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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

System clustering of fungal composition at the genus level.The names of several of the most abundant genera that included the terminal taxa shown in the heatmap are listed on the right of the figure. The sample names are listed at the top of the heatmap. “N” represents samples from different subjects, and the color bar at the top of the heatmap shows the percentages of <5% of the sequences in each sputum sample.
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pone.0130736.g004: System clustering of fungal composition at the genus level.The names of several of the most abundant genera that included the terminal taxa shown in the heatmap are listed on the right of the figure. The sample names are listed at the top of the heatmap. “N” represents samples from different subjects, and the color bar at the top of the heatmap shows the percentages of <5% of the sequences in each sputum sample.

Mentions: The fungal community in the lung microbiome of each patient was analyzed by ITS gene sequencing, and system clustering was performed to obtain a visual representation of the overall similarity among the sputum samples. Fig 4 shows the relative abundance and system clustering trees of the samples based on the percentage of fungal operational units in each community. Each patient exhibited an unstable microbial community during the observation period. The lung microbiomes of subjects N5, N7, and N12 were dominated by Aspergillus, whereas the other two subjects had intermediate or low levels of Aspergillus. The microbiome of subject N1 was dominated by Phialosimplex and Candida, whereas the microbiome of subject N3 was dominated by Aspergillus and Phialosimplex. The microbiome of subject N10 was dominated by Teratosphaeria and Sterigmatomyces after the patient entered the hospital and then by Aureobasidium afterward.


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)

System clustering of fungal composition at the genus level.The names of several of the most abundant genera that included the terminal taxa shown in the heatmap are listed on the right of the figure. The sample names are listed at the top of the heatmap. “N” represents samples from different subjects, and the color bar at the top of the heatmap shows the percentages of <5% of the sequences in each sputum sample.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0130736.g004: System clustering of fungal composition at the genus level.The names of several of the most abundant genera that included the terminal taxa shown in the heatmap are listed on the right of the figure. The sample names are listed at the top of the heatmap. “N” represents samples from different subjects, and the color bar at the top of the heatmap shows the percentages of <5% of the sequences in each sputum sample.
Mentions: The fungal community in the lung microbiome of each patient was analyzed by ITS gene sequencing, and system clustering was performed to obtain a visual representation of the overall similarity among the sputum samples. Fig 4 shows the relative abundance and system clustering trees of the samples based on the percentage of fungal operational units in each community. Each patient exhibited an unstable microbial community during the observation period. The lung microbiomes of subjects N5, N7, and N12 were dominated by Aspergillus, whereas the other two subjects had intermediate or low levels of Aspergillus. The microbiome of subject N1 was dominated by Phialosimplex and Candida, whereas the microbiome of subject N3 was dominated by Aspergillus and Phialosimplex. The microbiome of subject N10 was dominated by Teratosphaeria and Sterigmatomyces after the patient entered the hospital and then by Aureobasidium afterward.

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