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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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Distribution and dispersal of bacterial taxa across patients. (a) The number of patients for whom each bacterial taxon was observed, plotted against the mean abundance (log10 scale) across all patients (r2=0.44; F1,80=62.2; P<0.0001). (b) Random and non-random dispersal through space visualised by decomposing the overall distribution using an index of dispersion based on the ratio of variance to the mean abundance for each bacterial taxon from the 14 patients sampled. The line depicts the 2.5% confidence limit for the χ2 distribution. The 97.5% confidence limit was not plotted, as no taxon fell below that line.
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fig1: Distribution and dispersal of bacterial taxa across patients. (a) The number of patients for whom each bacterial taxon was observed, plotted against the mean abundance (log10 scale) across all patients (r2=0.44; F1,80=62.2; P<0.0001). (b) Random and non-random dispersal through space visualised by decomposing the overall distribution using an index of dispersion based on the ratio of variance to the mean abundance for each bacterial taxon from the 14 patients sampled. The line depicts the 2.5% confidence limit for the χ2 distribution. The 97.5% confidence limit was not plotted, as no taxon fell below that line.

Mentions: Positive relationships between mean abundance and distribution (number of sites occupied) have been observed at many spatial scales for taxa when classified into different types of ecological organisation (for example, guild or community) (Guo et al., 2000). Within the current study, we also observed a significant positive distribution–abundance relationship (Figure 1). This indicated that the bacterial taxa that were widely distributed throughout the CF airways sampled were more locally abundant than the taxa with a more restricted distribution. Therefore, as has been noted in studies of animal species, the commonness and rarity of bacterial taxa in the CF airway metacommunity were found to be related to their permanence (Magurran and Henderson, 2003).


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)

Distribution and dispersal of bacterial taxa across patients. (a) The number of patients for whom each bacterial taxon was observed, plotted against the mean abundance (log10 scale) across all patients (r2=0.44; F1,80=62.2; P<0.0001). (b) Random and non-random dispersal through space visualised by decomposing the overall distribution using an index of dispersion based on the ratio of variance to the mean abundance for each bacterial taxon from the 14 patients sampled. The line depicts the 2.5% confidence limit for the χ2 distribution. The 97.5% confidence limit was not plotted, as no taxon fell below that line.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig1: Distribution and dispersal of bacterial taxa across patients. (a) The number of patients for whom each bacterial taxon was observed, plotted against the mean abundance (log10 scale) across all patients (r2=0.44; F1,80=62.2; P<0.0001). (b) Random and non-random dispersal through space visualised by decomposing the overall distribution using an index of dispersion based on the ratio of variance to the mean abundance for each bacterial taxon from the 14 patients sampled. The line depicts the 2.5% confidence limit for the χ2 distribution. The 97.5% confidence limit was not plotted, as no taxon fell below that line.
Mentions: Positive relationships between mean abundance and distribution (number of sites occupied) have been observed at many spatial scales for taxa when classified into different types of ecological organisation (for example, guild or community) (Guo et al., 2000). Within the current study, we also observed a significant positive distribution–abundance relationship (Figure 1). This indicated that the bacterial taxa that were widely distributed throughout the CF airways sampled were more locally abundant than the taxa with a more restricted distribution. Therefore, as has been noted in studies of animal species, the commonness and rarity of bacterial taxa in the CF airway metacommunity were found to be related to their permanence (Magurran and Henderson, 2003).

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