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. 2025 Apr 15:15:1534750.
doi: 10.3389/fcimb.2025.1534750. eCollection 2025.

Development of the breastfed infant oral microbiome over the first two years of life in the BLOSOM Cohort

Roaa A Arishi  1   2   3   4 , Ali S Cheema  5 , Ching T Lai  1   2   3 , Matthew S Payne  6 , Donna T Geddes  1   2   3 , Lisa F Stinson  1   2   3
Affiliations

Development of the breastfed infant oral microbiome over the first two years of life in the BLOSOM Cohort

Roaa A Arishi et al. Front Cell Infect Microbiol. .

Abstract

Background: Acquisition and development of the oral microbiome are dynamic processes that occur over early life. This study aimed to characterize the temporal development of the oral microbiome of predominantly breastfed infants during the first two years of life.

Methods: Infant oral samples (n=667) were collected at ten time points from the first week to year two of life from 84 infants. Bacterial DNA profiles were analyzed using full-length 16S rRNA gene sequencing.

Results: The oral microbiome was dominated by Streptococcus mitis, Gemella haemolysans, and Rothia mucilaginosa. Bacterial richness decreased from 1 to 2 months (P = 0.043) and increased from 12 to 24 months (P = 0.038). Shannon diversity increased from 1 week to 1 month and again from 6 to 9 months and 9 to 12 months (all P ≤ 0.04). The composition of the infant oral microbiome was associated with multiple factors, including early pacifier use, intrapartum antibiotic prophylaxis, maternal allergy, pre-pregnancy body mass index, siblings, delivery mode, maternal age, pets at home, and birth season (all P < 0.01). Introduction of solid foods was a significant milestone in oral microbiome development, triggering an increase in bacterial diversity (richness P = 0.0004; Shannon diversity P = 0.0007), a shift in the abundance of seven species, and a change in beta diversity (P = 0.001).

Conclusion: These findings underscore the importance of multiple factors, particularly the introduction of solid foods, in shaping the oral microbiome of breastfed infants during early life.

Keywords: breastfeeding; human milk; infancy; infant diet; oral microbiome.

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Conflict of interest statement

DG, CL, and LS receive a salary from an unrestricted research grant from Medela AG administered through The University of Western Australia. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Sample collection and infant feeding mode at each of the 10 sample collection time points over the first two years of life.
Figure 2
Figure 2
Composition of the infant oral microbiome over the first two years of life. OTUs with an average relative abundance of >0.5% are displayed.
Figure 3
Figure 3
Genus-level interindividual variation in the infant oral microbiome. Individuals are represented by vertical bars. Genera that made up <2% relative abundance at all time points are grouped together as “Others”.
Figure 4
Figure 4
Relative abundance trends of key bacterial species in infant oral microbiomes over time, with loess-smoothed lines. The shaded area represents the 95% confidence intervals.
Figure 5
Figure 5
Infant oral microbiome evenness (a) and richness (b) increases after the first 6 months of life.
Figure 6
Figure 6
Pairwise Bray–Curtis dissimilarities between subsequent time points over two years of life. Each point represents the Bray-Curtis distance between samples at consecutive time points for an individual infant. Age on the X axis represents the latter sample time point in the comparison. Loess lines are fitted to the data with shaded areas representing the 95% confidence intervals.
Figure 7
Figure 7
Explained variance (R²) of factors influencing the oral microbiome.
Figure 8
Figure 8
Reduced levels of S. lugdunensis in the oral cavity of infants born to mothers who received antibiotics during delivery (n = 35) compared to those born to mothers who did not receive antibiotics (n = 44) (P = 0.023). Data shown for the 1-month time point, with 1 month as the reference for age comparisons.
Figure 9
Figure 9
A higher levels of S. salivarius group 1 and S. parasanguinis in the oral cavity of infants who used a pacifier in the first week post-partum (n = 18) compared to those who did not use pacifiers (n = 61) (P =0.031, P = 0.004, respectively). Data shown for the 1-month time point, with 1 month as the reference for age comparisons.
Figure 10
Figure 10
Introduction of solid foods is associated with multiple shifts in the infant oral microbiome.
Figure 11
Figure 11
The oral microbiome at 24 months of age differs based on breastfeeding. Those who were weaned at this age had increased S. mitis and S. lugdunensis and reduced N. subflava (P = 0.041, P = 0.006, and P = 0.007, respectively).
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