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Partitioning core and satellite taxa from within cystic fibrosis lung bacterial communities.

van der Gast CJ, Walker AW, Stressmann FA, Rogers GB, Scott P, Daniels TW, Carroll MP, Parkhill J, Bruce KD - ISME J (2010)

Bottom Line: Increasingly, culture-independent analyses are expanding the number of bacterial species associated with CF respiratory samples; however, the potential significance of these species is not known.The clinical significance of these core and satellite species findings in the CF lung is discussed.GenBank accession numbers: FM995625–FM997761

View Article: PubMed Central - PubMed

Affiliation: NERC Centre for Ecology and Hydrology, Wallingford, UK. cjvdg@ceh.ac.uk

ABSTRACT
Cystic fibrosis (CF) patients suffer from chronic bacterial lung infections that lead to death in the majority of cases. The need to maintain lung function in these patients means that characterising these infections is vital. Increasingly, culture-independent analyses are expanding the number of bacterial species associated with CF respiratory samples; however, the potential significance of these species is not known. Here, we applied ecological statistical tools to such culture-independent data, in a novel manner, to partition taxa within the metacommunity into core and satellite species. Sputa and clinical data were obtained from 14 clinically stable adult CF patients. Fourteen rRNA gene libraries were constructed with 35 genera and 82 taxa, identified in 2139 bacterial clones. Shannon-Wiener and taxa-richness analyses confirmed no undersampling of bacterial diversity. By decomposing the distribution using the ratio of variance to the mean taxon abundance, we partitioned objectively the species abundance distribution into core and satellite species. The satellite group comprised 67 bacterial taxa from 33 genera and the core group, 15 taxa from 7 genera (including Pseudomonas (1 taxon), Streptococcus (2), Neisseria (2), Catonella (1), Porphyromonas (1), Prevotella (5) and Veillonella (3)], the last four being anaerobes). The core group was dominated by Pseudomonas aeruginosa. Other recognised CF pathogens were rare. Mantel and partial Mantel tests assessed which clinical factors influenced the composition observed. CF transmembrane conductance regulator genotype and antibiotic treatment correlated with all core taxa. Lung function correlated with richness. The clinical significance of these core and satellite species findings in the CF lung is discussed. GenBank accession numbers: FM995625–FM997761

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Dendrograms of bacterial community composition in the 14 patients for (a) all taxa, (b) the core and (c) satellite taxa groups. Patient taxa profiles were compared using the Bray–Curtis quantitative index of similarity and average linkage clustering.
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fig4: Dendrograms of bacterial community composition in the 14 patients for (a) all taxa, (b) the core and (c) satellite taxa groups. Patient taxa profiles were compared using the Bray–Curtis quantitative index of similarity and average linkage clustering.

Mentions: A growing number of studies have observed that bacterial community composition is highly variable between CF patients (Rogers et al., 2005; Harris et al., 2007; Kelpac-Ceraj et al., 2010). Here, similarities and differences in the composition of CF bacterial communities were assayed using the Bray–Curtis quantitative index of similarity (SBC); dendrograms were generated for an average linkage cluster analysis of profiles from all taxa, and the core and satellite groups (Figure 4). The resulting cluster analyses for all taxa also revealed that community composition was highly variable between patients. The mean similarity of the bacterial communities taken pair-wise was 0.56, with a s.d. of ±0.24 (n=91 pair-wise comparisons) (Figure 4). When we examined compositional similarities and differences for members of core and satellite groups between patients, we found that similarity was more conserved for the core group (mean SBC=0.61±0.25) than in the satellite group, which comprised rarer spatially random distributed taxa (SBC=0.02±0.06). The presence and abundance of P. aeruginosa also affected the similarity between patients. When P1, in whom this taxon was not present, was removed from the analyses, the mean similarity of core group members between patients increased to SBC=0.70±0.14 (n=78 pair-wise comparisons).


Partitioning core and satellite taxa from within cystic fibrosis lung bacterial communities.

van der Gast CJ, Walker AW, Stressmann FA, Rogers GB, Scott P, Daniels TW, Carroll MP, Parkhill J, Bruce KD - ISME J (2010)

Dendrograms of bacterial community composition in the 14 patients for (a) all taxa, (b) the core and (c) satellite taxa groups. Patient taxa profiles were compared using the Bray–Curtis quantitative index of similarity and average linkage clustering.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3105771&req=5

fig4: Dendrograms of bacterial community composition in the 14 patients for (a) all taxa, (b) the core and (c) satellite taxa groups. Patient taxa profiles were compared using the Bray–Curtis quantitative index of similarity and average linkage clustering.
Mentions: A growing number of studies have observed that bacterial community composition is highly variable between CF patients (Rogers et al., 2005; Harris et al., 2007; Kelpac-Ceraj et al., 2010). Here, similarities and differences in the composition of CF bacterial communities were assayed using the Bray–Curtis quantitative index of similarity (SBC); dendrograms were generated for an average linkage cluster analysis of profiles from all taxa, and the core and satellite groups (Figure 4). The resulting cluster analyses for all taxa also revealed that community composition was highly variable between patients. The mean similarity of the bacterial communities taken pair-wise was 0.56, with a s.d. of ±0.24 (n=91 pair-wise comparisons) (Figure 4). When we examined compositional similarities and differences for members of core and satellite groups between patients, we found that similarity was more conserved for the core group (mean SBC=0.61±0.25) than in the satellite group, which comprised rarer spatially random distributed taxa (SBC=0.02±0.06). The presence and abundance of P. aeruginosa also affected the similarity between patients. When P1, in whom this taxon was not present, was removed from the analyses, the mean similarity of core group members between patients increased to SBC=0.70±0.14 (n=78 pair-wise comparisons).

Bottom Line: Increasingly, culture-independent analyses are expanding the number of bacterial species associated with CF respiratory samples; however, the potential significance of these species is not known.The clinical significance of these core and satellite species findings in the CF lung is discussed.GenBank accession numbers: FM995625–FM997761

View Article: PubMed Central - PubMed

Affiliation: NERC Centre for Ecology and Hydrology, Wallingford, UK. cjvdg@ceh.ac.uk

ABSTRACT
Cystic fibrosis (CF) patients suffer from chronic bacterial lung infections that lead to death in the majority of cases. The need to maintain lung function in these patients means that characterising these infections is vital. Increasingly, culture-independent analyses are expanding the number of bacterial species associated with CF respiratory samples; however, the potential significance of these species is not known. Here, we applied ecological statistical tools to such culture-independent data, in a novel manner, to partition taxa within the metacommunity into core and satellite species. Sputa and clinical data were obtained from 14 clinically stable adult CF patients. Fourteen rRNA gene libraries were constructed with 35 genera and 82 taxa, identified in 2139 bacterial clones. Shannon-Wiener and taxa-richness analyses confirmed no undersampling of bacterial diversity. By decomposing the distribution using the ratio of variance to the mean taxon abundance, we partitioned objectively the species abundance distribution into core and satellite species. The satellite group comprised 67 bacterial taxa from 33 genera and the core group, 15 taxa from 7 genera (including Pseudomonas (1 taxon), Streptococcus (2), Neisseria (2), Catonella (1), Porphyromonas (1), Prevotella (5) and Veillonella (3)], the last four being anaerobes). The core group was dominated by Pseudomonas aeruginosa. Other recognised CF pathogens were rare. Mantel and partial Mantel tests assessed which clinical factors influenced the composition observed. CF transmembrane conductance regulator genotype and antibiotic treatment correlated with all core taxa. Lung function correlated with richness. The clinical significance of these core and satellite species findings in the CF lung is discussed. GenBank accession numbers: FM995625–FM997761

Show MeSH
Related in: MedlinePlus