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

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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.

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Acknowledgments

We thank Theresa Rodger for providing outstanding technical assistance and Dr. Karla M. Stucker for her critical review and editing of the manuscript. The clinical sample and data collection for this study were supported by a National Institute of Allergy and Infectious Diseases grant (AI U19-AI-095277) and a Vanderbilt Institute for Clinical and Translational Research Grant (UL1 TR000445) from NCATS/NIH. The sequencing work was generously supported by the NIAID/NIH Genomic Centers for Infectious Diseases (GCID) program (U19-AI-110819). MHS and SRD are supported by U19AI095227 supplement. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

Authors’ Contributions

MHS, RSP, MLM, LJA, KEN, TVH, and SRD conceived and designed the study. CRS, RSP, and TH collected clinical samples, and MHS, MT, RH, and SRD performed sample processing and 16S rRNA gene sequencing. MHS, AT, KEN, and SRD performed the 16S rRNA gene sequence data analysis. MHS, CRS, AT, MLM, LJA, KEN, TVH, and SRD wrote the manuscript, and all authors reviewed and approved the final version.

Conflict of Interest

The authors declare that they have no competing interests.

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Authors and Affiliations

  1. Infectious Diseases Group, J. Craig Venter Institute, 9704 Medical Center Dr., Rockville, MD, 20850, USA

    Meghan H. Shilts, Asmik Akopov, Rebecca Halpin & Suman R. Das

  2. Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN, USA

    Christian Rosas-Salazar

  3. Genomic Medicine Group, J. Craig Venter Institute, Rockville, MD, USA

    Andrey Tovchigrechko, Manolito Torralba & Karen E. Nelson

  4. Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA

    Emma K. Larkin, R. Stokes Peebles & Tina V. Hartert

  5. Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA

    Martin L. Moore & Larry J. Anderson

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  1. Meghan H. Shilts
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Correspondence to Suman R. Das.

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Shilts, M.H., Rosas-Salazar, C., Tovchigrechko, A. et al. Minimally Invasive Sampling Method Identifies Differences in Taxonomic Richness of Nasal Microbiomes in Young Infants Associated with Mode of Delivery. Microb Ecol 71, 233–242 (2016). https://doi.org/10.1007/s00248-015-0663-y

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