A Study of the Infant Nasal Microbiome Development over the First Year of Life and in Relation to Their Primary Adult Caregivers Using cpn60 Universal Target (UT) as a Phylogenetic Marker

Abstract

Whereas the infant gut microbiome is the subject of intense study, relatively little is known regarding the nares microbiome in newborns and during early life. This study aimed to survey the typical composition and diversity of human anterior nare microflora for developing infants over time, and to explore how these correlate to their primary caregivers. Single nare swabs were collected at five time points over a one-year period for each subject from infant-caregiver pairs. Our study comprised of 50 infants (recruited at 2 weeks, post delivery) and their 50 primary caregivers. Applying the chaperonin-60 (cpn60) universal target (UT) amplicon as our molecular barcoding marker to census survey the microbial communities, we longitudinally surveyed infant nares microbiota at 5 time points over the course of the first year of life. The inter- and intra-subject diversity was catalogued and compared, both longitudinally and relative to their adult primary caregivers. Although within-subject variability over time and inter-subject variability were both observed, the assessment detected only one or two predominant genera for individual infant samples, belonging mainly to phyla Actinobacteria, Firmicutes, and Proteobacteria. Consistent with previously observed microbial population dynamics in other body sites, the diversity of nares microflora increased over the first year of life and infants showed differential operational taxonomic units (OTUs) relative to their matched primary caregiver. The collected evidence also support that both temporal and seasonal changes occur with respect to carriage of potentially pathogenic bacteria (PPBs), which may influence host predisposition to infection. This pilot study surveying paired infant/caregiver nare microbiomes provides novel longitudinal diversity information that is pertinent to better understanding nare microbiome development in infants.

Fig 1

Average relative abundance of phyla (A) and genera (B) in the nares microbiota of infants and their associated primary caregivers across five time points during the first year of life. Relative abundance depicted represents the average values derived from each subject grouping at each sampling time point T1-T5 (range: 22–35 subjects per time point, in a possible maximum n = 40 study subject pairs).

Fig 2

Relative abundance (A, B) and carriage (C, D) of potentially pathogenic bacteria (PPB) in the nares of infants and their primary caregivers over the first year of life. Relative abundance depicted represents the average values derived from each subject grouping at each sampling time point T1-T5 (range: 22–35 subjects per time point, in a possible maximum of (n = 40) study subject pairs). Carriage depicted represents the percentage of individuals carrying the organism at each time point.

Fig 3

Heatmap (A) and Phylogenetic Tree (B) of Morisita-Horn diversity indices between nares microbiota derived from infants (I) and their primary caregivers (P) at each time point (T1-T5). A) Gradations in the shading intensity reflect the degree of similarity for Morisita-Horn diversity indices between sampling time points, with darkest hue intensities denoting most dissimilarity (approaching a Morisita-Horn diversity index value of 0.0) and brightest hue intensities denoting the most similarity (diversity index value approaching 1.0). B) Phylogenetic distance was calculated using the unweighted pair group method with arithmetic mean (UPGMA) for each time point, based on a random subsampling of 25,000 OTUs from all subjects per group. The scale bar depicts an inferred phylogenetic distance (Morisita-Horn diversity index) of 0.04 (no units).