After birth,the infant’s skin and mucosal surfaces become rapidly colonized by complex microbial communities of bacteria, fungi, and viruses [1-3]. In early infancy, the composition and diversity of these microbial communities diverge by body site, driven by differences in nutrient availability, the chemical environment, and the host’s immune system across sites [3,4]. Multiple environmental factors influence the microbiome in infancy, including the maternal microbiome, the infant’s diet, delivery mode, and antibiotic exposure [1,5-8]. The microbiome plays a critical role in shaping multiple aspects of infant development, including the structure and function of the immune system and intestinal tract [9]. Alterations to the composition and diversity of the infant microbiome are associated with multiple morbidities including necrotizing enterocolitis (NEC), sepsis, growth failure, malnutrition, and others [10-14]. Furthermore, compelling evidence supports that alterations to the microbiome in early life have lasting effects on child development that may increase the risk of immune and metabolic diseases in later life [15-19]. This review will focus on the assembly of microbiome in infancy, its influence on infant health and development, and potential microbiome-targeted therapies to improve health outcomes.

The sources of microbes that seed the infant’s gut microbiome include strains present in the microbiomes of the mother, other caregivers, and the infant’s environment [5,20]. A diversity of organisms from the mother’s oral, vaginal, and skin microbiomes are transiently present in the early neonatal intestinal microbiome, but many are soon replaced by species better adapted to the intestinal environment (Table 1) [3,20]. Of all maternal body sites, the fecal microbiome contributes the highest number of strains that stably colonize the infant gut [5,20]. Approximately half of the species present in the infant’s gut microbiome are shared with the maternal microbiome [20]. Many of these shared species are present at a low relative abundance in the maternal fecal microbiome, as differences in diet and the biochemical environment in the infant gut exert unique selective pressures compared to the mother [20]. The specific bacterial features that confer a selective advantage for some strains to colonize and persist in the infant gut over others are only beginning to be elucidated, but they include genes involved in polysaccharide utilization, surface adhesion, and iron acquisition [21,22]. Bacterial strains within the Bacteroides, Bifidobacterium, and Escherichia genera are commonly shared between mothers and their infants. Infants born by cesarean delivery and infants of mothers who were administered peripartum antibiotics have a lower proportion of shared bacterial strains from the mother’s microbiome than those born by vaginal delivery without maternal antibiotic exposure [5,6,23]. In addition to bacteria, other elements of the microbiome, including bacterial viruses (bacteriophages) and fungi, may be vertically transmitted from mothers to their infants [24,25].

Human milk is another source of bacteria that may colonize the infant’s intestinal tract [20,26,27]. Breast milk contains viable microbial communities often dominated by Staphylococcus, Streptococcus, Acinetobacter, and Pseudomonas [26-28]. While the microbial profiles of human milk and infant stool are generally distinct, there are shared bacterial groups between mother’s milk and her infant’s stool [26,27]. Elucidating the contribution of the breast milk microbiome to the infant gut microbiome has been challenging due to several factors including contamination of milk samples with maternal skin flora, retrograde transfer of the infant’s oral bacteria to the mammary gland and milk during breastfeeding, and technical difficulties extracting and amplifying bacterial DNA from milk [27,29]. Milk from mothers who feed expressed breast milk has fewer bacterial types in common with the infant gut microbiome than that from mothers who directly breastfeed their infants, suggesting that the transfer of bacteria from the infant mouth could be a source of bacteria in mother’s milk [27].

Other sources of bacteria that seed the infant gut include microbes transmitted from other family members and microbes present in the physical environment [23]. The hospital environment may serve as a reservoir of strains that colonize the infant, particularly among infants born preterm [30-33]. In fact, preterm infants often share identical bacterial strains with other infants in the neonatal intensive care unit [21,34].

The assembly of the microbiome in infancy is a highly dynamic process [1,7,35]. Meconium samples collected from infants typically contain low or undetectable amounts of bacterial DNA, but a rapid rise in bacterial density occurs within the first postnatal days [2]. Many of the early colonizers of the infant’s intestinal tract are facultative anaerobes (e.g., Enterococcus, Escherichia, Staphylococcus) [1,2,36]. Over time, an increase is observed in the relative abundance of strictly anaerobic organisms. This is thought to reflect a shift from an aerobic to anerobic environment in the intestine. However, in silico modeling of the meconium microbiome suggests that bacterial growth occurs under anaerobic conditions within hours of birth [2]. After this transition, Bifidobacterium and Bacteroides spp. commonly dominate the infant gut microbiome [1,7,37,38]. In breastfeeding infants, these bacteria outcompete others secondary to their ability to digest human milk oligosaccharides (HMOs) [37,38]. In later infancy, the relative abundance of anaerobic taxa characteristic of the adult fecal microbiome increases (e.g., Ruminococcus, Roseburia) [1]. While the microbiome of young breastfeeding infants is enriched in genes involved in HMO degradation, the microbiome of older infants is enriched with genes required for the digestion of dietary fibers present in solid foods [1,37].

The infant microbiome is highly individualized. Variation among individual infants often exceeds the variation attributable to environmental exposures and treatments [6,39]. Environmental factors that have been consistently associated with microbiome composition and function include delivery mode, gestational age, diet, and antibiotics.

The microbiome has a broad range of effects on infant development, including roles in immunity, growth, metabolism, and neurodevelopment [9,59-63]. These effects occur through direct interactions of the microbiome with the host’s immune system at the skin and mucosal interfaces as well as through the production of bioactive metabolites by the microbiome that are absorbed into the circulation [19,61,63,64]. The infant’s immune system and gastrointestinal tract develop upon close interaction with the microbiome. Evidence from studies of germ-free animals reared in a sterile environment demonstrated the importance of the microbiome for normal intestinal and immune development. Germ-free rodents have enlarged ceca, reduced gastrointestinal motility, altered intestinal epithelial cell morphology including longer villi and shorter crypts, and structural and functional deficits in immune development [9,65-67]. Multiple studies reported a sensitive period in early life during which certain aspects of immune development are uniquely influenced by the microbiome, and perturbations of the microbiome during this period may have lasting health consequences [16,18,19,68,69]. Similarly, metabolic programming is uniquely influenced by the microbiome during early life, and disruption of the maternal and infant microbiomes may increase an individual’s susceptibility to later metabolic diseases including obesity [15,17,70,71].

The codevelopment of the microbiome, gastrointestinal tract, and immune system also influence physical growth in infancy. Young germ-free mice demonstrate slower weight gain, length gain, organ and bone growth as well as greater weight loss during periods of malnutrition than mice raised with a conventional microbiome, demonstrating the importance of the microbiome for supporting early life growth [60]. Germ-free mice have lower circulating levels of insulin-like growth factor 1 (IGF-1) and growth hormone sensitivity in the peripheral tissues than those raised with a microbiome [60]. In a mouse model of malnutrition, a select Lactobacillus plantarum strain was sufficient to increase IGF-1 production and sustain postnatal growth through a mechanism involving the interaction between its cell wall components and the pattern recognition receptor nucleotide-binding oligomerization domain–containing-2 in the intestinal epithelium [61]. In human infants and children, malnutrition is associated with persistent immaturity in the intestinal microbiome [14]. Transferring fecal bacteria from children with malnutrition to germ-free mice recapitulates phenotypic features of malnutrition in the animals, supporting a causal role of the microbiome in malnutrition [59]. A dietary intervention designed to modulate the microbiome of children with malnutrition to a composition similar to that of healthy children improves growth and nutritional biomarkers, demonstrating the potential ability of microbiome-targeted therapies to improve growth and nutrition in early life [72].

The commensal gut microbiome excludes pathogens from the gut and protects the host from infection through a phenomenon known as colonization resistance. There are multiple mechanisms of colonization resistance, including outcompeting pathogens for space and nutrients, bacterial secretion of antimicrobial peptides, and stimulation of the host immune system [73]. The relatively low bacterial diversity and increased luminal oxygen availability in the neonatal gut may impair the colonization resistance of the neonatal microbiome and increase susceptibility to pathogen invasion and sepsis [74-76]. Colonization resistance may be further impaired following disruption of the microbiome by antibiotic use [74].

Given the importance of the microbiome to infant health, there is high interest in understanding the best practices to support healthy microbiome development. Antimicrobial stewardship and breastfeeding support are sample practices that optimize the microbiome and improve infant health. Other microbiome-targeted interventions may include the administration of live bacteria (probiotics) or select nutrients that promote the growth of beneficial bacteria (prebiotics). Microbiome-targeted therapies have proven effective at reducing the incidence of NEC and sepsis, major causes of morbidity and mortality in infants (Table 2).

While the pathogenesis of NEC is not fully understood, interactions between an abnormal microbiome with the immature gut and immune system of preterm infants are central to its pathogenesis. Prolonged antibiotic use is associated with an increased risk of NEC, while breastfeeding is protective [77,78]. Breastmilk contains multiple bioactive components including HMOs and immunoglobulin A that likely contribute to its protective effects against NEC [53,79]. NEC is commonly preceded by a bloom in the relative abundance of Proteobacteria in the fecal microbiome [10]. Meta-analyses of randomized trials support that probiotics significantly reduce the risk of NEC and mortality in preterm infants (Table 2) [80-82]. Further, observational studies support the effectiveness of probiotics in clinical practice [83,84].

Sepsis is a major cause of morbidity and mortality in both full-term and preterm infants. A randomized controlled trial of an oral probiotic and prebiotic preparation (Lactobacillus plantarum plus fructooligosaccharide) in 4,556 term infants in rural India showed a striking reduction in the primary outcome of sepsis and death in the treatment arm [85]. The risk of lower-respiratory tract infections was also reduced among infants in the treatment group. Probiotics have been shown to reduce the risk of late-onset sepsis in preterm infants [86]. These studies demonstrate the promise of microbiome-targeted therapies to reduce infant morbidity and mortality rates.

The microbiome has a key role in health and development during infancy.Its composition and function are influenced by environmental exposures throughout infancy. Interventions to promote healthy microbiome development have already proven effective for multiple diseases that affect infants, but the discovery of other means to optimize microbiome development in early life has great potential to improve health outcomes across the lifespan.