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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 richness and abundance of (a) aerobic and anaerobic bacteria and (b) oral microbiota within the whole metacommunity, the core group and the satellite group. Also given are the actual values of taxa richness and abundance (number of clones). Shaded areas represent percentage abundance of Pseudomonas aeruginosa within the whole metacommunity and the core group of bacterial taxa.
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fig3: The richness and abundance of (a) aerobic and anaerobic bacteria and (b) oral microbiota within the whole metacommunity, the core group and the satellite group. Also given are the actual values of taxa richness and abundance (number of clones). Shaded areas represent percentage abundance of Pseudomonas aeruginosa within the whole metacommunity and the core group of bacterial taxa.

Mentions: The satellite group comprised 67 different bacterial taxa from 33 genera and accounted for only 11.1% of the total abundance (Table 2). From the satellite taxa, only 53 taxa were sampled from one individual patient. In contrast, the core group comprised 15 taxa from 7 genera (including Catonella (1 taxon), Neisseria (2), Porphyromonas (1), Prevotella (5), Pseudomonas (1), Streptococcus (2) and Veillonella (3)), accounting for 88.9% of the total abundance (Table 2). The core group was dominated by one taxon, P. aeruginosa, considered previously to be the predominant CF respiratory pathogen. This accounted for 70.6% of the total abundance and was found in all patients (except patient 1 (P1)) (Figure 3). With regard to the distribution of other recognised and candidate CF pathogens, the five recorded pathogens were randomly distributed throughout the patients and were therefore assigned to the satellite taxa group. Each of these CF pathogens was found only in low abundance and in single patients (Achromobacter xylosoxidans (P12, 5 clones), H. influenzae (P14, 5 clones), Staphylococcus aureus (P1, 1 clone), Stenotrophomonas maltophilia (P1, 4 clones) and Streptococcus intermedius/constellatus part of the Streptococcus milleri group (P10, 1 clone)). In total, these represented less than 0.75% of the total abundance. No taxa from the B. cepacia complex were recorded in any individual from the patient cohort.


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 richness and abundance of (a) aerobic and anaerobic bacteria and (b) oral microbiota within the whole metacommunity, the core group and the satellite group. Also given are the actual values of taxa richness and abundance (number of clones). Shaded areas represent percentage abundance of Pseudomonas aeruginosa within the whole metacommunity and the core group of bacterial taxa.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig3: The richness and abundance of (a) aerobic and anaerobic bacteria and (b) oral microbiota within the whole metacommunity, the core group and the satellite group. Also given are the actual values of taxa richness and abundance (number of clones). Shaded areas represent percentage abundance of Pseudomonas aeruginosa within the whole metacommunity and the core group of bacterial taxa.
Mentions: The satellite group comprised 67 different bacterial taxa from 33 genera and accounted for only 11.1% of the total abundance (Table 2). From the satellite taxa, only 53 taxa were sampled from one individual patient. In contrast, the core group comprised 15 taxa from 7 genera (including Catonella (1 taxon), Neisseria (2), Porphyromonas (1), Prevotella (5), Pseudomonas (1), Streptococcus (2) and Veillonella (3)), accounting for 88.9% of the total abundance (Table 2). The core group was dominated by one taxon, P. aeruginosa, considered previously to be the predominant CF respiratory pathogen. This accounted for 70.6% of the total abundance and was found in all patients (except patient 1 (P1)) (Figure 3). With regard to the distribution of other recognised and candidate CF pathogens, the five recorded pathogens were randomly distributed throughout the patients and were therefore assigned to the satellite taxa group. Each of these CF pathogens was found only in low abundance and in single patients (Achromobacter xylosoxidans (P12, 5 clones), H. influenzae (P14, 5 clones), Staphylococcus aureus (P1, 1 clone), Stenotrophomonas maltophilia (P1, 4 clones) and Streptococcus intermedius/constellatus part of the Streptococcus milleri group (P10, 1 clone)). In total, these represented less than 0.75% of the total abundance. No taxa from the B. cepacia complex were recorded in any individual from the patient cohort.

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