Early respiratory microbiota composition determines bacterial succession patterns and respiratory health in children

Am J Respir Crit Care Med. 2014 Dec 1;190(11):1283-92. doi: 10.1164/rccm.201407-1240OC.


Rationale: Many bacterial pathogens causing respiratory infections in children are common residents of the respiratory tract. Insight into bacterial colonization patterns and microbiota stability at a young age might elucidate healthy or susceptible conditions for development of respiratory disease.

Objectives: To study bacterial succession of the respiratory microbiota in the first 2 years of life and its relation to respiratory health characteristics.

Methods: Upper respiratory microbiota profiles of 60 healthy children at the ages of 1.5, 6, 12, and 24 months were characterized by 16S-based pyrosequencing. We determined consecutive microbiota profiles by machine-learning algorithms and validated the findings cross-sectionally in an additional cohort of 140 children per age group.

Measurements and main results: Overall, we identified eight distinct microbiota profiles in the upper respiratory tract of healthy infants. Profiles could already be identified at 1.5 months of age and were associated with microbiota stability and change over the first 2 years of life. More stable patterns were marked by early presence and high abundance of Moraxella and Corynebacterium/Dolosigranulum and were positively associated with breastfeeding in the first period of life and with lower rates of parental-reported respiratory infections in the consecutive periods. Less stable profiles were marked by high abundance of Haemophilus or Streptococcus.

Conclusions: These findings provide novel insights into microbial succession in the respiratory tract in infancy and link early-life profiles to microbiota stability and respiratory health characteristics. New prospective studies should elucidate potential implications of our findings for early diagnosis and prevention of respiratory infections. Clinical trial registered with www.clinicaltrials.gov (NCT00189020).

Keywords: children; microbial communities; microbiota; respiratory tract; succession.

Publication types

  • Randomized Controlled Trial
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Age Distribution
  • Anti-Bacterial Agents
  • Bacteria / isolation & purification*
  • Breast Feeding
  • Bronchodilator Agents / therapeutic use
  • Child, Preschool
  • Corynebacterium / isolation & purification
  • Corynebacterium / physiology
  • Disease Susceptibility
  • Humans
  • Infant
  • Microbiota / physiology*
  • Moraxella / isolation & purification
  • Moraxella / physiology
  • Nasopharynx / microbiology*
  • Netherlands
  • Respiratory Tract Infections / drug therapy
  • Respiratory Tract Infections / microbiology*


  • Anti-Bacterial Agents
  • Bronchodilator Agents

Associated data

  • ClinicalTrials.gov/NCT00189020