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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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Relative abundance of all bacterial phyla found in the NP microbiota of 96 infants 18 months of age.A cut-off of 0.1% is used for visual differentiation between predominant and less dominant phyla.
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pone-0017035-g001: Relative abundance of all bacterial phyla found in the NP microbiota of 96 infants 18 months of age.A cut-off of 0.1% is used for visual differentiation between predominant and less dominant phyla.

Mentions: We studied the NP microbiota composition of 96 healthy 18-months old children. Their characteristics are depicted in Table S1. Being aware of the current discussions on the artefacts that may be introduced by pyrosequencing [13], [14], we applied a stringent protocol for filtering and clustering of sequences. The approx. 1 100 000 generated sequences (on average 11000 sequences per sample) yielded about 92 000 unique sequences, representing 13 taxonomic phyla and 243 species-level phyla types (OTUs). The data were normalized for equal numbers of reads per sample. The 5 most predominant phyla were Proteobacteria (64%), Firmicutes (21%), Bacteroidetes (11%), Actinobacteria (3%) and Fusobacteria (1.4%) (Figure 1). In addition, we found representatives of Cyanobacteria, probably reflecting plant chloroplasts obtained through inhalation. Sporadically and/or in low abundance we found sequences for the candidate divisions OD1, TM7 and BRC1 and the phyla Deinococcus-Thermus, Nitrospira, Planctomycetes and Chloroflexi. On a lower taxonomic level, the most prevalent genera were Moraxella (40%), Haemophilus (20%), Streptococcus (12%), and Flavobacterium (10%). Other fairly common genera were Dolosigranulum (5%), Corynebacterium (2%), Neisseria (2%) and Fusobacterium (1%). The 30 most common OTUs representing almost 98% of all reads, and their relative and absolute presence are shown in Table 1 (For the complete list of OTUs; see Table S2). Although the top 6 predominant phyla are identical to those of neighbouring microbiota, the composition, i.e. relative contribution of each phyla to those microbiota seems fairly different. In the oral cavity, microbiota are dominated by Firmicutes followed by Proteobacteria and Bacteroidetes (overall 50% Gram-positive bacteria), whereas the microbiome of the nostril contains more than 80% gram-positive bacteria, mostly Actinobacteria and Firmicutes [15]. These data, therefore, suggest different dynamics (i.e., different biological equilibria) in the NP microbiome.


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)

Relative abundance of all bacterial phyla found in the NP microbiota of 96 infants 18 months of age.A cut-off of 0.1% is used for visual differentiation between predominant and less dominant phyla.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0017035-g001: Relative abundance of all bacterial phyla found in the NP microbiota of 96 infants 18 months of age.A cut-off of 0.1% is used for visual differentiation between predominant and less dominant phyla.
Mentions: We studied the NP microbiota composition of 96 healthy 18-months old children. Their characteristics are depicted in Table S1. Being aware of the current discussions on the artefacts that may be introduced by pyrosequencing [13], [14], we applied a stringent protocol for filtering and clustering of sequences. The approx. 1 100 000 generated sequences (on average 11000 sequences per sample) yielded about 92 000 unique sequences, representing 13 taxonomic phyla and 243 species-level phyla types (OTUs). The data were normalized for equal numbers of reads per sample. The 5 most predominant phyla were Proteobacteria (64%), Firmicutes (21%), Bacteroidetes (11%), Actinobacteria (3%) and Fusobacteria (1.4%) (Figure 1). In addition, we found representatives of Cyanobacteria, probably reflecting plant chloroplasts obtained through inhalation. Sporadically and/or in low abundance we found sequences for the candidate divisions OD1, TM7 and BRC1 and the phyla Deinococcus-Thermus, Nitrospira, Planctomycetes and Chloroflexi. On a lower taxonomic level, the most prevalent genera were Moraxella (40%), Haemophilus (20%), Streptococcus (12%), and Flavobacterium (10%). Other fairly common genera were Dolosigranulum (5%), Corynebacterium (2%), Neisseria (2%) and Fusobacterium (1%). The 30 most common OTUs representing almost 98% of all reads, and their relative and absolute presence are shown in Table 1 (For the complete list of OTUs; see Table S2). Although the top 6 predominant phyla are identical to those of neighbouring microbiota, the composition, i.e. relative contribution of each phyla to those microbiota seems fairly different. In the oral cavity, microbiota are dominated by Firmicutes followed by Proteobacteria and Bacteroidetes (overall 50% Gram-positive bacteria), whereas the microbiome of the nostril contains more than 80% gram-positive bacteria, mostly Actinobacteria and Firmicutes [15]. These data, therefore, suggest different dynamics (i.e., different biological equilibria) in the NP microbiome.

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