Variability and diversity of nasopharyngeal microbiota in children: a metagenomic analysis.

Department of Paediatric Infectious Diseases and Immunology, University Medical Center Utrecht-Wilhelmina Children's Hospital, Utrecht, The Netherlands.
PLoS ONE (Impact Factor: 3.73). 01/2011; 6(2):e17035. DOI: 10.1371/journal.pone.0017035
Source: PubMed

ABSTRACT The nasopharynx is the ecological niche for many commensal bacteria and for potential respiratory or invasive pathogens like Streptococcus pneumoniae, Haemophilus influenzae, and Neisseria meningitidis. Disturbance of a balanced nasopharyngeal (NP) microbiome might be involved in the onset of symptomatic infections with these pathogens, which occurs primarily in fall and winter. It is unknown whether seasonal infection patterns are associated with concomitant changes in NP microbiota. As young children are generally prone to respiratory and invasive infections, we characterized the NP microbiota of 96 healthy children by barcoded pyrosequencing of the V5-V6 hypervariable region of the 16S-rRNA gene, and compared microbiota composition between children sampled in winter/fall with children sampled in spring. The approximately 1,000,000 sequences generated represented 13 taxonomic phyla and approximately 250 species-level phyla types (OTUs). The 5 most predominant phyla were Proteobacteria (64%), Firmicutes (21%), Bacteroidetes (11%), Actinobacteria (3%) and Fusobacteria (1,4%) with Moraxella, Haemophilus, Streptococcus, Flavobacteria, Dolosigranulum, Corynebacterium and Neisseria as predominant genera. The inter-individual variability was that high that on OTU level a core microbiome could not be defined. Microbiota profiles varied strongly with season, with in fall/winter a predominance of Proteobacteria (relative abundance (% of all sequences): 75% versus 51% in spring) and Fusobacteria (absolute abundance (% of children): 14% versus 2% in spring), and in spring a predominance of Bacteroidetes (relative abundance: 19% versus 3% in fall/winter, absolute abundance: 91% versus 54% in fall/winter), and Firmicutes. The latter increase is mainly due to (Brevi)bacillus and Lactobacillus species (absolute abundance: 96% versus 10% in fall/winter) which are like Bacteroidetes species generally related to healthy ecosystems. The observed seasonal effects could not be attributed to recent antibiotics or viral co-infection.The NP microbiota of young children is highly diverse and appears different between seasons. These differences seem independent of antibiotic use or viral co-infection.

  • [Show abstract] [Hide abstract]
    ABSTRACT: Respiratory infections are among the most important causes of morbidity and mortality from infectious diseases worldwide. The most common causative bacterium, Streptococcus pneumoniae, frequently colonises the upper respiratory tract, where it resides mostly asymptomatically. Occasionally, however, S pneumoniae can cause severe disease such as pneumonia. Local host immunity is essential to control colonising pathogens by preventing overgrowth, spread, and invasion. However, age-related immune deficits in elderly people, known as immunosenescence, might contribute to increased disease burden. We review present knowledge about immunosenescence in the respiratory tract against Gram-positive bacteria, particularly S pneumoniae. We discuss the possible underdetection of pneumococcal colonisation in elderly people, and suggest changes to present surveillance methods to improve understanding of the relation between colonisation and disease. We conclude that present knowledge about alteration of host-pathogen interactions by immunosenescence in the respiratory tract is insufficient, and that research is needed to enable improved measures for prevention.
    The lancet. Respiratory medicine. 02/2014; 2(2):141-153.
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Seven-valent pneumococcal conjugate vaccine (PCV-7) is effective against vaccine serotype disease and carriage. Nevertheless, shifts in colonization and disease toward nonvaccine serotypes and other potential pathogens have been described. To understand the extent of these shifts, we analyzed nasopharyngeal microbial profiles of 97 PCV-7-vaccinated infants and 103 control infants participating in a randomized controlled trial in the Netherlands. PCV-7 immunization resulted in a temporary shift in microbial community composition and increased bacterial diversity. Immunization also resulted in decreased presence of the pneumococcal vaccine serotype and an increase in the relative abundance and presence of nonpneumococcal streptococci and anaerobic bacteria. Furthermore, the abundance of Haemophilus and Staphylococcus bacteria in vaccinees was increased over that in controls. This study illustrates the much broader effect of vaccination with PCV-7 on the microbial community than currently assumed, and highlights the need for careful monitoring when implementing vaccines directed against common colonizers.
    Emerging Infectious Diseases 02/2014; 20(2):201-10. · 6.79 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Rationale: The microbial communities inhabiting the upper respiratory tract protect from respiratory infection. The maturity of the immune system is believed to be a major influence on the composition of the microbiome and, in youth, the microbiota and immune system are believed to mature in tandem. With age, immune function declines and susceptibility to respiratory infections is increases. Whether these changes contribute to the microbial composition of the respiratory tract is unknown. Objectives: Our goal was to determine whether the resident microbes of the upper respiratory tract differ between mid-aged adults (18-40 yrs) and the elderly (>65 yrs). Methods: Microbiomes of the anterior nares and oropharynx of elderly individuals were evaluated by 16S rRNA gene sequencing. These communities were compared to data on mid-aged adults obtained from the Human Microbiome Project. Measurements and Main Results: The microbiota of the elderly showed no associations with gender, co-morbidities, residence, or vaccinations. Comparisons of mid-aged adults and elderly demonstrated significant differences in the microbial composition of the anterior nares and oropharynx with age, including a population in the anterior nares of the elderly that more closely resembled the oropharynx than the anterior nares of adults. The elderly oropharyngeal microbiota were characterized by increased abundance of streptococci, specifically, Streptococcus salivarius group species, but not Streptococcus pneumoniae, carriage of which was low (<3% of participants) as demonstrated by PCR (4/123). Conclusions: The Microbial populations of the upper respiratory tract in mid-aged adults and the elderly differ; it is possible these differences contribute to the increased risk of respiratory infections experienced by the elderly.
    Annals of the American Thoracic Society. 03/2014;

Full-text (2 Sources)

Available from
May 31, 2014