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. 2017 Aug;65(6):984-990.
doi: 10.1136/jim-2017-000414. Epub 2017 Mar 31.

Nasopharyngeal microbiome in premature infants and stability during rhinovirus infection

Geovanny F Perez  1   2   3   4 , Marcos Pérez-Losada  4   5   6 , Natalia Isaza  2   7 , Mary C Rose  1   2   3   4   8 , Anamaris M Colberg-Poley  2   3   4   8 , Gustavo Nino  1   2   3   4
Affiliations

Nasopharyngeal microbiome in premature infants and stability during rhinovirus infection

Geovanny F Perez et al. J Investig Med. 2017 Aug.

Abstract

Rationale: The nasopharyngeal (NP) microbiota of newborns and infants plays a key role in modulating airway inflammation and respiratory symptoms during viral infections. Premature (PM) birth modifies the early NP environment and is a major risk factor for severe viral respiratory infections. However, it is currently unknown if the NP microbiota of PM infants is altered relative to full-term (FT) individuals.

Objectives: To characterize the NP microbiota differences in preterm and FT infants during rhinovirus (RV) infection.

Methods: We determined the NP microbiota of infants 6 months to ≤2 years of age born FT (n=6) or severely PM<32 weeks gestation (n=7). We compared microbiota composition in healthy NP samples and performed a longitudinal analysis during naturally occurring RV infections to contrast the microbiota dynamics in PM versus FT infants.

Results: We observed significant differences in the NP bacterial community of PM versus FT. NP from PM infants had higher within-group dissimilarity (heterogeneity) relative to FT infants. Bacterial composition of NP samples from PM infants showed increased Proteobacteria and decreased in Firmicutes. There were also differences in the major taxonomic groups identified, including Streptococcus, Moraxella, and Haemophilus. Longitudinal data showed that these prematurity-related microbiota features persisted during RV infection.

Conclusions: PM is associated with NP microbiota changes beyond the neonatal stage. PM infants have an NP microbiota with high heterogeneity relative to FT infants. These prematurity-related microbiota features persisted during RV infection, suggesting that the NP microbiota of PM may play an important role in modulating airway inflammatory and immune responses in this vulnerable group.

Keywords: Infant, Premature; Microbiota.

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Conflict of interest statement

Competing interests: None declared.

Figures

Figure 1
Figure 1
Prematurity-related signatures in global nasopharyngeal microbiota. Bars represent taxonomic profiles of 19 nasopharyngeal microbiota from 12 children (6 paired samples and 7 single samples) analyzed via PacBio sequencing of 16S rRNA amplicons. Each color represents a different genus. FT, full term; PM, premature; rRNA, ribosomal RNA; RV, rhinovirus.
Figure 2
Figure 2
PCoA of seasonal groups (Bray-Curtis distances). These plots show dissimilarities or similarities between groups. PCoA clustered full-term subjects without viral infection (red squares within ellipse). FT, full term; PCoA, principal coordinates analysis; PM, premature.
Figure 3
Figure 3
Differences in OTUs abundance. (A) Extended error bar plot showing the bacterial taxa that have a significant difference (Welch’s t-test and ANOVA; p<0.05) in proportions between groups. (B) Extended error bar plot showing proportions for the most abundant bacterial genera between sample pairs. Significance was tested by Fisher’s test (p<0.05). ANOVA, analysis of variance; FT, full term; NV, no viral infection; OUT, operational taxonomic unit; PM, premature; RV, rhinovirus.
Figure 4
Figure 4
Procrustes analysis of PCoA plots of microbiota with and without RV infection. Nasopharyngeal pair samples collected from the same individual (n=6) are connected by a line that represents dissimilarity between healthy (no virus) and RV infection in the same subject. All pair samples showed dissimilarity (healthy vs RV) but dissimilarities were greater in the premature group. Red=premature; green=full term. PCoA, principal coordinates analysis; RV, rhinovirus.
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