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: 3.53). 02/2011; 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 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.

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Available from: Debby Bogaert, Aug 08, 2015
    • "Amplicon library preparation. Generation of a PCR amplicon library was performed by amplification of the 16S ribosomal RNA gene V5–V7 hypervariable region as previously described (Bogaert et al., 2011), except templates containing ⩽ 10 pg μl − 1 DNA were cycled 35 times instead of 30 times for adequate amplicon recovery. The library was sequenced in three runs with the 454 GS-FLX-Titanium Sequencer "
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    ABSTRACT: Bacterial pneumonia is a major cause of morbidity and mortality in elderly. We hypothesize that dysbiosis between regular residents of the upper respiratory tract (URT) microbiome, that is balance between commensals and potential pathogens, is involved in pathogen overgrowth and consequently disease. We compared oropharyngeal microbiota of elderly pneumonia patients (n = 100) with healthy elderly (n = 91) by 16S-rRNA-based sequencing and verified our findings in young adult pneumonia patients (n = 27) and young healthy adults (n = 187). Microbiota profiles differed significantly between elderly pneumonia patients and healthy elderly (PERMANOVA, Po0.0005). Highly similar differences were observed between microbiota profiles of young adult pneumonia patients and their healthy controls. Clustering resulted in 11 (sub)clusters including 95% (386/405) of samples. We observed three microbiota profiles strongly associated with pneumonia (Po0.05) and either dominated by lactobacilli (n = 11), Rothia (n = 51) or Streptococcus (pseudo)pneumoniae (n = 42). In contrast, three other microbiota clusters (in total n=183) were correlated with health (Po0.05) and were all characterized by more diverse profiles containing higher abundances of especially Prevotella melaninogenica, Veillonella and Leptotrichia. For the remaining clusters (n = 99), the association with health or disease was less clear. A decision tree model based on the relative abundance of five bacterial community members in URT microbiota showed high specificity of 95% and sensitivity of 84% (89% and 73%, respectively, after cross-validation) for differentiating pneumonia patients from healthy individuals. These results suggest that pneumonia in elderly and young adults is associated with dysbiosis of the URT microbiome with bacterial overgrowth of single species and absence of distinct anaerobic bacteria. Whether the observed microbiome changes are a cause or a consequence of the development of pneumonia or merely coincide with disease status remains a question for future research.
    The ISME Journal 07/2015; DOI:10.1038/ismej.2015.99 · 9.27 Impact Factor
    • "Amplicon library preparation. Generation of a PCR amplicon library was performed by amplification of the 16S ribosomal RNA gene V5–V7 hypervariable region as previously described (Bogaert et al., 2011), except templates containing ⩽ 10 pg μl − 1 DNA were cycled 35 times instead of 30 times for adequate amplicon recovery. The library was sequenced in three runs with the 454 GS-FLX-Titanium Sequencer "
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    ABSTRACT: Respiratory tract infections are a major global health concern, accounting for high morbidity and mortality, especially in young children and elderly individuals. Traditionally, highly common bacterial respiratory tract infections, including otitis media and pneumonia, were thought to be caused by a limited number of pathogens including Streptococcus pneumoniae and Haemophilus influenzae. However, these pathogens are also frequently observed commensal residents of the upper respiratory tract (URT) and form-together with harmless commensal bacteria, viruses and fungi-intricate ecological networks, collectively known as the 'microbiome'. Analogous to the gut microbiome, the respiratory microbiome at equilibrium is thought to be beneficial to the host by priming the immune system and providing colonization resistance, while an imbalanced ecosystem might predispose to bacterial overgrowth and development of respiratory infections. We postulate that specific ecological perturbations of the bacterial communities in the URT can occur in response to various lifestyle or environmental effectors, leading to diminished colonization resistance, loss of containment of newly acquired or resident pathogens, preluding bacterial overgrowth, ultimately resulting in local or systemic bacterial infections. Here, we review the current body of literature regarding niche-specific upper respiratory microbiota profiles within human hosts and the changes occurring within these profiles that are associated with respiratory infections. © 2015 The Author(s) Published by the Royal Society. All rights reserved.
    Philosophical Transactions of The Royal Society B Biological Sciences 07/2015; 370(1675). DOI:10.1098/rstb.2014.0294 · 6.31 Impact Factor
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    • "In the pharynx, many pathogenic species, including Streptococcus pneumonia, Staphylococcus aureus, H. influenza and Mycoplasma pneumonia, are well-adapted to the pharyngeal environment and become established in the resident microbiome, rendering the host asymptomatic [19] [20] [21]. Epidemiological studies suggested that the proportion of aforementioned resident pathogens in human hosts varies by season, as does the incidence of RTIs attributed to them [22]. Our recent study revealed that for each species in a set of common bacterial respiratory pathogens, there exists an abundance threshold, above which the risk of infection increases. "
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    ABSTRACT: The human pharyngeal microbiome, which resides at the juncture of digestive and respiratory tracts, may have an active role in the prevention of respiratory tract infections, similar to the actions of the intestinal microbiome against enteric infections. Recent studies have demonstrated that the pharyngeal microbiome comprises an abundance of bacterial species that interact with the local epithelial and immune cells, and together, they form a unique micro-ecological system. Most of the microbial species in microbiomes are obligate symbionts constantly adapting to their unique surroundings. Indigenous commensal species are capable of both maintaining dominance and evoking host immune responses to eliminate invading species. Temporary damage to the pharyngeal microbiome due to the impaired local epithelia is also considered an important predisposing risk factor for infections. Therefore, reinforcement of microbiome homeostasis to prevent invasion of infection-prone species would provide a novel treatment strategy in addition to antibiotic treatment and vaccination. Hence continued research efforts on evaluating probiotic treatment and developing appropriate procedures are necessary to both prevent and treat respiratory infections.
    Genomics Proteomics & Bioinformatics 06/2014; 12(3). DOI:10.1016/j.gpb.2014.06.001
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