Maturation of the infant respiratory microbiota, environmental drivers, and health consequences

Astrid A.T.M. Bosch, Wouter A.A. De Steenhuijsen Piters, Marlies A van Houten, Mei Ling J N Chu, Giske Biesbroek, Jolanda Kool, Paula Jm Pernet, Pieter-Kees C M de Groot, Marinus J.C. Eijkemans, Bart J F Keijser, Elisabeth A.M. Sanders, Debby Bogaert*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

5 Citations (Scopus)


Rationale: Perinatal and postnatal influences are presumed important drivers of the early-life respiratory microbiota composition. We hypothesized that the respiratory microbiota composition and development in infancy is affecting microbiota stability and thereby resistance against respiratory tract infections (RTIs) over time. Objectives: To investigate common environmental drivers, including birth mode, feeding type, antibiotic exposure, and crowding conditions, in relation to respiratory tract microbiota maturation and stability, and consecutive risk of RTIs over the first year of life. Methods: In a prospectively followed cohort of 112 infants, we characterized the nasopharyngeal microbiota longitudinally from birth on (11 consecutive sample moments and the maximum three RTI samples per subject; in total, n = 1,121 samples) by 16S-rRNA gene amplicon sequencing. Measurements and Main Results: Using a microbiota-based machine-learning algorithm, we found that children experiencing a higher number of RTIs in the first year of life already demonstrate an aberrant microbial developmental trajectory from the first month of life on as compared with the reference group (0-2 RTIs/yr). The altered microbiota maturation process coincided with decreased microbial community stability, prolonged reduction of Corynebacterium and Dolosigranulum, enrichment of Moraxella very early in life, followed by later enrichment of Neisseria and Prevotella spp. Independent drivers of these aberrant developmental trajectories of respiratory microbiota members were mode of delivery, infant feeding, crowding, and recent antibiotic use. Conclusions: Our results suggest that environmental drivers impact microbiota development and, consequently, resistance against development of RTIs. This supports the idea that microbiota form the mediator between early-life environmental risk factors for and susceptibility to RTIs over the first year of life.

Original languageEnglish
Pages (from-to)1582-1590
Number of pages9
JournalAmerican Journal of Respiratory and Critical Care Medicine
Issue number12
Publication statusPublished - 15 Dec 2017


  • Development
  • Nasopharynx
  • Respiratory microbiota
  • Respiratory tract infections
  • Risk factors


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