The human gut microbiome has a significant causal role in various aspects of human physiology and pathology, beyond its previously recognized associative roles. After birth, the human gut microbiome undergoes continuous changes, including increased microbial diversity, maturation and the emergence of site-specific microbial communities. While the composition of gut microbiota in adulthood is more stable than in infants, individual-specific gut microbiota shows personalized responses to diseases, dietary factors and drugs, indicating that individual microbiome may predict health outcomes (1). This raises a key question of when the impact of gut microbiome changes is the most significant.

Recent research has highlighted the significance of early-life gut microbiota in shaping host physiology, immunity and long-term health outcomes (2). The establishment of early gut microbiota is influenced by maternal factors during pregnancy, including microbiome transmission and metabolite transfer (3, 4). In addition, various factors such as gestational age, delivery mode and antibiotic exposure further impact the development and maturation of the early gut microbiota (5). Notably, the first 3 years from birth are considered a critical window for early intervention, as early-life colonization plays an important role in shaping long-term health outcomes even after the recovery from the gut microbial disruption (2, 6). Therefore, early intervention strategies are imperative to mitigate the long-lasting metabolic effects.

This review provides the basis for understanding the development of the gut microbiome in early life and emphasizes the importance of early interventions to normalize the microbiota from prenatal stages to 3 years after birth. These efforts aim not only to improve the health of infants but also to improve their long-term well-being.

Altered gut microbiome in various human diseases

The adult human gut microbiota is a dynamic ecosystem that co-evolves with its host. It is estimated to consist of 39 trillion microbial cells, approximately the same number as human cells in our bodies (7). Moreover, this ecosystem has over a thousand times more genes than the human genome, indicating its significant genetic and metabolic potential and its substantial impact on the host (1). The gut microbiome has been linked to various human diseases, not limited to the gut, including inflammatory bowel disease and colon cancer, and neurological and metabolic diseases such as Parkinson’s disease, Alzheimer’s disease, autism, depression, type 2 diabetes, cardiovascular diseases, atherosclerosis, non-alcoholic fatty liver diseases and obesity (1, 8, 9). The gut microbiome’s influence on diseases beyond the gut is thought to occur through various microbial metabolites that enter the host’s bloodstream from the gut and reach different host tissues (9).

Dynamics of the normal gut microbiota

The interaction between the host and the gut microbial ecosystem is crucial for regulating the immune system and maintaining metabolic homeostasis, and altered gut microbial ecosystems are associated with various human diseases (10). However, alteration of the gut microbiota induced by many perturbations can be stochastic, and studies indicate that even under normal, ecologically stable conditions, fluctuations in the gut microbiome can occur (11). One of the challenges in investigating the association between gut microbiota and specific human diseases is the lack of consistent signatures. This inconsistency can be partly attributed to the limitations of cross-sectional cohort studies that fail to consider normal variations and proper control groups, as well as technical variations in sample collection and analysis (12). Therefore, longitudinal studies with repeated data collection could be important to identify consistent and specific microbial biomarkers by considering the temporal dynamics of the gut microbiota. In addition, age should be considered as a confounding factor in microbiome analysis results given that age-specific differences have been observed in gut microbial change-related diseases among individuals aged 20 to 89 years (13).

Recent longitudinal studies have shown that highly diverse gut microbial compositions tend to be more stable over time in the normal gut microbiota (14, 15). Furthermore, the use of Whole Genome Sequencing (WGS)-based strain typing has revealed that genetically unstable microbial species are associated with various human diseases (16). Nevertheless, stable genomic features of a given microbiome, such as single nucleotide polymorphisms (SNPs) and structural variations (SVs), may serve as a host-specific fingerprint of the microbiome, potentially enabling the identification of individuals (14). These findings suggest that a comprehensive understanding of the normal variations in the gut microbiota across the lifespan and detailed strain-level analyses would facilitate the identification of “true disease-associated microbial signatures” and enable personalized treatment options.

Accumulating evidence shows that an alteration of the gut microbiome is not only a fingerprint that can track individual health conditions, but also its association and causality with various human diseases have been suggested (10). Consequently, there are many ongoing studies to find and understand factors that induce changes in the gut microbiome.

Lifestyle

Lifestyle factors can significantly impact the composition and function of the human gut microbiome. Among them, diet is a key determinant as it can regulate the microbial metabolic processes depending on the specific macronutrients and ingredients in a diet (17). For example, Mediterranean diets, which are high in fiber, monounsaturated fat and antioxidants, can lead to changes in the structure and metabolomic profile of the gut microbiome, resulting in higher levels of fecal short-chain fatty acids (SCFAs) and a reduced risk of obesity and cardiovascular diseases. Similarly, the Hadza hunter-gatherers who consume a diet rich in complex carbohydrates, have increased diversity of the gut microbiota (18). On the other hand, long-term consumption of Western diets or diets deficient in microbiota-accessible carbohydrates found in dietary fiber can lead to the extinction of several gut microbiota taxa over generations, emphasizing the role of diet as a driving force in microbiota composition and function, and consequently our health and disease (19).

Geographical differences in gut microbiome composition may also be related to dietary differences. The migration to the United States from non-western countries, which have diets dominated by maize and cassava, to the Western diet, which is high in sugar, fat, and protein, resulted in an immediate loss of gut microbiome diversity and function (20). Similarities in microbial communities between the U.S. control group and second-generation immigrants indicate that dietary changes may influence microbial community shifts, but other factors such as stress, exercise, antibiotics and antiparasitic treatment may play a role as well (20).

In addition to diet, other lifestyle factors such as smoking, alcohol consumption and exercise have been shown to impact the gut microbiome. Smoking and alcohol consumption reduce gut microbial diversity, increase intestinal permeability and decrease the production of SCFAs (21). Interestingly, smoking caused more severe gut dysbiosis than alcohol consumption, but the combination of smoking and alcohol does not worsen it compared to either group alone (21), suggesting that the interaction effect of tobacco and alcohol on the gut microbiota is complex. Moderate-intensity endurance exercise has been shown to reduce inflammation, improve body composition, contribute to the diversity and composition of gut microbiota, and have effects on metabolic contributions to human health. Conversely, irregular and exhausting training can increase intestinal barrier permeability, decrease intestinal mucus thickness, and may contribute to gut dysbiosis (22).

Individual physiological patterns, such as stool frequency, correlate with gut microbial richness, distribution, and composition (23). Taken together, lifestyle factors can have wide-ranging effects on human health by modulating the gut microbiome. Therefore, it is important to identify and understand the factors that influence the development of microbial communities to promote better health outcomes.

Medication

Orally administered medications reach the intestine, where they may interact with the gut microbiome, potentially affecting the effectiveness of the drugs (24). Notably, drugs designed to target human cells, not microbes, have also been shown to alter the composition and function of the gut microbiome (25). For example, metformin, a commonly used medication for type 2 diabetes, has been found to alter the gut microbiome composition in mice and humans, showing a positive correlation with the abundance of Escherichia and Akkermansia (26). Furthermore, the metformin-altered human microbiota or A. muciniphila improved glucose tolerance in mice, indicating that the altered gut microbiota plays a role in some of metformin’s antidiabetic effects (27). Similarly, rosuvastatin, a commonly used cholesterol-lowering drug of the statin class, has been shown to restore the altered gut microbiota induced by a high-fat diet. The composition of the gut microbiota can also affect the bioavailability of statins by modulating the metabolism of bile acids (28). Captopril, an antihypertensive drug, has been shown to increase the amounts of bacterial spores such as Parabacteroides, Mucispirillum and Allobaculum and induce long-lasting antihypertensive effects (29).

The gut microbiome can also, directly and indirectly, influence an individual’s response to a drug and immunotherapy in cancer treatment by enzymatically transforming the drug’s structure and altering its bioavailability, bioactivity, or toxicity. For example, digoxin, a cardiac glycoside, can be metabolized to cardio-inactive dihydrodigoxin by Eggerthella lenta, and brivudine, an antiviral drug, can be metabolized by Bacteroides, to a potentially toxic metabolite (30, 31). In addition, the gut microbiota can metabolize levodopa, a medication for Parkinson’s disease management, potentially reducing drug bioavailability. In addition, Enterococcus faecalis or E. lenta converts levodopa to m-tyramine leading to side effects (32).

The gut microbiome’s role in drug metabolism and efficacy underscores the importance of investigating the bidirectional interactions between the gut microbiome and drugs. Additionally, given that the human gut microbiota is highly individualized, it is speculated that the gut microbiota is one of the primary variables determining drug effectiveness in individuals (31).

Antibiotics

Antibiotics can disrupt the balance of the gut microbiota by increasing pathogenic bacteria including Enterobacteriaceae and Fusobacterium nucleatum, while reducing beneficial bacteria such as Bifidobacterium and butyrate producers, including Faecalibacterium prausnitzii and Eubacterium spp. (33). This disruption can have significant impacts on the host, affecting immune regulation, metabolic activities and overall health (34). Antibiotic-induced changes in the gut microbiota can have long-term effects on community structure, and individuals may have different recovery patterns (35). Additionally, the metabolic changes caused by antibiotic-induced alterations in the gut microbiota can contribute to various chronic and neurological diseases (36).

The human gut microbiota is a reservoir for antibiotic resistance genes (ARGs) and resistant microorganisms. The current knowledge on the “resistome” and “antibiotic resistance potential” suggests that the rapid development and dissemination of ARGs is largely due to antibiotic abuse and misuse, and bacteria carrying antibiotic resistance can persist in the human gut for years even after short-term antibiotic treatment (37).

Recent studies have investigated the use of the gut microbiome to restore dysbiosis caused by antibiotic use. For example, an engineered strain of Lactococcus lactis has been developed to degrade β-lactam antibiotics and alleviate their negative effects on commensal gut bacteria (38). Additionally, probiotics such as Bacillus clausii have shown to be promising in preventing antibiotic-associated diarrhea and improving Helicobacter pylori eradication rates (39). Fecal microbiota transplantation (FMT) is now widely used to treat antibiotic-induced gut dysbiosis, particularly in cases of Clostridium difficile and vancomycin-resistant E. faecium infections in both human cohorts and mouse models (40). The FDA recently approved SER-109, known as VOWST, oral capsules, composed of live and purified Firmicutes bacterial spores derived from healthy donors, for the prevention of recurrent C. difficile infection. This follows an earlier approval of REBYOTA, a microbiota suspension for rectal administration aiming at restoring the gut microbiota (41). These developments highlight the potential of microbiota-based live biotherapeutic products. Nevertheless, further research is needed to determine the optimal formulation and dosage, and ensure clinical safety and efficacy.

Epidemiological studies increasingly suggest that exposure to biological and psychosocial hazards during the first 3 years of life can have long-term effects on overall health, including cardiovascular, immune, metabolic and brain health (42). The colonization of the gut microbiota during this period is critical for long-term health outcomes (2).

Especially, exposure to antibitics affects the gut microbiome in early life. Notably, antibiotics are the most frequently prescribed medication to infants. Exposure to antibiotics in early life can lead to a rapid decrease in the diversity of the gut microbiome through a transient disruption. While this can recover over time, such changes can have long-lasting consequences on the immune and metabolic programming of infants, and may contribute to the development of chronic diseases later in life (6).

The use of antibiotics during pregnancy can affect the maternal gut microbiome, consequently influencing the transmission of microbiota from the mother to the newborn and potentially leading to various health conditions, including childhood atopy, asthma, allergies and obesity (43). Observational studies in humans have shown that antibiotics used during the second and third trimesters of pregnancy are associated with an increased risk of obesity, allergy and asthma in offsprings (43). In murine models, the administration of a low dose of penicillin during late pregnancy has been shown to alter the microbiota composition of the offspring, leading to metabolic changes associated with obesity, diabetes and non-alcoholic fatty liver disease (44). Interestingly, exposure to vancomycin during the prenatal period in neonatal mice models increased susceptibility to allergic asthma, while the same antibiotic exposure in adulthood had no such effect (45). Moreover, prenatal antibiotics exposure in murine models altered the gut microbiome profiles of offspring, including bacterial metabolic pathways, and influenced the immune function of post-weaned prepubescent offspring (46). The effects of antibiotic use during pregnancy varies across different types of antibiotics, with narrow-spectrum antibiotics such as pivmecillinam, erythromycin and clindamycin showing no association with overweight in offspring, while some broad-spectrum antibiotics such as ampicillin, amoxicillin and sulfamethizole may increase the risk of infant obesity in humans (47). Antibiotic use during the first year of life has also been associated with a higher risk of childhood obesity, pneumonia, asthma, allergies and related symptoms (48, 49).

Tracking antibiotic-exposed mice from infancy to old age revealed that, despite receiving the same antibiotics, distinct and functionally diverse changes in the microbial communities occur at different stages of life, suggesting that there is a critical period in life where antibiotic exposure has long-lasting effects on metabolism, immunity and lifespan (50). Indeed, antibiotic exposure in early life delays the development of the gut microbial community, with the most significant impact occurring between 6 and 12 months of age (5). This delay has been linked to the accelerated onset of childhood overweight and obesity between the ages of 1 and 2 and a half years in humans (49). In murine models, the early-life administration of antibiotics such as low-dose penicillin, tylosin and a mixture of amoxicillin and tylosin induced a significant increase in total and fat mass due to metabolic changes, demonstrated by the transfer of antibiotic-induced altered microbiome to germ-free mice (6, 51). Short-term antibiotic treatment, for less than 3 days, in infants has only a temporary and mild effect on the gut microbial composition and metabolites, while intensive antibiotic exposure can lead to a continuous decrease in the diversity of the microbiome (52). Interestingly, a recent study using rats suggests that selective reshaping of the gut microbiota through the use of appropriate antibiotics during the gestation and lactation period may have long-term benefits against pediatric hypertension (53). Therefore, it is important to use appropriate antibiotic combinations, doses and timing; this helps to minimize the risks associated with inevitable antibiotic exposure and achieve optimum therapeutic effects while promoting the rapid recovery of the gut microbial homeostasis.

The establishment and maturation of the gut microbiome in infants can vary, and microbiome perturbations during the first weeks to months of life can affect infant growth and health (54). The establishment of the gut microbiota during infancy is influenced by multiple factors, such as prenatal, peripartum and environmental factors (Fig. 1) (55). Given its close and causal relationship with later-life quality, we will discuss factors affecting the establishment of the early microbiome.

Maternal effect during pregnancy

Environmental factors such as diet, drug intake and stress can alter the maternal microbiome during pregnancy, consequently influencing the intrauterine environment and significantly affecting the fetal and infant microbiome (56-58). Maternal transmission of gut bacteria provides a microbial ‘starter kit’ for infants, promoting healthy growth and disease resistance (59). Microbial strains from multiple maternal body sites are transferred to the infant microbiome (4, 60). Metagenomic profiles have shown that maternal gut strains are more persistent in the infant’s gut, while maternal skin and vaginal strains colonize only transiently (60).

Metagenomics analysis has reported that excessive gestational weight gain in mothers (BMI > 25) alters the abundance and diversity of the gut microbiome, leading to a significant reduction in metabolic signaling and energy regulation-related bacterial communities, including Enterococcus, Acinetobacter and Pseudomonas (61). Moreover, research involving birth cohorts and murine models has demonstrated that the offspring born to mothers who consumed a high-fat diet or were overweight during pregnancy are enriched with Firmicutes and have impaired insulin sensitivity. These offsprings have a 5-fold higher risk of being overweight and developing metabolic diseases compared to those born to mothers of normal weight (62). Additionally, low-fiber diets during lactation can result in lasting microbiota dysbiosis in offsprings, characterized by reduced taxonomic diversity, increased abundance of Proteobacteria and increased adiposity when exposed to an obesogenic diet (56). Antibiotic intake during pregnancy can also disrupt the transmission of maternal-derived pioneer gut bacteria during birth, potentially affecting metabolic health. In a study involving pregnant spontaneously hypertensive rats treated with captopril water, changes in the gut microbiota were observed, and some of the changes were reflected in their male offsprings that showed persistently decreased systolic blood pressure and improvements in gut inflammation and permeability (57).

Maternal prenatal psychosocial stress is another factor that influences the long-term development of the infant microbiome (58). Continuous exposure to stress has been reported to disturb the vaginal bacterial structure and composition, which can be transmitted to the offsprings, affecting their gut microbiome composition and neurodevelopment (63). Prenatal depression, which affects 10-20% of pregnant women, can have various effects on the infant’s health, including behavior problems and increased susceptibility to physical illnesses (64). Infants born to mothers with high levels of depression and anxiety showed a reduction in the abundance of beneficial bacteria such as Bifidobacterium, and Lactobacillus, which have been shown to have a role in the gut-brain axis and immune modulation (65). For example, depression-induced maternal pro-inflammatory cytokines can promote dysfunctional neurodevelopment in offspring (65, 66).

Prenatal exposure to a smoking environment also greatly affects the composition of the gut microbiome in infants. The majority (78%) of infants born to mothers who smoked were born prematurely and infants from non-smoking families showed higher alpha diversity of gut microbiota compared to infants from smoking families. This suggests that secondhand smoke can affect the intestinal microbial community of neonates (67). Additionally, maternal smoking is associated with low birth weight in children and can also increase the abundance of Firmicutes during the first 3 months of life, thereby increasing the risk of obesity in children between the ages of 1 and 3 years (68).

Gestational age

The microbiota in infants undergoes dynamic changes in composition, and the temporal colonization pattern of the intestinal microbiota during the early stages of life may have an important contribution to long-term health (2, 69). However, most studies investigating the development of the gut microbiome in early life have primarily focused on full-term infants. In recent years, the prevalence of premature birth has increased, with approximately 5-18% of live births in 2019 classified as preterm (babies born before 37 weeks of gestational age) (70). Importantly, gestational age is considered a significant factor contributing to the development and maturation of the gut microbiome during early life (71).

Recent analyses of gut microbiota in infants have revealed significant differences in the meconium and stool between full-term and preterm infants (refer to Table 1). Although there were no significant differences in alpha diversity, the beta diversity analysis indicated distinct structures of the gut microbiota in each group (72). The most abundant bacteria at the phylum level in each group were Proteobacteria, Firmicutes and Bacteroidetes (72, 73).

Especially, there is a prediction that preterm infants may be colonized by potentially pathogenic facultative anaerobic bacteria such as Enterobacter, Escherichia and Klebsiella, with delayed colonization of commensal strict anaerobes such as Bifidobacterium, Bacteroides and Clostridium (74-77).

Preterm infants are predominantly born via cesarean section (CS), resulting in a gut microbiome that is more commonly colonized by the skin and environmental bacteria rather than the vaginal and rectal microbiome (78). Also, exposure to the neonatal intensive care unit, including sterile incubator nursing and broad-spectrum antibiotics, limits the acquisition and development of normal microbiota. This can lead to altered levels of Clostridium and B. fragilis, resulting in a different gut microbiome compared to full-term infants (74, 79). Antibiotic exposure in preterm infants increases the presence of antibiotic resistance genes or abundance of multi-drug resistant members of Klebsiella, Escherichia, Enterobacter and Enterococcus genera (80-82).

The delays and alterations in the colonization of commensal bacteria in the gut of preterm infants have been associated with the development of metabolic and gastrointestinal illnesses such as Type 1 diabetes, asthma and allergies, necrotizing enterocolitis (NEC) and late-onset sepsis (LOS), which leads to atopy and neurodevelopmental effects in childhood and later life (71, 83-86). For example, early Bifidobacterium deficiency in preterm infants seems to be a negative biomarker of adverse neurological outcomes and NEC (77, 87). Moreover, the transplantation of meconium microbiota from preterm infants into germ-free mice resulted in growth disorders, impaired intestinal immune function and metabolic abnormalities (88).

Current research provides evidence that premature birth impacts infant growth and development. However, our understanding of the gut microbiota in preterm infants from infancy to childhood is still limited. Future research is needed to identify the critical period during which interventions can be implemented to normalize infant growth, development and the microbiome. This knowledge would be invaluable for improving health outcomes in preterm infants.

Delivery mode

The delivery mode is a common major factor that can directly affect early microbial colonization (5). Vaginally delivered infants are enriched with bacteria such as Lactobacillus, Prevotella and Sneathia, which are present in the mother’s intestine and vagina. In particular, bacteria derived from the mother’s intestine persist more in the infant’s intestine (5, 60). However, infants born via CS are colonized with bacteria similar to those found on the mother’s skin and oral cavity since vertical transmission is blocked (78). This results in relatively reduced alpha diversity and lower levels of Bifidobacterium and Bacteroides, and higher levels of Clostridium, Lactobacillus, Enterobacter, Enterococcus, and Staphylococcus (84, 89). Within the first week after birth, there was no difference in the gut microbiota between vaginally delivered infants and CS-born infants (90). However, in the second week, Bacteroides in CS-born infants disappeared due to the absence of Bacteroides supporting species (4, 90). Furthermore, CS-born infants have lower alpha diversity during the first year (5, 91). Nevertheless, this difference normalizes in 3 to 5 years as the gut microbiota continued to mature (91). In contrast to term infants, the birth mode does not significantly impact microbial characteristics in preterm infants (92). This may be attributed to the dominant influence of neonatal intensive care unit (NICU) exposures, such as early antibiotic use and the absence of Bacteroides colonization in preterm infants (92).

Infant feeding type

Numerous studies have demonstrated that infant feeding type significantly influences the composition, development, and diversity of early microbiomes, which has a significant impact on immune function. Human breast milk considered the “gold standard” of infant nutrition, contains a wide spectrum of human milk microbiota that plays a crucial role in gastrointestinal colonization in infants. These microbiota include Firmicutes (i.e., Streptococcus, Staphylococcus, Lactobacillus), Proteobacteria (i.e., Serratia, Pseudomonas, Ralstonia, Sphingomonas), and Actinobacteria (i.e., Propionibacteria, Corynebacteria, Bifidobacterium) (93, 94). In addition to fulfilling the infant’s initial nutrition requirements, breast milk contains immunoglobulins, fatty acids, hormones and cytokines that contribute to the infant’s health and development (93). Furthermore, breastfeeding can play a vital role in enhancing gut microbiome diversity by selectively promoting the growth of beneficial bacteria such as Bifidobacterium and Lactobacillus species, which can break down specific oligosaccharides present in human milk (94). Consequently, the gut microbiome of breast-fed infants is typically dominated by Bifidobacterium and Lactobacillus species, which are associated with a lower risk of developing allergic diseases (78).

Infant formula milk formulation, including cow-milk-based formula and soy-based formula, mimics the nutritional composition of breast milk (95). However, cow’s milk-based formula contains higher levels of fat, minerals and proteins compared to human breast milk (96). Recent studies have shown that high protein content in infant formula is associated with excess weight gain in infants, which can lead to a 20% risk of being overweight later in life and an increased risk of food allergies (78, 97). Formula feeding is associated with a higher incidence of alterations in the infant gut microbiota compared to breast-fed infants such as in favor of proinflammatory taxa, increased gut permeability, and antibiotic resistance load (98). Despite efforts by formula manufacturers to replicate nutrients similar to those in human milk, the gut microbiota of breast-fed and formula-fed infants remain distinct (99).

In the relationship between delivery mode and infant feeding type, it has been observed that there was no difference in the abundance of Bifidobacterium according to feeding type in infants delivered vaginally. However, in CS-born infants, breast-fed infants have higher levels of B. longum, B. breve, B. bifidum, and B. pseudocatenulatum compared to formula milk-fed infants (100, 101). Interestingly, a recent report suggests that CS-born infants who do not have direct exposure to the birth canal may compensate for the transmission of the maternal microbiome through other routes, such as breast milk microbiota (4). Also, despite the high risk for dysbiosis of the gut microbiome in preterm babies, mother’s own milk has been shown to contribute to the development of a diverse and balanced microbial community in early life compared to donated human milk and formula milk (102).

Nevertheless, regardless of the delivery mode and infant feeding type, the introduction of solid food at around 1 year after birth leads to a more rapid and stable maturation of the gut microbiome, and an increase in diversity (100). As a result, by the age of 5 years, there is minimal difference in the initial gut microbial composition of infants based on the delivery method (91). However, even with the normalization of the microbiome, there may still be long-lasting effects from the previous microbiome associated with delivery modes, which could manifest in differences in disease prevalence (Fig. 1) (103).

The development of the gut microbiome in the early stages of life can be compromised in infants born via CS, preterm births, or exposure to antibiotics (5, 82, 104). Currently, commonly used intervention strategies to restore developmental impairment of the early gut microbiome in neonates include fecal microbiota transplantation (FMT), probiotics and nutrients (Fig. 2) (104-106). When maternal vaginal microbes were transplanted orally to CS-born infants, it did not show significant changes in gut microbiome composition and functional potential (107). Meanwhile, when CS-born infants immediately received a swab of the maternal vaginal microbiota, starting from the mouth, then the face and the rest of the body, a partial recovery of gut, oral and skin microbiota occurred similar to infants born vaginally, during the first 30 days (108). However, regardless of administration techniques, vaginal seeding has not sufficiently restored Bacteroides colonization and abundance in the gut microbiota of CS-born infants (108). Conversely, orally delivered maternal FMT exhibits a composition of the gut microbiota similar to that observed in infants born vaginally, indicating that the maternal fecal microbiota may be a more effective method for restoring Bacteroides levels in CS-born infants (104, 107). The restorative effect of FMT has also been observed in animal models, which affected the composition of the gut microbiota, prevented mucosal damage and NEC in a preterm pig model, and effectively reversed NEC damage in a preterm mouse model (109, 110). However, there are still risks associated with introducing living microorganisms, particularly the potential for disease occurrence due to the weakened immune system of the recipient (111). Therefore, as for safety, the importance of establishing donor screening criteria has been proposed. For example, current standard processes for the most successful and frequently performed treatment of C. difficile infection with FMT typically involve pre-screening with a medical history evaluation and blood and stool tests to detect the presence of infectious diseases, but the efficiency of screening is low and the focus is mainly on excluding infections and underlying diseases (112). Therefore, it is necessary to accumulate data on the occurrence of complications through longitudinal studies and understand how environmental factors or personal characteristics affect FMT clinical responses (112).

The supplementation of probiotics to preterm infants has been reported to be effective in preventing sepsis and major disorders such as NEC (106). Probiotic supplementation, containing species of Bifidobacterium, Lactobacillus and Streptococcus, in preterm infants and extremely preterm infants less than 5 days old, has been shown to increase the abundance of probiotic species in the gut microbiota of preterm infants, and effectively prevent serious morbidities associated with prematurity such as NEC and LOS (113). In addition, longitudinal analysis has demonstrated that the dominance of B. breve through probiotic supplementation is associated with accelerated maturation of the preterm infant gut. These findings suggest that the strain-specific effect is an important aspect to consider when designing an early intervention targeting the gut microbiome in preterm infants (114).

Breast and formula milk are the major sources of nutrition for newborns and can be used as strategies for nutritional supplementation (115). Human milk oligosaccharides (HMOs) are complex and unconjugated sugar structures in human milk, which are proposed to support infant growth, development and health. HMOs may have a protective impact on NEC in preterm infants by modulating the immune system and gut microbiota (105, 116). Furthermore, the addition of 2 HMOs (2’-fucosyllactose and lacto-N-neotetraose) in commercial formulas for term infants can produce gut microbiome compositions and functions, similar to those of breast-fed infants (78, 117). HMOs can promote the growth of Bifidobacterium and can be utilized by Akkermansia, suggesting the potential of enhancing the intestinal barrier function and immune system by guiding the healthy microbiota (105, 118). While various early intervention strategies have been proposed, further research is needed to understand the precise mechanisms for restoring disrupted or immature gut microbiota. It is crucial to establish reliable and effective strategies that ensure stability.

The gut microbiome and its metabolic processes are dynamic systems that can be easily altered by various factors. Antibiotic exposure often leads to the bloom of pathogens such as Enterococcus and Fusobacterium and the depletion of beneficial Bifidobacterium species, but most of the common microbiome composition is restored within 1.5 months after antibiotic exposure (119). However, in the long term, there may be “antibiotic scarring”, characterized by altered metabolic output and an increased antibiotic resistance burden even after the administration of antibiotics ceases (33). Persistent metagenomic signatures, such as enriched gut antibiotic resistome and carriage of multidrug-resistant Enterobacteriaceae, may remain and contribute to chronic pathology despite the recovery of the gut microbiota (120).

The early life period is particularly critical for host-microbial metabolic interactions, and altered metabolic phenotypes driven by delivery mode, infant feeding type and antibiotic exposure can persist and affect the long-term risk of chronic disease, even if early gut microbial perturbations recover (6, 121). Therefore, further research is needed to identify critical periods during which restoring the microbiome composition can lead to phenotype recovery.

The rising global preterm birth rates have emphasized the need to comprehensively investigate the complex microbial environment within the human gut using a combination of metagenomics and metabolomics approaches for a deeper understanding of maternal factors associated with infant health from the fetal stage (101). From a metagenomics perspective, taking probiotics during early pregnancy is an alternative treatment for preventing bacterial vaginosis-associated preterm birth and spontaneous preterm birth (122). In addition, starting supplementation of a probiotic mixture or human milk fortifier within a month after birth can have beneficial effects on the gut microbiome maturation as a critical developmental window of preterm infants, consequently improving clinical outcomes (123, 124).

From a metabolic perspective, the maternal gut microbiota can affect not only the maternal compartment but also the fetus in the sterile uterus through the modulation of microbial metabolites (3, 125). The microbial metabolites may modulate the infant gut microbial ecosystem, immunity and long-term metabolic effects on the offspring, including increased adiposity, glucose intolerance and neural development in adulthood (43, 126). Recently, the discovery of beneficial effects on infants through the release of indole-3-lactic acid and γ-linolenic acid via breast milk metabolization offers potential therapeutic applications, highlighting the possibility of harnessing the transmission of microbial metabolites from mother to infant for therapeutic purposes (127). In addition, as dynamic metabolic changes occur during pregnancy, potential biomarkers of gestational age prediction and preterm birth have been observed in blood and vaginal samples (128). For example, maternal metabolites can be used as early biomarkers for preterm birth which provides a basis for prevention and treatment. Moreover, considering the potential variation in transplantation outcomes based on subtle species-level donor differences (123), the use of validated metabolites that are more stable and reproducible than FMT can be considered as an alternative approach for gut microbiota restoration. It is also important to set the precise time point and dose of the early intervention to achieve the optimal efficacy and safety for the recovery of the early gut microbiota.

The authors have no conflicting interests.