Minimally Invasive Sampling Method Identifies Differences in Taxonomic Richness of Nasal Microbiomes in Young Infants Associated with Mode of Delivery

Abstract

To date, there is a limited understanding of the role of the airway microbiome in the early life development of respiratory diseases such as asthma, partly due to a lack of simple and minimally invasive sample collection methods. In order to characterize the baseline microbiome of the upper respiratory tract (URT) in infants, a comparatively non-invasive method for sampling the URT microbiome suitable for use in infants was developed. Microbiome samples were collected by placing filter paper in the nostrils of 33 healthy, term infants enrolled as part of the Infant Susceptibility to Pulmonary Infections and Asthma Following RSV Exposure (INSPIRE) study. After bacterial genomic DNA was extracted from the filters, amplicons were generated with universal primers targeting the V1-V3 region of the 16S rRNA gene. This method was capable of capturing a wide variety of taxa expected to inhabit the nasal cavity. Analyses stratifying subjects by demographic and environmental factors previously observed or predicted to influence microbial communities were performed. Microbial community richness was found to be higher in infants who had been delivered via Cesarean section and in those who had been formula-fed; an association was observed between diet and delivery, which confounds this analysis. We have established a baseline URT microbiome using a non-invasive filter paper nasal sampling for this population, and future studies will be performed in this large observational cohort of infants to investigate the relationship between viral infections, the URT microbiota, and the development of childhood wheezing illnesses.

Keywords: 16S rRNA; Microbiome; Next-generation sequencing; Upper respiratory tract.

Fig. 1

a Stacked bar graph showing genus level taxonomic composition for each individual sample, expressed as a proportion of reads. The 20 genera with the highest average relative abundance are shown. Samples are stratified by mode of delivery and sorted by Corynebacterium abundance. b. Box plots showing relative abundance of the top 20 most highly represented genera, averaged over all samples for each delivery mode.

Fig. 2

a Incidence-based richness estimates at the genus level and corresponding standard errors for samples grouped by delivery type. The Chao, first-order jackknife (jack1), and bootstrap (boot) indices were calculated after rarefying each sample to the minimum sequence count multiple times (n = 400) and averaging the results. Taxonomic richness at the genus level was consistently higher in the nasal microbiota of infants who had been delivered via Cesarean section. b. Heatmap of abundance profiles at the genus level. Infant age, in days, and delivery mode are labeled for each sample. Two clades emerge, colored green and orange. Clustering due to delivery mode can be observed.