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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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The abundance distributions for the bacterial metacommunity for (a) all taxa, (b) core taxa best predicted by the log-normal model (χ2(4)=2.71; P=0.607) and (c) satellite taxa best predicted by the log-series model (χ2(4)=4.61; P=0.330). The frequency of each log2 abundance class predicted by the log-normal and -series models is shown as a dot.
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fig2: The abundance distributions for the bacterial metacommunity for (a) all taxa, (b) core taxa best predicted by the log-normal model (χ2(4)=2.71; P=0.607) and (c) satellite taxa best predicted by the log-series model (χ2(4)=4.61; P=0.330). The frequency of each log2 abundance class predicted by the log-normal and -series models is shown as a dot.

Mentions: Following categorisation of the CF bacterial taxa into the two groups, the satellite taxa data were fitted with the log-series distribution model, whereas the core group was fitted with the log-normal distribution model (Figure 2). Both the χ2 and Kolmogorov–Smirnov goodness-of-fit tests were employed to evaluate whether the observed distributions were not significantly different from the expected distributions; for example, if P>0.05 for both tests, then a fit could be assumed. For fitting of the log-series model to the satellite taxa, the Kolmogorov–Smirnov test statistic was D=0.072, whereas the approximate critical value at the P<0.05 level was greater, D0.05=0.109. Similarly, for fitting the log normal to the core group, the values obtained were D=0.152 and D0.05=0.230. In addition, for both the log-series and -normal model fits, the χ2 values were not significantly different at the P<0.05 level (Figure 2). Therefore, as the observed distributions were not significantly different from the expected, the log-series and -normal models that had been fitted, respectively, to the satellite and core groups could be accepted. Conversely, no good fit was obtained for the overall empirical SAD by either of the two models (P<0.05 in each case for both types of goodness-of-fit tests). It has been generally accepted that empirical SADs for large communities of animal or plant species tend towards the log normal (Preston, 1948; Gaston and Blackburn, 2000; Magurran and Henderson, 2003). However, this view has begun to change, as increasing lines of evidence have demonstrated that large communities are typically characterised by an excess of rare species, resulting in a negatively skewed distribution (Gaston and Blackburn, 2000; Hubbell, 2001; Magurran, 2004). Despite the CF metacommunity investigated here having only relatively low bacterial diversity compared with other systems such as soil, when the distribution for all CF bacterial taxa was plotted (Figure 2), or rather when the core and satellite group distributions were superimposed, a negatively skewed distribution characterised by rare taxa was the result.


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)

The abundance distributions for the bacterial metacommunity for (a) all taxa, (b) core taxa best predicted by the log-normal model (χ2(4)=2.71; P=0.607) and (c) satellite taxa best predicted by the log-series model (χ2(4)=4.61; P=0.330). The frequency of each log2 abundance class predicted by the log-normal and -series models is shown as a dot.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig2: The abundance distributions for the bacterial metacommunity for (a) all taxa, (b) core taxa best predicted by the log-normal model (χ2(4)=2.71; P=0.607) and (c) satellite taxa best predicted by the log-series model (χ2(4)=4.61; P=0.330). The frequency of each log2 abundance class predicted by the log-normal and -series models is shown as a dot.
Mentions: Following categorisation of the CF bacterial taxa into the two groups, the satellite taxa data were fitted with the log-series distribution model, whereas the core group was fitted with the log-normal distribution model (Figure 2). Both the χ2 and Kolmogorov–Smirnov goodness-of-fit tests were employed to evaluate whether the observed distributions were not significantly different from the expected distributions; for example, if P>0.05 for both tests, then a fit could be assumed. For fitting of the log-series model to the satellite taxa, the Kolmogorov–Smirnov test statistic was D=0.072, whereas the approximate critical value at the P<0.05 level was greater, D0.05=0.109. Similarly, for fitting the log normal to the core group, the values obtained were D=0.152 and D0.05=0.230. In addition, for both the log-series and -normal model fits, the χ2 values were not significantly different at the P<0.05 level (Figure 2). Therefore, as the observed distributions were not significantly different from the expected, the log-series and -normal models that had been fitted, respectively, to the satellite and core groups could be accepted. Conversely, no good fit was obtained for the overall empirical SAD by either of the two models (P<0.05 in each case for both types of goodness-of-fit tests). It has been generally accepted that empirical SADs for large communities of animal or plant species tend towards the log normal (Preston, 1948; Gaston and Blackburn, 2000; Magurran and Henderson, 2003). However, this view has begun to change, as increasing lines of evidence have demonstrated that large communities are typically characterised by an excess of rare species, resulting in a negatively skewed distribution (Gaston and Blackburn, 2000; Hubbell, 2001; Magurran, 2004). Despite the CF metacommunity investigated here having only relatively low bacterial diversity compared with other systems such as soil, when the distribution for all CF bacterial taxa was plotted (Figure 2), or rather when the core and satellite group distributions were superimposed, a negatively skewed distribution characterised by rare taxa was the result.

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