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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

Comparison of the bacterial communities at the phylum level and of representative genera with highly abundant OTUs.(A) Taxonomic identification at the phylum level showing different phyla that varied with the period of hospitalization, the “other” represented for the phyla that did not being displayed directly. Patients with several significant changes in the OTU proportion over time: (B1) subject N1, (B2) subject N3, (B3) subject N5, (B4) subject N7, (B5) subject N10, and (B6) subject N12. The standardization of sequencing depth for each sample was 22000. N, case number; D, admission date.
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pone.0130736.g003: Comparison of the bacterial communities at the phylum level and of representative genera with highly abundant OTUs.(A) Taxonomic identification at the phylum level showing different phyla that varied with the period of hospitalization, the “other” represented for the phyla that did not being displayed directly. Patients with several significant changes in the OTU proportion over time: (B1) subject N1, (B2) subject N3, (B3) subject N5, (B4) subject N7, (B5) subject N10, and (B6) subject N12. The standardization of sequencing depth for each sample was 22000. N, case number; D, admission date.

Mentions: Twenty phyla were detected in the sputum samples. Firmicutes (37.57%), Proteobacteria (29.12%), Bacteroidetes (17.91%), Actinobacteria (11.31%), Fusobacteria (2.93%) and Cyanobacteria (1.02%) were found at high percentages. In contrast, Spirochaetes, Euryarchaeota, Planctomycetes, Deinococcus-Thermus, Acidobacteria, Aquificae, Chlamydiae, Nitrospira, Chloroflexi, Crenarchaeota, Euryarchaeota, Synergistetes, SR1, Tenericutes and TM7 appeared at low percentages. Firmicutes and Proteobacteria were distributed widely and abundantly among all samples, and the percentage of Proteobacteria remained nearly stable, except in samples N10 and N12. Subject N10 had an increased percentage of Neisseria and a decreased percentage of Moraxella, whereas subject N12 had decreased percentages of Neisseria and Moraxella. Firmicutes were found at decreased percentages in subjects N1, N3, and N7, whereas subjects N5, N10, and N12 showed increased percentages; these results were attributed to changes in the abundance of the genus Streptococcus. The amount of Fusobacteria also changed significantly over time, and this result was reflected at all taxonomic levels, down to the genera Leptotrichia and Fusobacterium. Streptophyta was found to be the most abundant among members of the phylum Cyanobacteria, and Rothia and Actinomyces were the most unstable genera among members of the phylum Actinobacteria (Fig 3).


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)

Comparison of the bacterial communities at the phylum level and of representative genera with highly abundant OTUs.(A) Taxonomic identification at the phylum level showing different phyla that varied with the period of hospitalization, the “other” represented for the phyla that did not being displayed directly. Patients with several significant changes in the OTU proportion over time: (B1) subject N1, (B2) subject N3, (B3) subject N5, (B4) subject N7, (B5) subject N10, and (B6) subject N12. The standardization of sequencing depth for each sample was 22000. N, case number; D, admission date.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0130736.g003: Comparison of the bacterial communities at the phylum level and of representative genera with highly abundant OTUs.(A) Taxonomic identification at the phylum level showing different phyla that varied with the period of hospitalization, the “other” represented for the phyla that did not being displayed directly. Patients with several significant changes in the OTU proportion over time: (B1) subject N1, (B2) subject N3, (B3) subject N5, (B4) subject N7, (B5) subject N10, and (B6) subject N12. The standardization of sequencing depth for each sample was 22000. N, case number; D, admission date.
Mentions: Twenty phyla were detected in the sputum samples. Firmicutes (37.57%), Proteobacteria (29.12%), Bacteroidetes (17.91%), Actinobacteria (11.31%), Fusobacteria (2.93%) and Cyanobacteria (1.02%) were found at high percentages. In contrast, Spirochaetes, Euryarchaeota, Planctomycetes, Deinococcus-Thermus, Acidobacteria, Aquificae, Chlamydiae, Nitrospira, Chloroflexi, Crenarchaeota, Euryarchaeota, Synergistetes, SR1, Tenericutes and TM7 appeared at low percentages. Firmicutes and Proteobacteria were distributed widely and abundantly among all samples, and the percentage of Proteobacteria remained nearly stable, except in samples N10 and N12. Subject N10 had an increased percentage of Neisseria and a decreased percentage of Moraxella, whereas subject N12 had decreased percentages of Neisseria and Moraxella. Firmicutes were found at decreased percentages in subjects N1, N3, and N7, whereas subjects N5, N10, and N12 showed increased percentages; these results were attributed to changes in the abundance of the genus Streptococcus. The amount of Fusobacteria also changed significantly over time, and this result was reflected at all taxonomic levels, down to the genera Leptotrichia and Fusobacterium. Streptophyta was found to be the most abundant among members of the phylum Cyanobacteria, and Rothia and Actinomyces were the most unstable genera among members of the phylum Actinobacteria (Fig 3).

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