Breastfeeding is a major determinant of the infant oral microbiome (Al-Shehri et al., 2016; Oba et al., 2020; Butler et al., 2022). The difference between breast-and formula-fed infants begins within days of birth, with the oral cavity of exclusively breastfed neonates 24–48 h post-partum exhibiting a higher abundance of Actinobacillus and Neisseria and a lower abundance of Haemophilus than those who received both breast milk and infant formula (mixed-fed) (Oba et al., 2020). At two months of age, breastfed infants harbor a higher abundance of Streptococcus and lower abundance of Veillonella (Oba et al., 2020; Butler et al., 2022), and at three months of age, lactobacilli are only detected in exclusively and partially breastfed infants (Holgerson et al., 2013). At six months of age a lower abundance of Weeksellaceae is seen compared with mixed-fed infants (Oba et al., 2020). At the phylum level, a higher abundance of Bacteroidetes and a lower abundance of Proteobacteria are observed in formula-fed infants (Al-Shehri et al., 2016; Butler et al., 2022). Studies comparing breast-and formula-fed infants consistently find a lower alpha diversity in the oral cavity of breastfed infants (Al-Shehri et al., 2016; Williams et al., 2019; Oba et al., 2020; Butler et al., 2022), consistent with the effect of breastfeeding on the infant gut microbiome (Ho et al., 2018).

Human milk is comprised of various microbial, bioactive, and nutritional components, which may influence the oral microbiome. However, direct evidence regarding these interactions is lacking. Studies to address this gap include cohort studies linking milk composition to oral microbiome composition, whole genome sequencing studies to identify metabolic genes of interest in the infant oral microbiome that may interact with various milk components, and culture supplementation studies to examine the impact of various milk components on cultured infant oral taxa. Potential mechanisms of action are discussed below.

Weaning is a critical transition point in infancy associated with growth and developmental changes (Nuzzi et al., 2022). It is well-known that cessation of breastfeeding drives maturation of the infant gut microbiome (Bäckhed et al., 2015), however, no such studies have been performed for the oral microbiome. Interestingly, in a study of the oral microbiome of donkey foals, significant changes were observed during the weaning period compared with pre-weaning period (Zhang Z. et al., 2022). While a direct comparison of pre-and post-weaning is yet to be performed in humans, there is some data to suggest that the duration of breastfeeding may impact the oral microbiome.

The effect of breastfeeding duration on the composition of the oral microbiome has been studied in a cohort of 90 children at 3, 6, 12, and 24 months and 7 years of age (Dzidic et al., 2018). Interestingly, at 24 months of age, infants who remained partially breastfed until at least 12 months of age differed significantly in their oral microbiomes compared to those who were no longer receiving human milk by 12 months of age (Dzidic et al., 2018). This effect was long lasting, with a distinct difference in the communities still detected at 7 years of age. Among children who breastfed until at least 12 months of age, a higher relative abundance of Streptococcus at 12 months and Veillonella at 7 years was observed. Among those who ceased breastfeeding before 12 months of age, a higher relative abundance of Porphyromonas at 12 months, Neisseria at 24 months, and Actinomyces at 7 years was observed (Dzidic et al., 2018). Porphyromonas is involved in periodontitis, which destroys gingiva (gums) and can lead to tooth loss (Mysak et al., 2014). This implies that early cessation of breastfeeding may put infants at risk of later-life oral diseases. However, given that cessation of breastfeeding prior to 12 months requires supplementation with infant formula, it is difficult to differentiate the effects of lack of breast milk per se from the effects of formula use. Further, the cariogenic effect of infant formula has been evaluated in 36 children aged 1–2 years, who were fed with infant formula milk three times a day for 21 days (Chaudhary et al., 2011). A significant increase in the colony-forming units of Streptococcus mutans, a caries associated species, was observed in the oral microbiome of supplemented infants (Chaudhary et al., 2011). Thus, the impact of infant formula on the oral microbiome and oral health should be evaluated in further research.

Evidence on the impact of breastfeeding duration on the oral microbiome is sparse. This is a significant gap in the evidence, due to the controversy surrounding the association between prolonged breastfeeding and dental caries (Li et al., 2000; Rosenblatt and Zarzar, 2004; Vachirarojpisan et al., 2004; Azevedo et al., 2005; van Palenstein Helderman et al., 2006; Yonezu et al., 2006; Avila et al., 2015; Tham et al., 2015; Cui et al., 2017; Peres et al., 2017; Chanpum et al., 2020; van Meijeren-van Lunteren et al., 2021; Suparattanapong et al., 2022). Some studies have shown a protective effect of breastfeeding against tooth decay compared to exclusively formula feeding (Avila et al., 2015; Cui et al., 2017) While others have shown that breastfeeding beyond 9 months increases the risk for tooth decay (Li et al., 2000; Rosenblatt and Zarzar, 2004; Vachirarojpisan et al., 2004; van Palenstein Helderman et al., 2006; Tham et al., 2015; Cui et al., 2017; Peres et al., 2017; Chanpum et al., 2020; van Meijeren-van Lunteren et al., 2021). This issue must be resolved in order to provide evidence-based recommendations to parents. Thus, breastfeeding duration and exclusivity should be considered in future studies to better understand the long-term consequences of breastfeeding duration on the oral microbial composition and oral health.

Human milk, often with fortification, is the nutrition recommended for preterm infants (Gu et al., 2021). However, mothers of preterm infants may be unable to produce sufficient volumes of milk to meet their infant’s needs, necessitating the use of alternative nutrition, such as donor human milk or formula. Further, preterm infants are often administered milk via nasogastric tubes, bypassing exposure to the oral cavity. As such, oral administration of colostrum has become standardized in many NICUs due to its ability to enhance the weight gain, decrease the duration of hospitalization, and decrease the risk of poor health outcomes (Huo et al., 2022). In a small study of 20 preterm neonates, the effect of oropharyngeal colostrum administration on the oral microbiome was investigated (Cortez et al., 2021). The study found a higher relative abundance of oral Staphylococcus, Bifidobacterium, and Bacteroides in the intervention group compared with those receiving standard care (Cortez et al., 2021). Similar findings, including increased oral Staphylococcus, were reported in another study of 12 very low birth weight infants (Sohn et al., 2016). Another consideration for preterm infants is the use of fortified human milk. While the impact of milk fortification on the gut microbiome has been studied (Underwood et al., 2013; Cong et al., 2017; Dahl et al., 2018; Cai et al., 2019), there is an absence of data about the effects on the oral microbiome. Such differences in neonatal nutrition may have consequences on the oral microbiome and long-term oral health.

Preterm birth is known to influence dental development and be associated with dental caries (Seow, 1997; Schüler et al., 2018). Delayed growth and development of both primary and permanent dentition has also been observed in preterm children (Seow, 1997). Children born preterm are also at a significantly higher risk for dental caries (50% prevalence in preterm children compared to 12.5% in term children) (Schüler et al., 2018). However, early feeding modes have not been investigated in these studies. The effect of preterm infant feeding practices on the composition of the oral microbiome should be examined in future cohorts to better support oral health in the preterm population.

In the first year of life, infants progress through their diet, from milk (either human milk or infant formula) to solid food. The WHO recommends that solid food is introduced at six months of age [World Health Organization (WHO), 2021b]. Introduction of solid foods not only introduces new substrates for bacterial metabolism, but also results in a gradual reduction in the dose of human milk, which may also lead to changes in the composition of the oral microbiome (Oba et al., 2020). However, limited studies have investigated the impact of the introduction of solid food on the oral microbiome (Sulyanto et al., 2019; Oba et al., 2020).

The dramatic change in nutrient sources that accompanies the introduction of solids is likely to influence the diversity and composition of the oral microbiome (Dzidic et al., 2018). In one study of 12 infants, oral samples collected immediately pre-and post-introduction of solid foods were compared. On average, solid food was introduced to the infant diet at 6.8 ± 0.9 months of age, following which the infant oral microbiome became richer and more diverse, and the relative abundance of Streptococcus mitis was reduced (Sulyanto et al., 2019). In another study of 12 infants sampled at birth and 2, 4, and 6 months of age, samples taken after the introduction of solids (n = 1 at 4 months, n = 10 at 6 months) had a high abundance of Gemella, Neisseria, Veillonella, and Fusobacterium compared to samples taken prior to the introduction of solids (Oba et al., 2020). While shifts in the oral microbiome have been detected around the time of introduction of solids, it is important to consider that introduction of solid food occurs close to the time of primary tooth eruption, which may contribute to the acquisition of new species by providing new surfaces for bacterial attachment (discussed further below) (Wan et al., 2001).

Overall, solid food introduction may increase the complexity of the infant oral microbiome. Due to limited evidence on the impact of solid food introduction on the oral microbiome, large longitudinal studies with detailed feeding data are needed. Such studies may aid in separating the effects of solid food introduction and tooth eruption events.

Tooth eruption may also impact the microbial composition of the oral cavity. Teeth begin to erupt in the infant oral cavity at approximately six months of age with a full complement of primary teeth at around 30 months of age, providing new surfaces for bacterial adhesion. As tooth emergence and the introduction of solid food often occur at the same time (Kageyama et al., 2019; Welch et al., 2020), it is difficult to differentiate between the effects of these two events.

The complexity of the oral microbiome increases with the emergence of primary teeth (Xu et al., 2022). In a study of 21 infants, saliva and plaque samples were taken across five detention states: prior to tooth eruption (~4–5 months old; saliva only), following the eruption of the first two teeth (~6 months old; saliva and plaque), following the eruption of the upper and lower primary incisors (~9 months old; saliva and plaque), following the eruption of the first molars (~14–19 months old; saliva and plaque), and at full dentition (~24–36 months old; saliva and plaque) (Xu et al., 2022). Approximately 30% of the OTUs in saliva and 70% of those in plaque remained across all dentition states, suggesting that the majority of saliva taxa are altered by tooth eruption, while the majority of plaque taxa remain. Streptococcus dominated the saliva across all dentition states, but declined gradually with teeth eruption, accompanied by a rise in community diversity. Following primary tooth eruption, new taxa colonize the oral cavity, including species of Streptococcus, Neisseria, Rothia, Veillonella, Corynebacterium, Gemella, Treponema, and Granulicatella (Shi et al., 2016; Mason et al., 2018; Xu et al., 2022).

Further maturation of the oral microbiome in childhood may be associated with the transition from primary to permanent dentition (Shi et al., 2018). There is a large overlap in taxa present prior to and following permanent dentition, with Actinomyces strongly associated with permanent teeth (Shi et al., 2016; Mason et al., 2018; Shi et al., 2018). These findings indicate that the oral microbiome at primary tooth eruption has a significantly higher alpha diversity compared to pre-dentate infants, mixed, and permanent dentations (Mason et al., 2018). Although dentition is a crucial milestone in infant oral microbiome development, few studies have specifically characterized the impact of tooth eruption on the oral microbiome. Further work is required to clarify whether the development of the oral microbiome is primarily influenced by age or by the emergence of teeth, with a focus on various sites within the oral cavity which may be differentially impacted by the emergence of teeth (Xiao et al., 2020).

Dental caries is the most prevalent childhood oral disease globally. It is estimated that 514 million children have primary teeth caries (Yu et al., 2021). Dental caries is also associated with alterations to the oral microbiome (Zhang J. S. et al., 2022). Factors such as consumption of sugar, frequency of breastfeeding, and night-time breastfeeding, have been impact the oral microbiome potentially increasing the incidence of dental caries (Carrillo-Diaz et al., 2021).

The etiology of dental caries occurs in three main steps. Firstly, biofilm is formed on the surface of teeth via formation of conditioning film, which allow cell-to-surface attachment of the primary colonizers and cell-to-cell interaction of the late colonizers. Then, teeth are coated with salivary components such as glycoproteins, mucins, sialic acid, and bacterial cells debris, which are absorbed on to the teeth enamel. After that, primary colonizer bacteria, such as Actinomyces viscosus and Streptococcus sanguis, interact with the biofilm by several cell-to-surface pathways (Lamont et al., 1991; Davey and O’toole, 2000). This interaction is influenced by carbon source, pH, and osmolarity (Davey and O’toole, 2000). The third step is adhesion of pathogenic bacteria such as S. mutans to the initial colonizers, leading to dental caries (Davey and O’toole, 2000). Although dental caries may be caused by many microorganisms (Aas et al., 2008; Holgerson et al., 2015; Hurley et al., 2019a), S. mutans has been identified as a common causative agent (Tanner et al., 2011; Holgerson et al., 2015; Hurley et al., 2019a). Streptococcus mutans is able to process monosaccharides to acid and to produce extracellular polysaccharides, leading to caries (Shellis and Dibdin, 1988; Zero, 2004).

The relationship between the oral microbiome and caries is likely bidirectional: the oral microbiome can cause caries, and caries can impact the oral microbiome. The oral microbiome of caries-active children is reduced in alpha diversity and Veillonella, and enriched in Streptococcus mutans and other streptococci, Cutibacterium, Prevotella, and Lactobacillus (Belstrøm et al., 2014; Richards et al., 2017; Wang et al., 2017; Xu et al., 2018; Wang et al., 2019; Hurley et al., 2019a; Yang et al., 2021).

While dental caries alter the oral microbiome, differences in the infant oral microbiota may precede childhood caries. The ability of the infant oral microbiome to predict later childhood caries has been investigated prospectively (Xu et al., 2018; Dashper et al., 2019;Grier et al., 2021; Blostein et al., 2022). In a recent case–control study, the oral microbiome prior to the onset of caries was depleted in Neisseria, Haemophilus parainfluenzae, and Fusobacterium periodonticum compared to controls (Blostein et al., 2022). This shift in the microbiome was also associated with a decrease in saliva pH and an increased risk of acquiring S. mutans. Importantly, this study controlled for numerous potential confounders, including maternal education, primary dentition, mode of delivery, breastfeeding, and antibiotic exposure (Blostein et al., 2022). In a similar prospective study of 134 children, 65 of whom developed caries by age of 5 years, the oral microbiome was characterized at seven time points from 1.9 months to 5 years of age (Dashper et al., 2019). While children who would go on to develop caries and those who would remain healthy could not be discriminated based on their oral microbiota at prior to 20 months of age, distinctions began to develop by 39 months of age. A number of taxa were identified as discriminatory between children who would go on to develop caries and those who would remain healthy; however, presence of S. mutans was the largest predictor of later disease. Similarly, in a study of 56 children 1–3 year old children who were sampled 6-monthly, 36 of which went on to develop caries, machine learning models were able to predict the onset of early childhood caries with an AUC of 0.71 at 1 year of age, and an AUC of 0.89 in the visit immediately before disease onset, suggesting a progression in the oral microbiome toward disease (Grier et al., 2021). In these models, Rothia mucilaginosa, Streptococcus sp., and Veillonella parvula were the most discriminatory species. While alpha diversity is known to be reduced in children with caries (Belstrøm et al., 2014; Hurley et al., 2019a), alpha diversity has not been reported to be predictive of caries (Grier et al., 2021; Blostein et al., 2022). This suggests that the reduction in alpha diversity that occurs in caried-affect children occurs as a result of the disease. Together, a shift in composition of the oral microbiome of children who developed caries compared to those who remained healthy suggests a role for the infant oral microbiome in dental caries susceptibility. If such shifts can be identified early, timely intervention may be applied to promote oral health in children.

Respiratory bacteria may also contribute to the infant oral microbiome. Anatomically, the oral cavity is also a route for the respiratory tract. Mutual exchange of microbes between the respiratory tract and the oral cavity may occur due to mouth breathing and coughing (Dong et al., 2022). Typical taxa of the respiratory system, such as Haemophilus and Pseudomonas, are regularly identified in the infant oral cavity (Segal et al., 2013).

Several studies in adults have shown an association between oral bacteria and the risk of respiratory diseases such as influenza, pneumonia, and chronic obstructive pulmonary disease (Scannapieco and Ho, 2001; Pragman et al., 2019; Takeuchi et al., 2019; Gomes-Filho et al., 2020; Imai et al., 2021). This finding indicates that respiratory health may be associated with the oral microbiome. However, this association has not been examined in infants. Therefore, studies of the infant microbiome should include data on respiratory health to clarify this link.

Many infections are treated by antibiotics in early life, which have systemic effects regardless of the site of infection. Antibiotic use is widespread in infants, with 82.3% of children prescribed antibiotics within the first two years of life in New Zealand (Leong et al., 2020). Exposure to antibiotics therefore has the potential to disrupt the oral microbiome (Lazarevic et al., 2013; Dzidic et al., 2018; Kennedy et al., 2019).

Studies have reported an association between antibiotic use in early life and perturbations to the oral microbiome (Lazarevic et al., 2013; Dzidic et al., 2018; Kennedy et al., 2019). However, the long-term effects of this are not fully understood. Recently, the impact of antibiotic intake in the first two years of life on the oral microbiota was assessed in Swedish children (n = 90), who were followed from birth to 7 years of age (Dzidic et al., 2018). Of those, 30% had been treated with amoxicillin or phenoxymethylpenicillin in their first year of life, while 44% had been treated with those antibiotics in their second year of life. Interestingly, the oral cavities of unexposed children exhibited a higher relative abundance of Neisseria spp., S. mitis, and Streptococcus dentisani-species associated with childhood caries (Gross et al., 2010). Thus, antibiotics exposure may influence early oral health. However, to date, no association has been reported between early-life antibiotic use and dental caries. Similar results were reported from another cohort in which the use of antibiotics was categorized according to “ever-used” and “used within the last three months” at the time of sample collection. Antibiotics were prescribed for 6, 3, and 16% of children at ages 6, 12 and 24 months, respectively. Exposure to antibiotics within the three months prior to sample collection was positively associated with Pasteurellaceae and Neisseriaceae, and negatively associated with Prevotellaceae (Kennedy et al., 2019). Corresponding results were reported from a smaller study of 18 children aged 12–72 months treated with amoxicillin and a control group (n = 15) who were not exposed to antibiotics. Saliva samples were collected at the initial visit (at the prescription of amoxicillin), approximately 10 days later (at the end of treatment), and a month after commencement of antibiotics (approximately 3 weeks after cessation of treatment). Samples were collected from the control group at the same three time points. Exposure to amoxicillin was associated with a major shift in the relative abundances of various taxa and a reduction in species diversity and richness in the oral cavity. At the end of the treatment period, a reduction in Streptococcus, Gemella, Rothia, Fusobacterium, and Prevotella was observed in the treated group. Notably, the oral microbiome exhibited partial recovery three weeks after the course of amoxicillin but remained distinct from pre-antibiotic samples in terms of richness and diversity (Lazarevic et al., 2013). These findings together imply a significant and lasting impact of antibiotics on the early oral microbiome.

Aside from the factors discussed here, there are various potential factors that may influence the early-life oral microbiome. A small number of studies have shown an association between oral microbiome composition in early life and maternal delivery mode (Li et al., 2005; Holgerson et al., 2011; Nelun Barfod et al., 2011; Thakur et al., 2012; Dominguez-Bello et al., 2016; Li H. et al., 2018; Hurley et al., 2019b), intrapartum antibiotic prophylaxis (Gomez-Arango et al., 2017; Li et al., 2019), gestational diabetes mellitus (He et al., 2019), infant pacifier use (Plonka et al., 2012), and ethnicity (Premaraj et al., 2020; Table 2). However, study numbers and consistency between studies is low. Additionally, there are other early-life factors and events which may influence the development oral microbiome, such as second-hand smoke exposure, teething interventions (gels, toys, washcloths), and teeth brushing behavior (cloth, silicon or plastic bristle, brushing frequency, age of introduction to toothpaste). However, to date, these have not been explored in infants.