Dynamics of oral microbiome acquisition in healthy infants: A pilot study

Abstract

Objectives: The human oral microbiota is one of the most complex bacterial communities in the human body. However, how newborns initially acquire these bacteria remains largely unknown. In this study, we examined the dynamics of oral microbial communities in healthy infants and investigated the influence of the maternal oral microbiota on the acquisition of the infant's oral microbiota. We hypothesized that the infant oral microbial diversity increases with age.

Methods: One hundred and sixteen whole-salivary samples were collected from 32 healthy infants and their biological mothers during postpartum and 9- and 15-month well-infant visits. Bacterial genomic DNA was extracted and sequenced by Human Oral Microbe Identification using Next Generation Sequencing (HOMINGS) methods. The Shannon index was used to measure the microbial diversity of the infant-mother dyads (alpha diversity). The microbial diversity between the mother-infant dyads (beta-diversity) was calculated using the weighted non-phylogenetic Bray-Curtis distance in QIIME 1.9.1. Core microbiome analysis was performed using MicrobiomeAnalyst software. Linear discriminant analysis coupled with effect size analysis was used to identify differentially abundant features between mother and infant dyads.

Results: A total of 6,870,571 16S rRNA reads were generated from paired mother-infant saliva samples. Overall, oral microbial profiles significantly differed between the mother and infant groups (p < 0.001). The diversity of the salivary microbiomes in the infants increased in an age-dependent manner, whereas the core microbiome of the mothers remained relatively stable during the study period. Breastfeeding and gender did not affect the microbial diversity in infants. Moreover, infants had a greater relative abundance of Firmicutes and a lower abundance of Actinobacteria, Bacteroidetes, Fusobacteria, and Proteobacteria than their mothers. The SparCC correlation analysis demonstrated constant changes in infants' oral microbial community network (p < 0.05).

Conclusions: This study provides new evidence that the oral cavities of infants are colonized by a distinct group of bacterial species at birth. The acquisition and diversity of changes in oral microbial composition are dynamic during the first year of an infant's life. Before reaching the second birthday, the composition of the oral microbial community could be more similar to that of their biological mothers.

Keywords: infant-mother dyads; microbial diversity; microbial initial acquisition; oral microbiota; postpartum.

Figure 1

Comparison of the oral microbial alpha diversity between the infant and mother groups. (A) The figure shows a significant difference in the alpha diversity measured by the Shannon index among the three visits in the infant group. *The Kruskal–Wallis one-way analysis of variance. (B) Beta diversity, measured by the Bray-Curtis Index, of mothers and infants. A significant difference was detected between mothers and infants at all three-time points (postpartum, 9 months, and 15 months) for the Shannon index and Bray-Curtis index. (p < 0.001, Wilcoxon–Mann–Whitney test). (C) Relative abundance at the phylum, genus, and species levels. The top 25 most abundant genera and species are plotted. * and ^ indicate that the relative abundance of taxa is significantly different across times in infants and mothers, separately, with adjusted p-value <0.05.

Figure 2

Comparison of core oral microbiome between mothers and infants. The core genera for infants (A) and mothers (B) were defined with 20% sample prevalence and 0.01% relative abundance. The core microbiome of the mothers was relatively stable, while the core oral microbiome in infants evolved over time. For infants, Neisseria, Alloprevotella, and Haemophilus gained abundance after 9 months.

Figure 3

Differentially abundant oral microorganisms between mothers and infants in early life. The genera with significant differences between the mothers and the infants were detected by Linear discriminant analysis effect size test (LEfSe, FDR 0.05, LDA 2.0) using Kruskal–Wallis test for the three visits (A) postpartum, (B) 9 months, and (C) 15 months. Among the genera with a significant difference, mothers have a higher number of genera with higher abundance. The differences in Corynebacterium and Staphylococcus between the mothers and the infants became less significant from postpartum to 15 months of age.

Figure 4

Network analysis of the oral microbiota evolution in infants. The figure indicates the network of microbial communities at the genus level built from SparCC correlation coefficients stratified by feeding methods. The nodes represent genera of bacteria. The edges between the nodes represent the correlation coefficients between genera. The results show that the relationship between the oral microbiomes in infants is constantly changing and that more genera begin to be interconnected over time. The correlation threshold is set at 0.5, p < 0.05.