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

Bogaert D, Keijser B, Huse S, Rossen J, Veenhoven R, van Gils E, Bruin J, Montijn R, Bonten M, Sanders E - PLoS ONE (2011)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Paediatric Infectious Diseases and Immunology, University Medical Center Utrecht-Wilhelmina Children's Hospital, Utrecht, The Netherlands. d.bogaert@umcutrecht.nl

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.

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Principal component analysis of the individual NP communities.We observed three individual clusters/axes surrounding a centre of profiles, with in green individual profiles depicting predominantly (>50% of sequences) Moraxella OTU 1, in blue microbiota profiles depicting predominantly H. influenzae OTU 2, and in red microbiota profiles depicting predominantly Streptococcus OTU 3. Mixed phyla profiles (no single OTU is representing >50% of sequences) cluster in the centre of this PCA plot.
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pone-0017035-g002: Principal component analysis of the individual NP communities.We observed three individual clusters/axes surrounding a centre of profiles, with in green individual profiles depicting predominantly (>50% of sequences) Moraxella OTU 1, in blue microbiota profiles depicting predominantly H. influenzae OTU 2, and in red microbiota profiles depicting predominantly Streptococcus OTU 3. Mixed phyla profiles (no single OTU is representing >50% of sequences) cluster in the centre of this PCA plot.

Mentions: Principal component analysis identified 3 distinct clusters of microbiota profiles correlating strongly with a predominance (>50% of sequences per sample) of single OTU's, i.e. Moraxella (OTU 1), Haemophilus influenzae (OTU 2), and Streptococci (OTU 3), respectively, connected by a group of community profiles representing mixed microbiota (Figure 2). Additionally, we observed transition zones for microbiota profiles between the Haemophilus- and Moraxella-dominated clusters, but not between Haemophilus- or Moraxella-dominated clusters and the Streptococci-dominated cluster, which might implicate potential interactions between microbiota profiles.


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

Bogaert D, Keijser B, Huse S, Rossen J, Veenhoven R, van Gils E, Bruin J, Montijn R, Bonten M, Sanders E - PLoS ONE (2011)

Principal component analysis of the individual NP communities.We observed three individual clusters/axes surrounding a centre of profiles, with in green individual profiles depicting predominantly (>50% of sequences) Moraxella OTU 1, in blue microbiota profiles depicting predominantly H. influenzae OTU 2, and in red microbiota profiles depicting predominantly Streptococcus OTU 3. Mixed phyla profiles (no single OTU is representing >50% of sequences) cluster in the centre of this PCA plot.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3046172&req=5

pone-0017035-g002: Principal component analysis of the individual NP communities.We observed three individual clusters/axes surrounding a centre of profiles, with in green individual profiles depicting predominantly (>50% of sequences) Moraxella OTU 1, in blue microbiota profiles depicting predominantly H. influenzae OTU 2, and in red microbiota profiles depicting predominantly Streptococcus OTU 3. Mixed phyla profiles (no single OTU is representing >50% of sequences) cluster in the centre of this PCA plot.
Mentions: Principal component analysis identified 3 distinct clusters of microbiota profiles correlating strongly with a predominance (>50% of sequences per sample) of single OTU's, i.e. Moraxella (OTU 1), Haemophilus influenzae (OTU 2), and Streptococci (OTU 3), respectively, connected by a group of community profiles representing mixed microbiota (Figure 2). Additionally, we observed transition zones for microbiota profiles between the Haemophilus- and Moraxella-dominated clusters, but not between Haemophilus- or Moraxella-dominated clusters and the Streptococci-dominated cluster, which might implicate potential interactions between microbiota profiles.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Paediatric Infectious Diseases and Immunology, University Medical Center Utrecht-Wilhelmina Children's Hospital, Utrecht, The Netherlands. d.bogaert@umcutrecht.nl

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 MeSH
Related in: MedlinePlus