterium and Bacteroides in their intestinal tracts, and that exclusive breastfeeding partially mitigates this discrepancy, resulting in greater similarity in the microbiomes of infants born by C-section and exclusively breastfed versus infants who are delivered vaginally (39).

Antibiotics

The use of drugs, especially antibiotics, not only has an immediate impact on the gut microbiota, but may also bring about disturbances of longer duration (40). Antibiotics are the most common type of medication prescribed to children in Western countries. Although the use of antibiotics has transformed previously fatal infections into relatively mild illnesses, antibiotic treatment may also have adverse effects (41). Data from the US Centers for Disease Control and Prevention show that US children receive an average of three antibiotic courses before age of 2 years, while this figure reaches 11 by age of 10 years. Repeated use of antibiotics in the treatment of ear, nose, and throat inflammation has been common in children up to the age of 3 years (42). The most widely used antibiotics include penicillin, cephalosporins, and fluoroquinolone antibiotics, for which inappropriate antibiotic prescribing by physicians and the indiscriminate use of antibiotics not in accordance with prescriptions can significantly increase the incidence of antibiotic resistance worldwide (43). Antibiotics are one of the most common types of medications prescribed in the early years, which is also a critical period for gut microbiota formation. Indeed, from birth to 3 years of age, the composition of gut microbiota is constantly changing as the phylogenetic diversity gradually increases. For example, the reduction in maternal feeding and the introduction of solid foods reduced the abundance of Bifidobacteria & Clostridia and increased the abundance of Bacteroidetes. This strain can induce a switch in gene expression from promoting predominantly lactose utilization to promoting linked carbohydrate utilization, vitamin synthesis, and xenobiotic degradation (44). The use of antibiotics, however, can significantly affect these changes, leading to a decrease in the stability, diversity and abundance of the infant gut microbiota and a reduction in phylogenetic diversity, as well as an increase in the abundance of Aspergillus spp. (44). In addition, antibiotic misuse may trigger an inflammatory response in the gut and exacerbate bacterial resistance to antibiotics, as evidenced by an increased pro-inflammatory state and increased activity of antibiotic resistance genes. One study showed a significant increase in the proportion of several unknown taxa belonging to the Bacteroides spp. (gram-negative bacteria) in a trial of an intervention with β-lactams (45). Unexpectedly, an increase in the total number of microbial cells per gram of sample can result from an increase in Bacteroides spp. during antibiotic treatment. Thus, antibiotic use induces a decrease in microbial diversity and the growth of resistant species, and can even lead to an increase in the overall microbial load.

On the other hand, the misuse of antibiotics early in life can have potentially serious effects on health later in life. A systematic review highlighted that the use of specific probiotic strains (e.g., Saccharomyces boulardii CNCM I-745 and Lactobacillus rhamnosus GG) within 48 hours of antibiotic treatment reduces antibiotic-induced microbial dysbiosis and promotes intestinal microbial restoration as evidenced by a 32% increase in microbial diversity (alpha diversity) and a 41% reduction in gastrointestinal symptoms (46). Probiotics [≥10⁹ colony-forming unit (CFU)/day] modulate gut-brain axis via short-chain fatty acids (SCFAs) production, improving abdominal pain and reversing antibiotic-induced dysbiosis in 76% of patients (47).

Studies have shown that the development and maturation of gut microbiota in infants who are given antibiotics early in life tends to be delayed, diverting them from their normal developmental trajectory. Due to the existence of a certain natural recovery function of the human gut microbiota, when a small amount or occasional use of antibiotics, the distribution of microecological microbiota has the potential to naturally return to normal levels. In this case, recovery of their gut microbiota is more difficult and takes longer than in adults treated with antibiotics (41). However, this damage to the micro-ecology can become permanent if the use of antibiotics in large quantities or repeatedly exceeds the micro-ecology’s ability to repair itself. Probiotics alleviate antibiotic-induced microbiota dysbiosis by competitively inhibiting the colonization of pathogenic bacteria and reinforcing intestinal barrier integrity (48). Normal microbial colonization during early life critically regulates the establishment of intestinal crypts, maturation of barrier components (mucosal layer and immunoglobulins), development of Peyer’s patches, differentiation of mucosal and systemic T lymphocytes, and activation of innate immune signaling pathways. Therefore, early microecological disruption can significantly affect later immune function and metabolic homeostasis, leading to immunodeficiency, commensal intolerance, and invasion of pathogens due to defects in bacterial colonization and resistance, thus increasing the risk of various preexisting diseases (Figure 2).

Figure 2 The effect of antibiotics on the organism. Bacterial colonization and the emergence of drug-resistant pathogens intensify infections, while antibiotic misuse exacerbates this pathological cascade by disrupting gut microbial homeostasis—ultimately driving antimicrobial resistance evolution and pro-inflammatory microenvironment formation.

Prenatal factors

Maternal microbiota during pregnancy may shape the initial microbial seeding of the fetus. One study indicates that maternal gut bacteria can translocate to the amniotic cavity via bloodstream or dendritic cells, potentially influencing fetal immune programming (8). Factors such as maternal diet, stress, and antibiotic use in pregnancy may alter this prenatal microbial exposure, though the mechanisms require further elucidation. From prenatal exposure to postnatal maturation, the gut microbiota evolves dynamically. Prenatal microbial influences, though still under investigation, may prime fetal development, while postnatal colonization remains pivotal for immune and metabolic programming. Table 1 summarizes the factors influencing the early establishment of infant gut microbes and changes in microbiota status.

The use of metabolic substances including probiotics and their associated metabolites and personalised treatment plans may be promising preventive strategies to counteract the destruction of gut microbiota due to antibiotic misuse. As research has progressed, specific probiotic strains have been found to have antimicrobial activity against pathogenic bacteria. An in vitro study demonstrated that Lactobacillus plantarum PA21 exhibited antimicrobial activity against all nine methicillin-resistant Staphylococcus aureus (MRSA) species as well as three of the 13 clinical isolates of Klebsiella pneumoniae tested (51). The probiotic Bacillus licheniformis MCC 2514 produces lasso peptide, which is an antimicrobial peptide that has shown efficacy in the treatment of Salmonella typhimurium infections in vivo (52). In another study, Bacillus licheniformis and Bacillus subtilis were shown to have anti-inflammatory effects and, in some therapeutic combinations, antioxidant effects. Specifically, B. licheniformis inhibited the adhesion of S. Typhimurium and E. coli, and B. subtilis inhibited the adhesion of E. coli to IPEC-J2 cells (53). For children, antibiotics are the most common medication prescribed to children in hospitals and in the community, and this is associated with a high proportion of inappropriate prescriptions. Antibiotic misuse increases the risk of toxicity and raises healthcare costs and resistance options. A systematic review analysing studies of antimicrobial stewardship programs (ASPs) conducted globally in children aged 0–18 years showed that almost all studies (79.6%) showed a significant reduction in inappropriate prescribing (54). Demonstrated significant impact on personalised treatment regimens reducing empirical antibiotic use, healthcare costs and antibiotic resistance.

Microecological regulators and their mechanisms of action

Microecological regulators, also known as microecological agents, can be categorized into probiotics, prebiotics, synbiotics, and postbiotics. Microecological regulators are a class of products developed based on the principles of microecology to correct imbalances microbiota, to maintain ecological balance, and to enhance the health of the host or improve its health status (55). These products not only contain living beneficial microorganisms or inanimate microorganisms, but also cover the components of these inanimate microorganisms, the metabolites of all these microorganisms, as well as additives that promote the growth of beneficial microbiota. Microecological regulator is a very inclusive concept, which can specifically include live bacteria, inactivated bacteria, bacterial components, metabolites and colony growth promoters. In clinical practice, probiotics are most widely used as a type of microecological regulator. Many probiotics were originally isolated from the gastrointestinal tract and gradually used in many fermented foods, pills, powders, and liquids, and these preparations are now widely used in the community, even as prescription medications (56). The main probiotic drugs used in the clinic are more common in complex bacterial preparations, containing strains ranging from two to four, such as Bifidobacterium bifidum, Lactobacillus acidophilus, Streptococcus thermophilus, Bacillus licheniformis, and so on. Table 2 summarizes the types and roles of microecological regulators.

A variety of microecological regulators have been used in pediatric and neonatal populations with very good results and are of great value. In extremely preterm infants, Lactobacillus reuteri DSM 17938 supplementation significantly increased gut microbial diversity (Shannon index increased by 0.38, P=0.003) and reduced Enterobacteriaceae abundance by 42% at 1 week of age, demonstrating early modulation of dysbiosis (2). Synbiotics (mixed probiotics and fructooligosaccharides) increased fecal Bifidobacterium by 3.2-fold and serum motilin by 28% in constipated children, accelerating gastrointestinal transit (P<0.01) via SCFA-mediated neural activation. HMOs as prebiotics enhanced Bifidobacterium longum colonization in preterm infants, correlating with 65% lower necrotizing enterocolitis risk (63). Postbiotics (5× concentrated bacterial lysate) reduced loperamide-induced constipation in mice by increasing fecal water content 32% and SCFA production by 41% for acetic acid and 29% for propionic acid, demonstrating therapeutic potential for pediatric functional gastrointestinal disorders (64).

Gut microbiota dysbiosis may amplify allergic responses through Th2 polarization and impaired Treg differentiation. Probiotic supplementation (e.g., Lactobacillus rhamnosus GG) reduces vaccine-triggered urticaria by downregulating interleukin (IL)-4 and IL-13 while enhancing immunoglobulin A (IgA) production. Aluminum adjuvants show no association with autoimmune or atopic disorders in a Danish cohort of 1.22 million children (65). Postbiotics (bacterial lysates) may attenuate aluminum-induced local inflammation by suppressing NLRP3 inflammasome activation and IL-1β release, as demonstrated in murine models of vaccine hypersensitivity.

Recent studies have demonstrated that intestinal microbiota significantly influences vaccine efficacy in children. A 2025 prospective clinical trial revealed that antibiotic-induced gut microbiota disruption reduces antibody responses to rabies vaccine by altering metabolic pathways (e.g., secondary bile acid metabolism) and Th1/Tfh cell balance (66). This “microbiota-metabolism-immune” axis provides a theoretical basis for developing microbiota-based vaccine adjuvants. Emerging evidence links early-life gut microbiota composition to pediatric allergy development. A systematic review and meta-study analyzing evidence from 19 intervention trials suggests that oral supplementation with non-pathogenic microorganisms such as probiotics during late pregnancy and lactation may reduce the risk of eczema (67). A mechanistic, double-blind, controlled trial that included 100 patients with atopic dermatitis between the ages of 6 and 36 months demonstrated that probiotic Lacticaseibacillus rhamnosus GG can be used as an adjunctive treatment for pediatric atopic dermatitis, with improvements in disease severity and quality of life paralleled by beneficial modulation of the gut and skin microbiota (68).

Probiotics mechanisms of action include resistance to potential pathogens, improvement of the intestinal environment, enhancement of the intestinal barrier, down-regulation of the inflammatory response, and up-regulation of the immune response to antigenic challenge (69). These phenomena are thought to mediate most of the beneficial effects, including reducing the incidence and severity of diarrhea, which is one of the most widely recognized uses of probiotics. Probiotic strains can mediate health effects through one or more mechanisms. Probiotics may affect the ecosystem of the gut by influencing mucosal immune mechanisms, interacting with commensal or potentially pathogenic microorganisms, producing metabolic end-products such as SCFA, and interacting with host cells through chemical signaling, and microbiota and probiotics interact with the host through metabolic activity and immune function to prevent colonization of opportunistic and pathogenic microorganisms, and prebiotics may affect the intestinal bacterial ecosystem by increasing the beneficial bacterial numbers or activity to influence gut bacteria. Endo et al. found that intervention of Bifidobacteria cultured in vitro with sucrose trisaccharides and sucrose tetrasaccharides, the main components of fructooligosaccharides, significantly increased the number of Bifidobacteria (70). This may reduce the population of potentially pathogenic microorganisms or reduce potentially harmful metabolic activity of the host microbial community. In addition, prebiotics may affect immune function. Figure 3 illustrates the mechanism of probiotic-host interaction.

Figure 3 Diagram of probiotic-host interaction mechanism. Probiotics maintain intestinal microecological homeostasis and enhance the integrated mechanisms of host defense through synergistic pathways such as direct bacterial inhibition, ecological niche competition, and immunomodulation.

Clinical application of microecological regulators in childhood diseases

Diarrhea treatment and prevention

Treatment and prevention of acute diarrhea

Some probiotic strains help reduce the severity and duration of acute infectious diarrhea in children. Oral administration reduces the duration of acute diarrhea in children by approximately 1 day, and several published meta-analyses of clinically controlled trials of other probiotic strains have shown consistent results suggesting that probiotics may be safe and effective (71). In the prevention of diarrhea in children, there is evidence that certain probiotics are effective in specific situations (72). For persistent and prolonged diarrhea, probiotics may not be effective and may need to be given early.

Prevention of antibiotic-associated diarrhea (AAD)

AAD is defined as diarrhea accompanied by antibiotic use that cannot be explained by other causes, and is now mainly considered to be related to intestinal microecological imbalance triggered by antibiotic use (73). AAD can be classified as simple diarrhea, colitis, or pseudomembranous colitis according to the degree of disease and clinical manifestations. For example, pseudomembranous enteritis is caused by the disruption of the microecological balance after heavy use of antibiotics, and drug-resistant Clostridium difficile, unaffected by antibiotics, multiplies rapidly and causes a series of serious illnesses such as abdominal pain, diarrhea, and fever (74). In the prevention of AAD, it has been suggested that probiotics are effective in adults or children undergoing antibiotic therapy, and that their mechanism of action is that by rebalancing the microbial community in the intestinal tract, they can reduce the likelihood of pathogens settling (75). Probiotics may be moderately effective in preventing AAD in children, adults, and the elderly. Probiotics currently used in the treatment of AAD include Bifidobacterium, Lactobacillus, Yeast, Streptococcus, and Enterococcus. A study has shown that Lactobacillus rhamnosus shows the best efficacy and tolerability in the prevention of AAD, while Lactobacillus casei demonstrates more significant efficacy in the treatment of AAD (76). Another study showed that Saccharomyces boulardii was effective and safe in preventing AAD in both infants and elderly patients (77). In addition, Saccharomyces boulardii was able to significantly reduce the risk of diarrhea from 20.9% to 8.8% when used as monotherapy in children compared to placebo or no treatment (78).

Prevention of Clostridium difficile-associated diarrhea and radiotherapy-associated diarrhea

Studies have shown that probiotics are effective in preventing Clostridium difficile-associated diarrhea in children treated with antibiotics. Probiotics are generally safe for use in pediatric patients who are not immunodeficient or severely debilitated, and pediatric patients at high risk of developing Clostridium difficile-associated diarrhea would benefit from probiotic prophylaxis. Whereas Lactobacillus casei seems to be the most effective option for patients with severe Clostridium difficile infections, there is a lack of sufficient evidence for other strains (76).

Gut microbiota may play an important role in radiotherapy-associated diarrhea through mechanisms such as enhancing intestinal barrier function, improving innate immunity, and stimulating intestinal repair, and related studies have shown that probiotics may be helpful in pediatric oncology prevention and treatment of radiotherapy-associated diarrhea (79). The results of the meta-analysis showed that supplemental probiotic therapy significantly reduced the incidence of chemotherapy-associated diarrhea and improved the overall effectiveness of treatment as well as shortened the duration of diarrhea in pediatric oncology chemotherapy patients (80).

Treatment of malnutrition in children

The main signs of malnutrition in children are diarrhea, anorexia, loss of appetite, wasting and poor immunity. Chronic malnutrition can lead to other diseases in children, and malnutrition is influenced by a variety of factors, such as infections, nutritional intake, and physical and psychological factors. Of these, infection and nutritional intake are the most common causative factors and can therefore be focused on during treatment. A common treatment option for malnutrition in children is to modulate their intestinal motility and enhance their ability to absorb nutrients. Children can increase the number of gut microbiota survival through the intake of factors that promote the growth and reproduction of Bifidobacteria, such as oligofructose, oligosaccharides and so on, which can play a role as bifidobacterial factors in the large intestine, promote the reproduction of Bifidobacteria, and improve the nutrient absorption ability of children. Lactobacillus rhamnosus is a probiotic present in the human intestinal tract, which is not only acid-resistant but also bile salt-resistant, and can attach to the intestinal epithelial cells to form an intestinal mucosal barrier and improve the digestive and assimilative capacity of the human intestinal tract. This bacterial group can effectively regulate the gut microbiota structure, commonly used in the treatment of acute diarrhea, dyspepsia, constipation, can effectively improve the body’s immunity, enhance gastrointestinal function, alleviate the symptoms of insufficient nutrient absorption. Therefore, increasing the number of Lactobacillus rhamnosus colonies in the gut may also be used in the treatment of malnutrition in children (81). Bacillus subtilis is a bacterium that lives in soil and decaying materials and can survive in small amounts in the human body. This microbiota can secrete large amounts of proteins and other metabolites, as well as synthesize a variety of enzymes and vitamins, which work together with digestive enzymes in the body to promote digestion and absorption. It is often used in the medical field for the treatment of children’s nutritional deficiencies, and Bacillus subtilis Dictyostelium granules is a special medicine for children, which can effectively treat dyspepsia, loss of appetite, diarrhea, enteritis, malnutrition and other conditions (82). In addition, probiotics such as Bacillus licheniformis, Enterococcus and Clostridium typhimurium can also be used to treat malnutrition in children. These probiotics can be combined with foods and medicines to improve children’s digestive system, enhance their nutrient absorption, help prevent colds and strengthen immunity. In particular, the combination of probiotics and food is one of the most effective ways to treat malnutrition in children, as it can play a therapeutic role in health care and is also beneficial for children to take.

Notably, pediatric obesity and metabolic syndrome, as emerging nutritional disorders intertwined with gut microbiota dysbiosis, have been recognized as part of the broader spectrum of pediatric malnutrition-related conditions. Emerging evidence highlights the potential of probiotics in modulating gut microbiota to address pediatric obesity and metabolic syndrome. Studies have shown that specific probiotic strains, such as Bifidobacterium and Lactobacillus, may improve metabolic function by enhancing intestinal barrier integrity, reducing low-grade inflammation, and regulating energy homeostasis. For instance, a randomized controlled trial demonstrated that supplementation with Bifidobacterium-rich prebiotics significantly reduced body fat mass and serum triglycerides in overweight children, suggesting a metabolic benefit (83). Additionally, probiotics may influence appetite-regulating hormones, though further research is needed to optimize strain-specific interventions (84). Recent reviews also suggest potential benefits of synbiotics in modulating anthropometric parameters in adolescents with metabolic syndrome (85). A randomized controlled trial demonstrated that supplementation with B. lactis HNO19 significantly reduced body mass index (BMI), total cholesterol, and inflammatory cytokines [tumor necrosis factor-alpha (TNF-α), IL-6] with metabolic syndrome (86). Mechanistically, probiotics may enhance intestinal barrier function, reduce endotoxemia, and regulate bile acid metabolism, thereby improving insulin sensitivity and lipid profiles (87).

Applications in autism spectrum disorders (ASDs)

ASD is a group of neurodevelopmental disorders with a high degree of genetic heterogeneity that begin in the early stages of life and are characterized by social impairments, a narrow range of interests or activities, and repetitive and stereotyped behaviors that seriously affect children’s health. These neurodevelopmental abnormalities can lead to impaired socialization within the first few years of life, which can severely affect the cognitive, emotional, and behavioral well-being of children with ASD. The etiology of ASD is unclear and involves a complex interplay of genetic and environmental factors, with genetic factors such as single-gene mutations, copy number variants, and de novo variants playing a major role in the pathogenesis of ASD.

Several studies have reported abnormalities in microbiota composition and abnormalities in microbiota metabolites in children with ASD. Gastrointestinal disturbances often occur in children with ASD, and food selection and picky eating are also more common in children with ASD. The potential mechanisms by which nutrition, gut microbiota, and ASD interact through the microbiota-gut-brain axis are being investigated. Children with ASD have reduced abundance and altered structure of the gut microbiota and significantly higher abundance of actinomycetes and significantly higher levels of toxin genes in Clostridium perfringens as well as beta2 toxin-producing Clostridium perfringens (88). In animal models of autism, individuals with ASD may have a defective gastrointestinal barrier, which leads to the entry of toxins and bacterial products into the bloodstream, which in turn affects brain function (89). Patients with ASD may present with comorbidities including immune dysregulation and gastrointestinal disorders, in which the gut microbiota plays an important role in regulating immune homeostasis and intestinal function (90). Over the past decade, there has been a rapid increase in research on the role of gut microbes in regulating neurological function, suggesting that microbes may be important susceptibility factors for neurological disorders. In addition, it has been shown that probiotics have a positive effect on improving depression and neurodevelopmental disorders (91). Therefore, modulation of gut microbiota may be a potential approach to improve ASD symptoms.

Application to inflammatory bowel disease (IBD) in children

It has been suggested that certain probiotics may be as safe and effective as conventional treatments in terms of therapeutic response and remission rates in mild to moderately active ulcerative colitis (UC) in children (92). However, studies have also concluded that the certainty of the evidence regarding the role of induction of remission in mild to moderate UC is low and that there is no evidence that probiotics are effective in more severe disease states. Research on probiotics in Crohn’s disease suggests that there is currently no evidence that they are beneficial in inducing or maintaining remission in Crohn’s disease. Related studies on irritable bowel syndrome have shown that probiotic treatment may reduce bloating and flatulence, and some strains may relieve pain and overall symptoms. Certain probiotics may improve symptoms and quality of life in patients with functional abdominal pain (93). IBD is a chronic inflammatory disease characterised by remission and relapse. UC is one of the main forms of IBD and is treated using corticosteroids and anti-inflammatory drugs as standard therapy. Oral corticosteroid therapy alters the gut microbiota in part by reducing colonic mucin (94). B. longum infantis BB-02 results in a lower dose of meso-secretory IgA, reduced neutrophil infiltration and KC/CXCL-1 levels, and reduced intestinal permeability, leading to a reduction in colonic inflammation as well (95).

Application to IBD in children

Prevention of systemic infections

There is a lack of sufficient evidence to support the use of probiotics or synbiotics in critically ill adult patients in the intensive care unit, and relevant studies have demonstrated that probiotics and prebiotics affect a wide range of clinical outcomes unrelated to intestinal disorders, and some have suggested that gut microbiota may affect a wide range of non-gastrointestinal disorders, including through the brain-gut-microbe signaling system, which may establish a link between these disorders and the gastrointestinal tract (96). There is also a large body of research showing that probiotics can improve bacterial vaginitis, prevent atopic dermatitis in infants, reduce oral pathogens and dental caries, and reduce the incidence and duration of common upper respiratory tract infections. Evidence from one study has shown that the use of probiotics for mothers during late pregnancy and breastfeeding, as well as for infants after birth, can be effective in preventing the development of eczema in infants and young children (97). This precaution is especially critical for infants who are at high risk for allergic diseases. In addition, probiotics and prebiotics have been used to prevent certain manifestations of metabolic syndrome, including overweight, type 2 diabetes, and dyslipidemia (98).

Prevention and treatment of respiratory infections

The microbiota of the oral cavity is diverse, containing more than 700 different species on the tongue, teeth, gums, inner cheeks, palate and tonsils. Although saliva does not contain native bacteria, it does contain bacteria shed from biofilms in other areas of the mouth. More than 20% of these strains of bacteria are of the genus Streptococcus, which occupies the largest number of occupants in the oral cavity. Probiotics can trigger immunomodulatory mechanisms in the body to enhance immune function, and it has been clinically proven that the preventive use of probiotics can reduce the incidence of acute respiratory infections in both children and adults, and reduce the use of antibiotics. It has been suggested that Streptococcus salivarius K12 may theoretically play a role in reducing the incidence and/or severity of acute otitis media (AOM) and secretory otitis media in children (72). However, Sarlin et al. evaluated the efficacy of an oral probiotic preparation of Streptococcus salivarius K12 in the prevention of AOM in children, and showed that the use of this probiotic did not significantly reduce the incidence of AOM, and there was no statistically significant difference compared to the placebo group (99). This suggests that Streptococcus salivarius K12 probiotic may not be as effective as expected in preventing AOM in children in practical clinical applications, suggesting that we still need to explore new prevention strategies and methods. Furthermore, among many well-studied probiotic formulations, one of them, the oral probiotic Bactoblis^® containing the commensal strain ENT-K12 from the human oral mucosa, has been widely used in several clinical observations targeting upper respiratory tract infections, and it was found that the daily dosing of ENT-K12 could be an effective strategy and highly safe for the prevention of streptococcal and viral respiratory tract infections (74). Table 3 summarizes recent studies of probiotics in children with respiratory infections.

Antifungal treatment

In fungal infectious diseases in children, probiotics mainly play an antifungal role by inhibiting adhesion, inhibiting the formation of fungal biofilm and mycelial differentiation, secreting antimicrobial peptides, altering the microenvironment of the body, and immunomodulation. Probiotics have strong inhibitory effects on fungi such as yeast and Trichophyton. Adhesion, invasion, penetration, and biofilm formation are virulence factors of fungal pathogenicity, among which adhesion is the first step for pathogenic fungi to invade and colonize the host, which is the key attribute of fungal virulence, and the fungal biofilm is a complex three-dimensional structure consisting of yeast cells and hyphae embedded in each other’s extracellular matrix, a habitat created by the microorganisms for themselves, and fungi in the biofilm are much less susceptible to the host’s defense. Probiotics produce antimicrobial substances that inhibit the growth of pathogenic bacteria. These antimicrobial substances include sugar breakdown metabolites such as lactic acid and organic acids such as acetic acid, which are produced by probiotics to effectively retard the growth of fungal hyphae. Lactobacillus is the most common probiotic preparation, and it has been found to secrete a variety of metabolites, including organic acids, hydrogen peroxide, and antimicrobial peptides, which prevent the colonization and overgrowth of pathogenic fungi. In addition, the acidic products it secretes can maintain the acidic environment of the vagina and keep the local microbiota balance (75).

Discussion

The gut microbiota and the host have formed an inextricable and mutually beneficial symbiotic relationship over a long period of co-evolution, and they play an important role in host nutrition, immunity, and health and well-being by participating in many basic physiological and metabolic activities in the human body (104,105). Symbiotic gut microbiota can provide the host with a rich diversity of genes and metabolic functions that aid in the uptake of nutrients from food and can provide factors needed for biosynthetic pathways to facilitate the biosynthesis of essential nutrients.

Studies have shown that gut microbiota plays an integral role in early life brain development, cognitive abilities, and stressful emotions (106-108). Gut microbiota affects the brain as well as the brain-gut axis system through neural and immune factors, endocrine and metabolic pathways (30). The mechanism of action involves bacterial metabolites, cytokines released by mucosal immune cells, and enterohormones (e.g., 5-hydroxytryptamine secreted by enteroendocrine cells) that enter the brain via the bloodstream. Signals are then transmitted to the central nervous system through afferent nerve pathways, including the vagus nerve (106). This suggests that there is not only a physiological link between gut microbiota and the brain, but may also be involved in emotional and behavioral regulatory processes (109).

During this critical period of establishing gut microbiota, early supplementation of high-quality probiotics to infants and young children can promote the formation of a healthy microbiota, which will have a profound positive impact on the health of infants and young children as well as adults. For example, the addition of probiotics and/or prebiotics to infant formulas is one way to achieve purposeful regulation and optimization of the gut microbiota of infants and young children (61). Savino et al. found that four-month-old infants fed formula containing a specific strain of Limosilactobacillus reuteri DSM 17938 showed a significant increase in the number of Lactobacillus in their fecal samples, as well as a significant decrease in the number of Escherichia coli and the amount of ammonia in their feces (110). Another study showed that probiotic- and prebiotic-fortified cow’s milk formulated with B. breve M-16V, galactooligosaccharides, and fructooligosaccharides promoted the growth of Bifidobacteria in the intestinal tract of young children (111). This finding highlights the benefits of microecological regulators in shaping the gut microbiota of infants and young children. Over time, common bacteria in the adult body, such as Bacteroides, Eubacterium, and Digestive Coccus, gradually colonize the gut and become the major gut microbiota, and the composition of the gut microbiota is basically close to that of an adult.

Conclusions

In conclusion, microecological agents, as active microbial supplements that produce health benefits in humans, have been widely used in a number of clinical areas, including pediatrics. Microecological agents can colonize the respiratory, genitourinary and intestinal tracts and regulate the microbiota in various parts of the body, thereby regulating lactose metabolism, calcium absorption, vitamin synthesis, and inhibiting cancer (112-115). The emergence of multiple new therapeutic strategies demonstrates the vast promise of microecological modulators. The scientific principle and mechanism of action of microecological agents are the important cornerstone for analyzing their efficacy. Microecological agents have a complex mechanism of action and material basis for their health effects, which can be realized through the regulation of gut microbiota and its metabolism, including SCFAs, bile acids and neurotransmitters. With the development of sequencing and artificial intelligence technologies, the intrinsic mechanisms underlying the efficacy of microecological agents are being actively explored (116,117). In the future, more research on microecological preparations and related products will be based on clinical applications to solve clinical problems. Conducting standardized clinical trials is a key part of the efficacy evaluation of microecological preparations. Clinical trials based on guidelines or consensus of evidence-based medicine are the best decision-making tools to guide the practice of probiotic application, which can lay the foundation for the industrialization of probiotics to provide better evidence-based evidence for microecological agents, represented by probiotics, to better serve patients of all ages, including children.

Acknowledgments

None.

Footnote

Peer Review File: Available at https://tp.amegroups.com/article/view/10.21037/tp-2025-303/prf

Funding: This study was supported by Municipal Financial Subsidy of Nanshan District Medical Key Discipline Construction, Shenzhen Nanshan District Health System Science and Technology Major Project (No. NSZD2023018).

Conflicts of Interest: All authors have completed the ICMJE uniform disclosure form (available at https://tp.amegroups.com/article/view/10.21037/tp-2025-303/coif). The authors have no conflicts of interest to declare.

Ethical Statement: The authors are accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved.

Open Access Statement: This is an Open Access article distributed in accordance with the Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International License (CC BY-NC-ND 4.0), which permits the non-commercial replication and distribution of the article with the strict proviso that no changes or edits are made and the original work is properly cited (including links to both the formal publication through the relevant DOI and the license). See: https://creativecommons.org/licenses/by-nc-nd/4.0/.

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