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Alterations of Bacteroides sp., Neisseria sp., Actinomyces sp., and Streptococcus sp. populations in the oropharyngeal microbiome are associated with liver cirrhosis and pneumonia.

Lu H, Qian G, Ren Z, Zhang C, Zhang H, Xu W, Ye P, Yang Y, Li L - BMC Infect. Dis. (2015)

Bottom Line: The microbiomes of humans are associated with liver and lung inflammation.Study components were as follows: (1) determination of the temporal stability of the oropharyngeal microbiome; (2) identification of oropharyngeal microbial variation in 90 subjects; (3) quantitative identification of disease-associated bacteria.Whole genome amplification combined with denaturing gradient gel electrophoresis analysis monitored successfully oropharyngeal microbial variations and showed that the composition of each subject's oropharyngeal microbiome remained relatively stable during the follow-up.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou, 310003, People's Republic of China. seawindlu@126.com.

ABSTRACT

Background: The microbiomes of humans are associated with liver and lung inflammation. We identified and verified alterations of the oropharyngeal microbiome and assessed their association with cirrhosis and pneumonia.

Methods: Study components were as follows: (1) determination of the temporal stability of the oropharyngeal microbiome; (2) identification of oropharyngeal microbial variation in 90 subjects; (3) quantitative identification of disease-associated bacteria. DNAs enriched in bacterial sequences were produced from low-biomass oropharyngeal swabs using whole genome amplification and were analyzed using denaturing gradient gel electrophoresis analysis.

Results: Whole genome amplification combined with denaturing gradient gel electrophoresis analysis monitored successfully oropharyngeal microbial variations and showed that the composition of each subject's oropharyngeal microbiome remained relatively stable during the follow-up. The microbial composition of cirrhotic patients with pneumonia differed from those of others and clustered together in subgroup analysis. Further, species richness and the value of Shannon's diversity and evenness index increased significantly in patients with cirrhosis and pneumonia versus others (p < 0.001, versus healthy controls; p < 0.01, versus cirrhotic patients without pneumonia). Moreover, we identified variants of Bacteroides, Eubacterium, Lachnospiraceae, Neisseria, Actinomyces, and Streptococcus through phylogenetic analysis. Quantitative polymerase chain reaction assays revealed that the populations of Bacteroides, Neisseria, and Actinomycetes increased, while that of Streptococcus decreased in cirrhotic patients with pneumonia versus others (p < 0.001, versus Healthy controls; p < 0.01, versus cirrhotic patients without pneumonia).

Conclusions: Alterations of Bacteroides, Neisseria, Actinomyces, and Streptococcus populations in the oropharyngeal microbiome were associated with liver cirrhosis and pneumonia.

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Related in: MedlinePlus

Phylogenetic tree analysis based on bacterial PCR-DGGE profiles. (a) Nucleotide sequence identification of the bands from the PCR-DGGE profiles. The number corresponds to the number of band-classes in the phylogenetic tree. (b) The phylogenetic tree generated using a neighbor-joining method of the sequences derived from the DGGE profiles. The fragment sequences were designated according to their positions in gels using the band-matching tool with BioNumerics software version 6.01. The plot was prepared using MEGA5 software
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Fig4: Phylogenetic tree analysis based on bacterial PCR-DGGE profiles. (a) Nucleotide sequence identification of the bands from the PCR-DGGE profiles. The number corresponds to the number of band-classes in the phylogenetic tree. (b) The phylogenetic tree generated using a neighbor-joining method of the sequences derived from the DGGE profiles. The fragment sequences were designated according to their positions in gels using the band-matching tool with BioNumerics software version 6.01. The plot was prepared using MEGA5 software

Mentions: In the 90 PCR-DGGE profiles analyzed in this study, 39 band-classes were identified (Fig. 4a). Firmicutes (20 band-classes) was the most common phylum, followed by Actinobacteria (8 band-classes), Bacteroidetes (4 band-classes), Proteobacteria (4 band-classes), and Fusobacteria (3 band-classes) (Fig. 4b). Seven band-classes were highly prevalent (median intensity in at least one of the groups was >2 %), including band-classes 30.1, 33.0, and 65.6 of Streptococcus, band-class 8.3 of Fusobacterium, band-class 59.4 of Veillonella, as well as band-classes 80.6 and 63.0 of Actinomyces, in which there was little variance among band-classes 65.6, 59.4, and 80.6 (Additional file 3: Table S3).Fig. 4


Alterations of Bacteroides sp., Neisseria sp., Actinomyces sp., and Streptococcus sp. populations in the oropharyngeal microbiome are associated with liver cirrhosis and pneumonia.

Lu H, Qian G, Ren Z, Zhang C, Zhang H, Xu W, Ye P, Yang Y, Li L - BMC Infect. Dis. (2015)

Phylogenetic tree analysis based on bacterial PCR-DGGE profiles. (a) Nucleotide sequence identification of the bands from the PCR-DGGE profiles. The number corresponds to the number of band-classes in the phylogenetic tree. (b) The phylogenetic tree generated using a neighbor-joining method of the sequences derived from the DGGE profiles. The fragment sequences were designated according to their positions in gels using the band-matching tool with BioNumerics software version 6.01. The plot was prepared using MEGA5 software
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4477430&req=5

Fig4: Phylogenetic tree analysis based on bacterial PCR-DGGE profiles. (a) Nucleotide sequence identification of the bands from the PCR-DGGE profiles. The number corresponds to the number of band-classes in the phylogenetic tree. (b) The phylogenetic tree generated using a neighbor-joining method of the sequences derived from the DGGE profiles. The fragment sequences were designated according to their positions in gels using the band-matching tool with BioNumerics software version 6.01. The plot was prepared using MEGA5 software
Mentions: In the 90 PCR-DGGE profiles analyzed in this study, 39 band-classes were identified (Fig. 4a). Firmicutes (20 band-classes) was the most common phylum, followed by Actinobacteria (8 band-classes), Bacteroidetes (4 band-classes), Proteobacteria (4 band-classes), and Fusobacteria (3 band-classes) (Fig. 4b). Seven band-classes were highly prevalent (median intensity in at least one of the groups was >2 %), including band-classes 30.1, 33.0, and 65.6 of Streptococcus, band-class 8.3 of Fusobacterium, band-class 59.4 of Veillonella, as well as band-classes 80.6 and 63.0 of Actinomyces, in which there was little variance among band-classes 65.6, 59.4, and 80.6 (Additional file 3: Table S3).Fig. 4

Bottom Line: The microbiomes of humans are associated with liver and lung inflammation.Study components were as follows: (1) determination of the temporal stability of the oropharyngeal microbiome; (2) identification of oropharyngeal microbial variation in 90 subjects; (3) quantitative identification of disease-associated bacteria.Whole genome amplification combined with denaturing gradient gel electrophoresis analysis monitored successfully oropharyngeal microbial variations and showed that the composition of each subject's oropharyngeal microbiome remained relatively stable during the follow-up.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou, 310003, People's Republic of China. seawindlu@126.com.

ABSTRACT

Background: The microbiomes of humans are associated with liver and lung inflammation. We identified and verified alterations of the oropharyngeal microbiome and assessed their association with cirrhosis and pneumonia.

Methods: Study components were as follows: (1) determination of the temporal stability of the oropharyngeal microbiome; (2) identification of oropharyngeal microbial variation in 90 subjects; (3) quantitative identification of disease-associated bacteria. DNAs enriched in bacterial sequences were produced from low-biomass oropharyngeal swabs using whole genome amplification and were analyzed using denaturing gradient gel electrophoresis analysis.

Results: Whole genome amplification combined with denaturing gradient gel electrophoresis analysis monitored successfully oropharyngeal microbial variations and showed that the composition of each subject's oropharyngeal microbiome remained relatively stable during the follow-up. The microbial composition of cirrhotic patients with pneumonia differed from those of others and clustered together in subgroup analysis. Further, species richness and the value of Shannon's diversity and evenness index increased significantly in patients with cirrhosis and pneumonia versus others (p < 0.001, versus healthy controls; p < 0.01, versus cirrhotic patients without pneumonia). Moreover, we identified variants of Bacteroides, Eubacterium, Lachnospiraceae, Neisseria, Actinomyces, and Streptococcus through phylogenetic analysis. Quantitative polymerase chain reaction assays revealed that the populations of Bacteroides, Neisseria, and Actinomycetes increased, while that of Streptococcus decreased in cirrhotic patients with pneumonia versus others (p < 0.001, versus Healthy controls; p < 0.01, versus cirrhotic patients without pneumonia).

Conclusions: Alterations of Bacteroides, Neisseria, Actinomyces, and Streptococcus populations in the oropharyngeal microbiome were associated with liver cirrhosis and pneumonia.

Show MeSH
Related in: MedlinePlus