Limits...
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

Show MeSH

Related in: MedlinePlus

The relationships between bacterial taxa richness and lung function (FEV1 in litres) for (a) the whole metacommunity, (b) the core group and (c) the satellite group. In each case linear regression lines have been fitted. For the whole metacommunity, r2=0.43, F1,12=9.2, P<0.01; core group, r2=0.40, F1,12=7.82, P<0.02; and satellite group, r2=0.42, F1,12=8.67, P<0.01.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3105771&req=5

fig5: The relationships between bacterial taxa richness and lung function (FEV1 in litres) for (a) the whole metacommunity, (b) the core group and (c) the satellite group. In each case linear regression lines have been fitted. For the whole metacommunity, r2=0.43, F1,12=9.2, P<0.01; core group, r2=0.40, F1,12=7.82, P<0.02; and satellite group, r2=0.42, F1,12=8.67, P<0.01.

Mentions: We also investigated which clinical factors correlated with bacterial taxa richness across the patient cohort (Figure 5). We found that only lung function measured by forced expiratory volume in 1 s significantly correlated with richness, demonstrating significant positive linear relationships for total taxa richness, and the core and satellite group member richness (Figure 5), whereby taxa richness decreased with a reduction in lung function. More research is needed to be able to explain this observation, particularly given the fact that forced expiratory volume in 1 s is the single best predictor of mortality and is an important determinant of the timing of transplantation (Kerem et al., 1992; Doershuk and Stern, 1999; Oikonomou et al., 2002). In addition, however, our findings agree, in part, with those of the study by Kelpac-Ceraj et al. (2010) on paediatric CF patients, in that we also found that similarities in community composition correlated with similarities in CFTR genotype and antibiotic treatments. However, we did not find a relationship between patient age and richness. We postulate that this may be a result of bacterial community composition and richness being highly dynamic in younger patients, and that these community dynamics may stabilise with increase in patients' age.


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 relationships between bacterial taxa richness and lung function (FEV1 in litres) for (a) the whole metacommunity, (b) the core group and (c) the satellite group. In each case linear regression lines have been fitted. For the whole metacommunity, r2=0.43, F1,12=9.2, P<0.01; core group, r2=0.40, F1,12=7.82, P<0.02; and satellite group, r2=0.42, F1,12=8.67, P<0.01.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig5: The relationships between bacterial taxa richness and lung function (FEV1 in litres) for (a) the whole metacommunity, (b) the core group and (c) the satellite group. In each case linear regression lines have been fitted. For the whole metacommunity, r2=0.43, F1,12=9.2, P<0.01; core group, r2=0.40, F1,12=7.82, P<0.02; and satellite group, r2=0.42, F1,12=8.67, P<0.01.
Mentions: We also investigated which clinical factors correlated with bacterial taxa richness across the patient cohort (Figure 5). We found that only lung function measured by forced expiratory volume in 1 s significantly correlated with richness, demonstrating significant positive linear relationships for total taxa richness, and the core and satellite group member richness (Figure 5), whereby taxa richness decreased with a reduction in lung function. More research is needed to be able to explain this observation, particularly given the fact that forced expiratory volume in 1 s is the single best predictor of mortality and is an important determinant of the timing of transplantation (Kerem et al., 1992; Doershuk and Stern, 1999; Oikonomou et al., 2002). In addition, however, our findings agree, in part, with those of the study by Kelpac-Ceraj et al. (2010) on paediatric CF patients, in that we also found that similarities in community composition correlated with similarities in CFTR genotype and antibiotic treatments. However, we did not find a relationship between patient age and richness. We postulate that this may be a result of bacterial community composition and richness being highly dynamic in younger patients, and that these community dynamics may stabilise with increase in patients' age.

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