1. Introduction

The infant gut microbiome is the collection of microorganisms residing in the gastrointestinal tract of newborns and infants (i.e., children between 1 and 23 months of age) [1]. This microbial community is composed of different microorganisms, including bacteria, viruses, fungi, parasites, archaea, and other microbes. Bacteria are the most abundant and diverse group within the gut microbiome ^[2][3][2,3]. Generally, the human gut microbiome is fundamental in shaping the health and well-being of individuals throughout their lifespan [4]. The critical role of this microbial community is even more pronounced during infancy, the period that lays the groundwork for an individual’s long-term health trajectory ^[5][6][5,6]. Multiple recent research works have underscored the significance of the gut microbiome in infants concerning different facets of health and illness ^[7][8][7,8], shedding light on the intricate interactions among microbial populations, nutrition, genetics, and the body’s immune mechanisms ^[5][6][5,6]. The quantitative and qualitative composition of the gut microbiome is heavily dependent on the diet. This is particularly true during the first two years of life due to the many changes that take place during this period of life, including breast and/or formula feeding, weaning and gradual introduction of different solid foods ^[9][10][11][9,10,11].

The maturation of the gut microbiota in early life is deeply influenced by the methods of infant nutrition, which are breast milk and formula feeding ^[12][68]. The type of feeding significantly influences the composition and function of the infant gut microbiota mainly because of differences in nutrient composition, particularly related to the Human Milk Oligosaccharides (HMOs) ^[13][69].

The primary role of breast feeding in establishing a healthy infant gut microbiome has been increasingly recognized in recent years [5]. Breast milk contains different components, including proteins, fats, carbohydrates, and immunoglobulins ^[14][70]. A significant component of breast milk is the HMOs, such as GOS, which undergo only partial digestion in the small intestine, mainly reaching the colon ^[15][71]. In the colon, HMOs are fermented, largely by Bifidobacteria, resulting in the production of SCFAs ^[16][72] that inhibit the growth of opportunistic pathogens, specifically belonging to the Clostridiaceae, Enterobacteriaceae, and Staphylococcaceae families ^[17][18][19][25,73,74]. Sakurama and colleagues showed that Bifidobacteria produce an enzyme, lacto-N-biosidase, that contributes to the digestion of GOS ^[20][75]. As shown by Matsuki et al. ^[21][76], Bifidobacterium numbers increase, HMO content in stool decreases, and the levels of acetic and lactic acid increase in one-month-old infants. Consequently, HMOs exhibit a pronounced prebiotic impact by selectively fostering the growth of a Bifidobacterium-dense microbiota.

Bifidobacteria, particularly the Bifidobacterium infantis, exhibit a direct correlation with the levels of mucosal Immunoglobulin A (IgA) secreted by the gut ^[22][77]. Additionally, this bacterium is known for its anti-inflammatory properties.

Therefore, the synergy between HMOs and Bifidobacteria not only enhances the variety and equilibrium of the baby’s intestinal microbiota but is also crucial in supporting the host’s immune system and general well-being. Moreover, remnants of HMO metabolism, such as fucose, lactate, and 1,2 propanediol, as well as aromatic amino acid-derived co-HMO metabolism products like indolelactate and 4-hydroxypheyllactate, are typically present in breastfed (BF) infants ^[1][23][1,78].

Additionally, human milk is also a source of bacteria that colonize the infant gut ^[24][79]. Mother-to-infant transmission studies, accounting for both cultured and non-cultured bacteria, provide strong evidence that this bacterial transfer takes place through breastfeeding ^[25][26][24,80]. This transmission has been verified by detecting the same bacterial strains in both maternal milk and the stool of breastfed infants ^[27][81]. Furthermore, research by Pannaraj and colleagues ^[28][82] suggests that bacterial transmission via breast milk has a more profound influence on the early bacterial colonization of a newborn than the bacteria from the areolar skin.

Human breast milk is comprised of a diverse array of microbiota, encompassing both skin-related and non-skin-related Gram-positive bacterial strains ^[29][83]. Notably, Streptococci (specifically S. mitis and S. salivarius) and coagulase-negative Staphylococci prevail in both human milk and stool of breastfed babies ^[30][84]. These microorganisms can compete with undesirable pathobionts, such as Staphylococcus aureus, for space and resources within the infant gut.

The origin of the microbial population in breast milk remains uncertain. The entero-mammary pathway theory suggests that immune cells selectively transport bacteria from the gut to the mammary gland ^[31][85]. This idea is supported by data indicating a resemblance in the bacterial profiles of a mother’s feces and her breast milk ^[32][86]. This hypothesis is further supported by clinical studies finding probiotic strains previously ingested by the mother in her breast milk ^[33][34][87,88].

Infant feeding also influences significantly the host gene expression, as demonstrated by transcriptomic studies conducted on intestinal epithelial cells ^[35][89]. It has been observed that breastfeeding increases the transcription of genes related to immunological processes and metabolic functions ^[35][89]. Breastfeeding plays a key role in rectifying disruptions in the infant’s gut microbiota resulting from cesarean birth, highlighting its essential function in forming a robust intestinal microbiota, regardless of the method of delivery ^[36][90].

The duration and exclusivity of breastfeeding are major drivers of infant gut microbiota composition ^[37][91]. Both exclusive breastfeeding (EBF), defined as the consumption of only breast milk without any additional formula milk, food, or drink, not even water, and its duration, shape specifically the infant gut microbiota ^{[37][38][39][40]}[91,92,93,94]. A meta-analysis of seven studies revealed that during the first 6 months of life non-exclusively breastfed infants exhibited consistently higher gut bacterial diversity and microbiota age compared to exclusively breastfed infants ^[38][92]. Furthermore, relative abundances of Bacteroidetes and Firmicutes and their respective energy pathway were consistently higher in non-exclusively breastfed infants ^[38][92]. These differences persisted until 2 years of age. In the CHILD study ^[37][91], the relationship between exclusive breastfeeding and duration of EBF and the prevalence and relative abundance of different bacteria in the infant gut, represented by amplicon sequencing variants (ASVs), was analyzed, with notable differences in the overall relative abundance of ASVs at 3 and 12 months in exclusive vs. non-exclusive BF. In a recent work by Chichlowski ^[40][94], the gut microbiome of EBF infants was less diverse but more stable compared to formula-fed infants. Bifidobacterium, known for selectively using HMOs as growth substrates, was the dominant genus in the infants’ stools at all points in time, regardless of EBF duration. Infants who experienced EBF for more than six months exhibited a greater relative abundance of Bifidobacterium bifidum compared to those who were EBF for less than three months ^[40][94].

Laursen identified a positive correlation between the duration of breastfeeding and the occurrence of Bifidobacterium, Veillonella, Megasphaera, Haemophilus, lactic acid bacteria, and Enterobacteriaceae. Conversely, longer breastfeeding duration had a negative effect on the abundance of Lachnospiraceae and Ruminococcaceae, bacteria known for breaking down complex carbohydrates ^[41][95].

Formula-fed (FF) infants show more diverse colonization compared to their breastfed counterparts ^[42][96]. Infants who are FF show a greater prevalence of Clostridiales and Proteobacteria in their gut microbiome ^[24][79]. Additionally, the gut microbiota of these infants tends to have a higher concentration of Atopobium and Bacteroides but less Bifidobacteria compared to breastfed infants ^[43][97]. Formula feeding has also been observed to decrease the overall quantity of gut bacteria while simultaneously increasing the diversity within the gut microbiome ^[40][44][94,98].

This difference in microbiota composition is primarily attributed to the absence of HMOs and the increased protein content in formula milk. Infant formulas often contain supplemental FOS and/or GOS, but these are not as selective as HMOs ^[45][99]. They can stimulate the growth of various bacterial species, leading to a significantly different microbiota composition compared to that seen in breastfed infants ^[46][47][100,101].

Interestingly, the gut microbiota of FF infants, even when the formula contains GOS, show a predominance of proteolytic over saccharolytic metabolism ^[48][49][102,103]. This is evidenced by the elevated concentrations of protein breakdown byproducts ^[43][97]. Unfortunately, some of these metabolites can be converted in the liver into detrimental metabolites, such as p-cresol-sulfate and phenylacetateglutamine; these compounds can contribute to enterocyte toxicity, promote inflammation and increased gut permeability and disrupt normal metabolic functions by competing with other substances for sulfation in the liver, a pathway used to detoxify a variety of compounds ^[50][51][104,105].

Efforts to promote the development of a gut microbiome in FF infants that closely resembles that of a breastfed infant in order to emulate health advantages conferred by breast milk include the supplementation of infant formula with prebiotics, probiotics or symbiotics ^[52][53][54][106,107,108], which are synergistic combinations of both.

Numerous research efforts have been conducted to explore the impact of prebiotic addition on the composition of the infant gut microbiome ^[45][55][99,109]. Research has demonstrated the advantages of enriching infant formula with HMOs like 2′ fucosyllactose and lacto-N-neotetraose ^[56][110]. The goal of this strategy is to replicate the positive impacts that breast milk has on the intestinal microbiota. Initial studies have shown promising results, as the gut microbiota of infants fed with HMO-supplemented formula showed a greater resemblance to that of breastfed infants ^[57][111]. These supplements not only support optimal growth in infants, but also promote the growth of beneficial Bifidobacteria, achieving a gut microbial composition closer to that of breastfed infants. The supplementation of infant formula with GOS and FOS can lead to an increased abundance of Bifidobacteria and lower fecal pH, mirroring attributes of breastfed infants ^[58][112].

Although infant formula products are engineered to replicate the macronutrient profile of human milk, currently, the majority of them do not incorporate substantial levels of prebiotics and/or probiotics, as reported by Salminen et al. in 2020 ^[59][113]. Babies fed with formula enhanced with HMOs exhibited increased Bifidobacteria and decreased Enterobacteriaceae and Peptostreptococcaceae ^[53][107]. A study by Borewicz ^[45][99] compared the fecal microbiota composition in infants who were breastfed with that of babies fed with an infant formula fortified with prebiotics (GOS and/or FOS) or receiving mixed feeding. These findings were compared with those from infants who were given conventional formulas. By next-generation sequencing analysis, this study demonstrated a bifidogenic effect of prebiotic-fortified formulas as compared to traditional formulas. Infants who were fed formulas fortified with prebiotics showed gut microbiota compositions that were more similar to those found in breastfed babies. This was not the case in formula-fed infants who were given formulas without any added prebiotics. This study also demonstrated lower bifidogenic activity in formulas combined with breastmilk feeding, suggesting a possible interference between the components of the two ^[45][99].

The addiction of bovine milk-derived oligosaccharides (MOS) to infant formula was evaluated in a three-arm RCT including a control group fed on regular cow milk-based formula, an experimental group receiving the same formula but with added MOS, and a reference group of exclusively breast milk-fed infants ^[60][114]. The overall gut microbiota composition in the experimental group showed more similarities with that of breast milk-fed infants than with the control group. Bifidobacteria were found in higher abundance in the experimental group compared to the control group. Moreover, infants born via cesarean in the experimental group also showed a microbiota composition that was more similar to breast milk-fed and vaginally born infants than to the control group infants. By the age of 4 months, counts of harmful bacteria, Clostridioides difficile and Clostridium perfringens, were significantly reduced in the experimental group than in the control group. The experimental group also showed twice the amount of fecal secretory IgA compared to the control group.

Two comprehensive systematic reviews carried out by Rao et al. ^[55][109] and Mugambi ^[61][115] examined the effects of adding prebiotics to formula milk. Both showed higher stool colony counts of Bifidobacteria, regardless of differences in dosage, duration of supplementation, and method of reporting results. However, three specific studies using supplementation with GOS, FOS or a GOS/FOS mix found no difference in Bifidobacteria levels between the infant formula-supplemented groups and their controls ^[62][63][64][116,117,118]. Prebiotic supplementation had an inconsistent impact on ^{[63][64][65][66]}[117,118,119,120] while decreasing the levels of C. difficile ^[67][68][121,122]. A double-blinded RCT comparing an infant formula supplemented with a symbiotic composed of bovine MOS and the probiotic Bifidobacterium animalis vs. the same formula alone caused a significant increase in Bifidobacteria abundance and lower microbiota diversity in the experimental group vs. controls, similarly to breastfed infant ^[69][123].

Currently, the most frequently examined and utilized probiotic species belong to the Lactobacillus, Bifidobacterium, and Saccharomyces genera ^[70][71][124,125]. Researchers are also exploring the potential application of bacteria extracted from breast milk to develop infant formulas that closely resemble the nutritional composition of natural breast milk [5]. Supplementation of the formula with Bifidobacterium species and/or lactic acid bacteria, such as Lactobacillus strains, is deemed secure and generally accepted ^[72][73][74][126,127,128] and may potentially enhance their immune response ^[75][76][129,130].

Studies investigating the effect of probiotic supplementation of infant formulas did not find a strong correlation between fecal Bifidobacterium concentration and Bifidobacterium supplementation ^[77][78][79][131,132,133]. Bifidobacteria colonization in the infant gut was indeed found to be unstable over time, most likely due to competition among members of the gut microbial ^[80][81][134,135]. This finding has been supported by a systematic review ^[66][120] of 12 RCTs, reporting that supplementation of probiotics did not increase the counts of Bifidobacteria or Lactobacilli nor decreased the levels of pathogens such as Bacteroides and E. coli. ^[61][115].

In a recent observational study, neonates undergoing varied probiotic administration for six months showed an elevation in stool Bifidobacteria levels only during the first week after birth, implying that probiotics might potentially expedite the initial colonization of this taxon, together with a concomitant reduction in the Enterobacteriaceae family, without differences in alpha diversity ^[82][136]. Regardless of the probiotic species, fecal Lactobacillus levels were higher in infants supplemented with a probiotic ^[82][83][136,137]. Another investigation revealed that healthy infants given formula supplemented with Lactobacillus rhamnosus GG (LGG) showed a greater frequency of Lactobacilli colonization compared to those who were fed with a standard formula ^[84][138]. Additionally, in very low birth weight infants, the supplementation of Bifidobacterium breve Bb12 favored gut colonization by the added bacteria and expedited the growth of Lactobacilli compared to those infants who did not receive the probiotic supplement ^[85][139].

To foster a beneficial gut microbiota, the most opportune time for administering probiotics is prior to the establishment and colonization of individual microbial taxa ^[86][140]. This crucial window is typically within the initial months of life. Nonetheless, the colonization timings vary across different microbial taxa ^[87][141]. Therefore, identifying these specific periods of opportunity for each taxon is of paramount importance. However, the optimal duration of probiotic supplementation required to guarantee a protracted beneficial impact on gut microbiota remains unclear.

During the fourth month of life, the infant’s renal and gastrointestinal systems reach physiological maturation, enabling them to process non-milk alimentary substances ^[88][142]. Upon reaching the sixth month, the nutritional and energetic benefits procured solely from breast milk become insufficient to meet the growing metabolic demands of the infant ^[89][143]. Thus, the inclusion of complementary food is needed for the appropriate somatic and neurodevelopmental trajectory ^[88][90][142,144].

The implementation of complementary feeding presents a heterogeneous pattern across Europe and worldwide. Certain European regions, exemplified by the UK and Sweden, adhere to the World Health Organization’s endorsement of starting such feeding regimens from six months. However, other territories, including Belgium and Spain, advocate for the initiation of these diets between the fourth and sixth month, a strategy that is in alignment with the guidelines of the European Society for Paediatric Gastroenterology, Hepatology, and Nutrition (ESPGHAN) Committee on Nutrition ^[91][145]. According to this committee, the introduction of complementary alimentary substances should not precede the fourth month and should not be delayed beyond the sixth month, including those containing potential allergenic substances.

Despite remarkable advancements in our knowledge of early-life gut microbial interaction and our growing understanding of the microbial capacity to metabolize various dietary compounds, the understanding of the effects of diet on gut microbiota during the complementary feeding period is still limited ^[92][146].

The shift from exclusive milk feeding to the inclusion of family foods in the infant’s diet corresponds with substantial changes in the gut microbiota ^[93][147]. During this period, the alpha diversity increases, with a shift from Bifidobacterium-dominant community to Bacteroidetes- and Firmicutes-dominant communities ^[94][148]. For instance, there is a rapid decrease in the population of Bifidobacterium species that can degrade HMO ^[95][96][20,149]. Simultaneously, there is a significant increase in diversity and the emergence of Bacteroidaceae, Lachnospiraceae, and Ruminococcaceae species, reflecting the more complex diet that comes with the introduction of fibers and new proteins ^[97][98][150,151]. A longitudinal study by Stewart et al. ^[99][152] reported a clear increase in gut microbial diversity after the introduction of solid foods. Further, this increased diversity correlated with enhanced immunological and metabolic development in infants, suggesting the potential health benefits of diverse solid food introduction. A recent study by Pannaraj et al. ^[28][82] provided similar findings, reporting the association of diversified solid food intake with the enrichment of specific microbial groups, particularly Bifidobacterium and Bacteroides.

Diverse solid foods act as new sources of microbiota-accessible carbohydrates, therefore stimulating the growth of beneficial taxa such as Bifidobacterium, Lactobacillus, and Bacteroides ^[100][153]. These microbes produce SCFAs, such as butyrate, propionate, and acetate, promoting a healthy gut environment and influencing the immune system ^[101][154]. The introduction of fruits and vegetables, rich in fermentable fibers, leads to an increase in beneficial microbes like Bacteroides and Bifidobacterium ^[102][155]. On the other hand, protein-rich foods like meats and eggs can stimulate proteolytic microbes such as Clostridium and Streptococcus ^[103][156]. Hence, the introduction of a diverse diet could ensure a balance between these microbes, leading to a more resilient and healthier gut microbiota.

Since gut microbes primarily derive their energy from dietary fibers and secondarily from proteins/peptides, these macronutrients are likely to have the greatest influence on the microbial composition ^[104][105][49,157]. The primary outputs of metabolizing dietary fiber include SCFAs like acetate, butyrate, and propionate ^[106][107][158,159]. High levels of acetate are generated during the initial stages of infancy, whereas the levels of butyrate and propionate start at a markedly reduced state, subsequently elevating as the infant grows older [9]. Correspondingly, the products of protein degradation, notably branched-chain fatty acids (BCFAs), remain essentially unobservable during the lactation period yet exhibit a parallel trajectory of augmentation with advancing age ^[41][95]. These changes align with the beginning of solid food intake and the end of breastfeeding ^[108][160]. In agreement with the typical gut microbiota developmental pattern, key species within the Lachnospiraceae and Ruminococcaceae families produce butyrate, while Bacteroides species are common propionate producers ^[109][161]. These species possess a comprehensive array of enzymes for breaking down dietary fibers into these SCFAs ^[110][162]. Moreover, certain species more abundant in older infants, such as Bacteroides and Clostridium, might employ a range of amino acids derived from dietary proteins to produce BCFAs ^[111][163]. Thus, complementary feeding might have a causative effect on microbiota composition and metabolism ^[13][112][69,164].

In a study of nine-month-olds infants, the diversity of gut microbiota was found to increase with the introduction of solid food, particularly fibers and protein, independent of whether the infants were breastfed or formula-fed ^[113][165]. A study by Marrs ^[114][26] suggests that the introduction of allergenic food, in conjunction with continued breastfeeding between 3 to 6 months of age, resulted in the increase of the overall gut microbiota Shannon diversity. Specifically, this diversification was characterized by the emergence of various microbial taxa, notably Prevotellaceae and Escherichia/Shigella. Of note, the presence of Prevotella has been linked with high-fiber diets ^[97][150].

Elevated protein intake has been associated with a heightened abundance of Lachnospiraceae and a decrease in saccharolytic organisms, such as those in the Bifidobacteriaceae family ^[115][166]. Simultaneously, the consumption of fiber was linked to an increase in the proportions of Prevotellaceae ^[116][117][167,168].

The timing of complementary food introduction is known to influence gut microbiota composition. A study by Bäckhed et al. ^[118][169] suggests that the delayed introduction of solid food could cause a lag in microbial maturation and increase susceptibility to allergies and obesity. On the other hand, an earlier introduction could expose infants to potential pathogens and allergens ^{[119][120][121]}[170,171,172]. Hence, the timing of solid food introduction should balance between these risks and benefits.

Differding and coworkers found that the introduction of complementary feeding before 3 months of age can lead to enhanced microbial diversity and a higher concentration of fecal butyrate and that these effects may continue up to the age of 12 months ^[94][148]. In an RCT comparing traditional spoon feeding to a baby-led approach (involving self-feeding with complementary “finger foods”), the authors found that babies weaned through a baby-led approach were introduced to solid foods approximately 20 days beyond the initial six months (at the age of seven months) ^[122][173]. At this age, their consumption of both vegetables and fibrous nutrients was markedly reduced.

By contrast, Laursen and colleagues discovered that the length of time infants were breastfed had a greater influence on both the variety and the proportion of intestinal microbiota and their overall microbial richness at the age of nine months than when they began eating solid complements ^[93][147]. This conclusion aligns with the latest findings from Bäckhed et al. ^[118][169], which indicate an increase in Lachnospiraceae populations correlating with increased consumption of household meals, as opposed to a decline in Bifidobacteriaceae numbers. This alteration likely mirrors the dietary shift from mother’s milk, which is rich in Bifidobacteriaceae, to solid foods typical of late infancy that are abundant in fiber and protein, thus supporting the growth of Lachnospiraceae species ^[93][147].

In another study, Differding and coworkers ^[123][174] investigated how the timing of introducing complementary foods can significantly affect the infant’s gut microbiota composition, in turn potentially impacting their gut health and overall nutrition: Ruminococcus bromii, which is able to digest resistant starches ^[124][19] was found in greater amounts in infants who were breastfed for less than four months and given complementary foods early. In infants fed with a diet rich in resistant starches, R. bromii could potentially outperform other commensal bacteria that are not as efficient in energy extraction, potentially causing a shift in metabolic processes and dysbiosis. Additionally, these infants had a reduced number of Bifidobacterium animalis, a dominant bacterial species in young gut ecosystems, which generally diminishes with the infant’s growth and the onset of weaning ^[99][123][152,174]. An increased presence of Bifidobacterium animalis may be advantageous for the gastrointestinal health of infants, as indicated by a randomized controlled trial which demonstrated that its supplementation reduced the levels of fecal calprotectin (an indicator of gut inflammation) and decreased gastrointestinal leakiness in infants born before term ^[125][175].