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Sputum Bacterial and Fungal Dynamics during Exacerbations of Severe COPD.

Su J, Liu HY, Tan XL, Ji Y, Jiang YX, Prabhakar M, Rong ZH, Zhou HW, Zhang GX - PLoS ONE (2015)

Bottom Line: Sequence analysis showed 261 bacterial genera representing 20 distinct phyla, with an average number of genera per patient of >157, indicating high diversity.Acinetobacter, Prevotella, Neisseria, Rothia, Lactobacillus, Leptotrichia, Streptococcus, Veillonella, and Actinomyces were the most commonly identified genera, and the average total sequencing number per sputum sample was >10000 18S ITS sequences.The fungal population was typically dominated by Candia, Phialosimplex, Aspergillus, Penicillium, Cladosporium and Eutypella.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Organ Failure Research, Department of Environmental Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, China; Department of Respiratory Physicians, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.

ABSTRACT
The changes in the microbial community structure during acute exacerbations of severe chronic obstructive pulmonary disease (COPD) in hospitalized patients remain largely uncharacterized. Therefore, further studies focused on the temporal dynamics and structure of sputum microbial communities during acute exacerbation of COPD (AECOPD) would still be necessary. In our study, the use of molecular microbiological techniques provided insight into both fungal and bacterial diversities in AECOPD patients during hospitalization. In particular, we examined the structure and varieties of lung microbial community in 6 patients with severe AECOPD by amplifying 16S rRNA V4 hyper-variable and internal transcribed spacer (ITS) DNA regions using barcoded primers and the Illumina sequencing platform. Sequence analysis showed 261 bacterial genera representing 20 distinct phyla, with an average number of genera per patient of >157, indicating high diversity. Acinetobacter, Prevotella, Neisseria, Rothia, Lactobacillus, Leptotrichia, Streptococcus, Veillonella, and Actinomyces were the most commonly identified genera, and the average total sequencing number per sputum sample was >10000 18S ITS sequences. The fungal population was typically dominated by Candia, Phialosimplex, Aspergillus, Penicillium, Cladosporium and Eutypella. Our findings highlight that COPD patients have personalized structures and varieties in sputum microbial community during hospitalization periods.

No MeSH data available.


Related in: MedlinePlus

Distributions of the indices.(A) PD_whole_tree index, i.e., evenness index. (B) Shannon index, i.e., sample distribution index. (C, D) PCoA of unweighted UniFrac distance. (C) Community comparison of the 6 different subjects. (D) Two different groups based on the CRP value.
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pone.0130736.g001: Distributions of the indices.(A) PD_whole_tree index, i.e., evenness index. (B) Shannon index, i.e., sample distribution index. (C, D) PCoA of unweighted UniFrac distance. (C) Community comparison of the 6 different subjects. (D) Two different groups based on the CRP value.

Mentions: The sputum bacterial community structure varied among the different participants; Fig 1 shows the alpha- and beta-diversity results. We used the PD_whole_tree and Shannon indices to compare the alpha diversities of the different samples. There was considerable variability in the alpha diversity of each subject; however, no consistent patterns were observed. In subjects N1, N5, and N12, the PD_whole_tree and Shannon indices initially declined and then gradually increased over time. In subjects N3 and N10, there was an increase in the Shannon index throughout the observation period, whereas the PD_whole_tree index showed the opposite trend. For subject N7, the PD_whole_tree index showed a descending trend, with a mild increase over time, whereas the Shannon index showed a consistently descending trend. We additionally studied the PCoA of the UniFrac distances among the different subjects. The PCoA analysis of the sample distribution based on the unweighted UniFrac distance of each patient showed that the samples were separated, revealing that patients with severe COPD have a unique microbial community structure. These samples could be divided into two separate groups based on the CRP value.


Sputum Bacterial and Fungal Dynamics during Exacerbations of Severe COPD.

Su J, Liu HY, Tan XL, Ji Y, Jiang YX, Prabhakar M, Rong ZH, Zhou HW, Zhang GX - PLoS ONE (2015)

Distributions of the indices.(A) PD_whole_tree index, i.e., evenness index. (B) Shannon index, i.e., sample distribution index. (C, D) PCoA of unweighted UniFrac distance. (C) Community comparison of the 6 different subjects. (D) Two different groups based on the CRP value.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4493005&req=5

pone.0130736.g001: Distributions of the indices.(A) PD_whole_tree index, i.e., evenness index. (B) Shannon index, i.e., sample distribution index. (C, D) PCoA of unweighted UniFrac distance. (C) Community comparison of the 6 different subjects. (D) Two different groups based on the CRP value.
Mentions: The sputum bacterial community structure varied among the different participants; Fig 1 shows the alpha- and beta-diversity results. We used the PD_whole_tree and Shannon indices to compare the alpha diversities of the different samples. There was considerable variability in the alpha diversity of each subject; however, no consistent patterns were observed. In subjects N1, N5, and N12, the PD_whole_tree and Shannon indices initially declined and then gradually increased over time. In subjects N3 and N10, there was an increase in the Shannon index throughout the observation period, whereas the PD_whole_tree index showed the opposite trend. For subject N7, the PD_whole_tree index showed a descending trend, with a mild increase over time, whereas the Shannon index showed a consistently descending trend. We additionally studied the PCoA of the UniFrac distances among the different subjects. The PCoA analysis of the sample distribution based on the unweighted UniFrac distance of each patient showed that the samples were separated, revealing that patients with severe COPD have a unique microbial community structure. These samples could be divided into two separate groups based on the CRP value.

Bottom Line: Sequence analysis showed 261 bacterial genera representing 20 distinct phyla, with an average number of genera per patient of >157, indicating high diversity.Acinetobacter, Prevotella, Neisseria, Rothia, Lactobacillus, Leptotrichia, Streptococcus, Veillonella, and Actinomyces were the most commonly identified genera, and the average total sequencing number per sputum sample was >10000 18S ITS sequences.The fungal population was typically dominated by Candia, Phialosimplex, Aspergillus, Penicillium, Cladosporium and Eutypella.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Organ Failure Research, Department of Environmental Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, China; Department of Respiratory Physicians, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.

ABSTRACT
The changes in the microbial community structure during acute exacerbations of severe chronic obstructive pulmonary disease (COPD) in hospitalized patients remain largely uncharacterized. Therefore, further studies focused on the temporal dynamics and structure of sputum microbial communities during acute exacerbation of COPD (AECOPD) would still be necessary. In our study, the use of molecular microbiological techniques provided insight into both fungal and bacterial diversities in AECOPD patients during hospitalization. In particular, we examined the structure and varieties of lung microbial community in 6 patients with severe AECOPD by amplifying 16S rRNA V4 hyper-variable and internal transcribed spacer (ITS) DNA regions using barcoded primers and the Illumina sequencing platform. Sequence analysis showed 261 bacterial genera representing 20 distinct phyla, with an average number of genera per patient of >157, indicating high diversity. Acinetobacter, Prevotella, Neisseria, Rothia, Lactobacillus, Leptotrichia, Streptococcus, Veillonella, and Actinomyces were the most commonly identified genera, and the average total sequencing number per sputum sample was >10000 18S ITS sequences. The fungal population was typically dominated by Candia, Phialosimplex, Aspergillus, Penicillium, Cladosporium and Eutypella. Our findings highlight that COPD patients have personalized structures and varieties in sputum microbial community during hospitalization periods.

No MeSH data available.


Related in: MedlinePlus