Variability and Diversity of Nasopharyngeal Microbiota in Children: A Metagenomic Analysis

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 1000000 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.

Viruses and bacteria in Th2‐biased allergic airway disease

“…Here, bacteria that cause airway diseases are listed in Table 2. In infants, the nasopharynx microbiome is qualitatively dominated by six common genera: Haemophilus, Streptococcus, Moraxella (those three genera are common in ARI), Staphylococcus, Alloiococcus, and Corynebacterium (more common in healthy samples) (6), which is consistent with previous studies in children (25,26) and in adults (27). Similarly, Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, Streptococcus pyogenes, and Staphylococcus aureus (S. aureus) were also observed in the nasopharynx swabs of Asian infants (28).…”

Culture and molecular-based profiles show shifts in bacterial communities of the upper respiratory tract that occur with age

“…When all samples were clustered based on phylogenetic differences, four groups emerged two of which were enriched with samples from the nasopharynx of children (Figure 2c). Similarly, an ordination of NP microbial profiles from children in the Netherlands of similar age revealed four clusters, three dominated by a single OTU (Moraxella, Haemophilus or Streptococcus) and one, which was mixed (Bogaert et al, 2011). It is unknown if the fourth mixed group of child samples resembled adult profiles, as none were included, however, this aligns well with our data, suggesting that NP bacterial communities of young children often have low diversity owing to the dominance by a small number of bacterial species.…”

“…A few microbiome studies have focused on describing the communities at these sites (Lemon et al, 2010;Charlson et al, 2011;Faust et al, 2012), however, only Bogaert et al (2011) looked in depth at children under 2 years of age, the population at greatest risk of respiratory illness and invasive pneumococcal disease. No reports, however, have looked at the healthy URT microbiota from both the perspective of molecular profiling and quantitative culture for all bacteria, an approach that provides a more complete picture of bacterial colonization.…”

Phlyctenular Keratoconjunctivitis Associated withDolosigranulum pigrum

“…pigrum was isolated from the conjunctivae of this patient, who had no exposures that put her at risk of contracting tuberculous or parasitic infections that have been associated with phlyctenulosis. D. pigrum has been found to be part of the core upper respiratory microbiota, 7 but evidence regarding whether it is commensal conjunctival flora is currently lacking. The organism has emerged as a potential pathogen in humans and has been identified in a broad spectrum of diseases, including nosocomial pneumonia and 9 and cystic fibrosis pneumonia.…”