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

• Authors: Meghan H. Shilts, J. Craig Venter Institute; Christian Rosas-Salazar, Vanderbilt University; Andrey Tovchigrechko, J. Craig Venter Institute; Emma K. Larkin, Vanderbilt University; Manolito Torralba, J. Craig Venter Institute; Asmik Akopov, J. Craig Venter Institute; Rebecca Halpin, J. Craig Venter Institute; R. Stokes Peebles, Vanderbilt University; Martin Moore, Emory University; Larry Anderson, Emory University; Karen E. Nelson, J. Craig Venter Institute; Tina V. Hartert, Vanderbilt University; Suman R. Das, J. Craig Venter Institute
• Journal Title: Microbial Ecology
• Volume: Volume 71, Number 1
• Publisher: Springer | 2016-01-01, Pages 233-242
• Type of Work: Article | Post-print: After Peer Review
• Publisher DOI: http://doi.org/10.1007/s00248-015-0663-y
• Subjects: Health Sciences, General; Biology, Genetics
• Keywords: Science & Technology; Life Sciences & Biomedicine; Ecology; Marine & Freshwater Biology; Microbiology; Environmental Sciences & Ecology; Microbiome; 16S rRNA; Next-generation sequencing; Upper respiratory tract; SYNCYTIAL-VIRUS BRONCHIOLITIS; CESAREAN DELIVERY; GUT MICROBIOTA; MORAXELLA-CATARRHALIS; BODY HABITATS; ASTHMA; DISEASE; HEALTH; COLONIZATION; ALLERGY

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.