Bacterial community structure and effects of picornavirus infection on the anterior nares microbiome in early childhood

Abstract

Background: Little is known regarding the nasal microbiome in early childhood and the impact of respiratory infection on the infants' nasal microbial composition. Here we investigated the temporal dynamics and diversity of the bacterial composition in the anterior nares in children attending daycare centers.

Results: For our investigation, we considered 76 parental-taken nasal swabs of 26 children (aged 13 to 36 months) collected over a study period of 3 months. Overall, there was no significant age-specific effect or seasonal shift in the nasal bacterial community structure. In a sub-sample of 14 healthy children the relative abundance of individual taxa as well as the overall diversity did not reveal relevant changes, indicating a stable community structure over the entire study period. Moreover, the nasal bacterial profiles clustered subject-specific with Bray-Curtis similarities being elevated in intra-subject calculations compared to between-subject calculations. The remaining subset of 12 children provided samples taken during picornavirus infection (PVI) and either before or after a PVI. We detected an association between the relative abundance of members of the genus Streptococcus and PV when comparing both (i) samples taken during PVI with samples out of 14 healthy children and (ii) samples taken during PVI with samples taken after PVI within the same individual. In addition, the diversity was higher during PVI than after infection.

Conclusions: Our findings suggest that a personalized structure of the nasal bacterial community is established already in early childhood and could be detected over a timeframe of 3 months. Studies following infants over a longer time with frequent swab sampling would allow investigating whether certain parameter of the bacterial community, such as the temporal variability, could be related to viral infection.

Keywords: Anterior nares; Early childhood; Picornavirus infection; Temporal diversity; Temporal dynamics.

Fig. 1

Average relative abundance of bacterial phyla and genera in the anterior nares. a phyla and b genera of 14 healthy children at three different collection days roughly 1 month apart (M1, n = 14; M2, n = 14; M3 n = 14). Comparison of the mean relative abundance of (c) phyla and (d) genera in children infected with picornavirus (n = 12) and healthy children (n = 12)

Fig. 2

Alpha-diversity of the anterior nares bacterial community by Shannon diversity. a Shannon diversity of 14 healthy children on three different collection days, roughly 1 month apart (M1, n = 14; M2, n = 14; M3 n = 14). b Shannon diversity was compared between samples of healthy children (n = 12) and samples of additional 12 infected children taken during picornavirus infection (PVI) (n = 12). c Shannon diversity from samples taken before and during PVI within the same infected children (n = 6). d Shannon diversity from samples taken during and after PVI within the same infected children (n = 8). The Shannon diversity of each child is represented by one dot

Fig. 3

Non-metric multidimensional scaling (nMDS) of the global nasal bacterial community structure and index of multivariate dispersion (IMD). a nMDS and c IMD in 14 healthy children between the bacterial profiles of three sampling times for each healthy child (n = 42). b nMDS and d IMD of 12 infected children, where each child is represented by one color with either two or three samples per child (during picornavirus infection (PVI) n = 12, before PVI n = 9, after PVI n = 13). The color assignment for the IMD corresponds to the ones in the nMDS plot of each child. R: R-value, indicates the degree of separation between groups; P: p-value; 2D Stress: indicates the two-dimensional stress level on the plot

Fig. 4

Comparison of the average distance between bacterial profiles of three different collection days roughly 1 month apart of 14 healthy children (left) with mean of mean distances based on permutations using the Bray-Curtis similarity algorithm (right)