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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

RT-qPCR analysis of the key bacterial species accounting for variations in microbiome compositions. Number of key bacteria: log # per 10 ng original swab DNA. The figure shows the numbers of key bacteria, including Streptococcus, Streptococcus mitis, Actinomycetes, Lachnospiraceae, Eubacterium, Bacteroides, and Neisseria
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Fig6: RT-qPCR analysis of the key bacterial species accounting for variations in microbiome compositions. Number of key bacteria: log # per 10 ng original swab DNA. The figure shows the numbers of key bacteria, including Streptococcus, Streptococcus mitis, Actinomycetes, Lachnospiraceae, Eubacterium, Bacteroides, and Neisseria

Mentions: To verify the key bacteria present in infected subjects, which were associated with oropharyngeal microbial variation, quantitative PCR was used to analyze the original (non-WGA) DNA samples using bacterial species-specific primers. The abundances of Bacteroides sp., Neisseria sp., and Actinomycetes sp. and those of Streptococcus sp. in the oropharyngeal mucosa of group CI were higher and lower, respectively, compared with those of groups CC and HC (3.23, IQR 2.07–4.10 versus 1.08, IQR 0–1.91 and 1.97, IQR 1.27–2.85 for Bacteroides sp.; 1.78, IQR 1.33–3.60 versus 0, IQR 0–1.10 and 0 IQR 0–0 for Neisseria sp.; 2.42, IQR 0–3.77 versus 0, IQR 0–3.02 and 0, IQR 0–3.18 for Actinomycetes sp.; 3.26, IQR 2.48–4.66 versus 4.74, IQR 4.08–6.03 and 4.03, IQR 3.01–5.44 for Streptococcus sp.) (p < 0.05) (Fig. 6). The abundances of Bacteroides sp. and Streptococcus mitis were higher in group CC versus group HC (p < 0.05).Fig. 6


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)

RT-qPCR analysis of the key bacterial species accounting for variations in microbiome compositions. Number of key bacteria: log # per 10 ng original swab DNA. The figure shows the numbers of key bacteria, including Streptococcus, Streptococcus mitis, Actinomycetes, Lachnospiraceae, Eubacterium, Bacteroides, and Neisseria
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig6: RT-qPCR analysis of the key bacterial species accounting for variations in microbiome compositions. Number of key bacteria: log # per 10 ng original swab DNA. The figure shows the numbers of key bacteria, including Streptococcus, Streptococcus mitis, Actinomycetes, Lachnospiraceae, Eubacterium, Bacteroides, and Neisseria
Mentions: To verify the key bacteria present in infected subjects, which were associated with oropharyngeal microbial variation, quantitative PCR was used to analyze the original (non-WGA) DNA samples using bacterial species-specific primers. The abundances of Bacteroides sp., Neisseria sp., and Actinomycetes sp. and those of Streptococcus sp. in the oropharyngeal mucosa of group CI were higher and lower, respectively, compared with those of groups CC and HC (3.23, IQR 2.07–4.10 versus 1.08, IQR 0–1.91 and 1.97, IQR 1.27–2.85 for Bacteroides sp.; 1.78, IQR 1.33–3.60 versus 0, IQR 0–1.10 and 0 IQR 0–0 for Neisseria sp.; 2.42, IQR 0–3.77 versus 0, IQR 0–3.02 and 0, IQR 0–3.18 for Actinomycetes sp.; 3.26, IQR 2.48–4.66 versus 4.74, IQR 4.08–6.03 and 4.03, IQR 3.01–5.44 for Streptococcus sp.) (p < 0.05) (Fig. 6). The abundances of Bacteroides sp. and Streptococcus mitis were higher in group CC versus group HC (p < 0.05).Fig. 6

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