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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

The applicability, feasibility, and validity of the WGA method for enriching microbial DNA. (a) DGGE profiles of WGA-amplified oropharyngeal DNAs (lanes A1, B1, C1, and D1) and the original oropharyngeal DNA (lanes A0, B0, C0, and D0); (b) the WGA-amplified fecal DNA (lanes A1–3 and B1–3) represented the most predominant microbial bands that were similar to those detected in the original fecal DNA (lanes A0 and B0), and were reproducible; (c) Seven oropharyngeal microbial DNA samples were amplified in duplicate using WGA for DGGE analysis. Clustering was performed using Dice’s coefficient and UPGMA with BioNumerics software
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Fig1: The applicability, feasibility, and validity of the WGA method for enriching microbial DNA. (a) DGGE profiles of WGA-amplified oropharyngeal DNAs (lanes A1, B1, C1, and D1) and the original oropharyngeal DNA (lanes A0, B0, C0, and D0); (b) the WGA-amplified fecal DNA (lanes A1–3 and B1–3) represented the most predominant microbial bands that were similar to those detected in the original fecal DNA (lanes A0 and B0), and were reproducible; (c) Seven oropharyngeal microbial DNA samples were amplified in duplicate using WGA for DGGE analysis. Clustering was performed using Dice’s coefficient and UPGMA with BioNumerics software

Mentions: We first analyzed the applicability of the WGA method for characterizing oropharyngeal microbial DNA samples. We compared the DGGE profiles between WGA-amplified DNA (Fig. 1a, lanes A1, B1, C1, and D1) and the original DNA (Fig. 1a, lanes A0, B0, C0, and D0) and found that the WGA-positive samples comprised more bands than those of WGA-negative samples, suggesting that the WGA method was capable of enriching oropharyngeal microbial DNA samples for DGGE analysis.Fig. 1


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)

The applicability, feasibility, and validity of the WGA method for enriching microbial DNA. (a) DGGE profiles of WGA-amplified oropharyngeal DNAs (lanes A1, B1, C1, and D1) and the original oropharyngeal DNA (lanes A0, B0, C0, and D0); (b) the WGA-amplified fecal DNA (lanes A1–3 and B1–3) represented the most predominant microbial bands that were similar to those detected in the original fecal DNA (lanes A0 and B0), and were reproducible; (c) Seven oropharyngeal microbial DNA samples were amplified in duplicate using WGA for DGGE analysis. Clustering was performed using Dice’s coefficient and UPGMA with BioNumerics software
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig1: The applicability, feasibility, and validity of the WGA method for enriching microbial DNA. (a) DGGE profiles of WGA-amplified oropharyngeal DNAs (lanes A1, B1, C1, and D1) and the original oropharyngeal DNA (lanes A0, B0, C0, and D0); (b) the WGA-amplified fecal DNA (lanes A1–3 and B1–3) represented the most predominant microbial bands that were similar to those detected in the original fecal DNA (lanes A0 and B0), and were reproducible; (c) Seven oropharyngeal microbial DNA samples were amplified in duplicate using WGA for DGGE analysis. Clustering was performed using Dice’s coefficient and UPGMA with BioNumerics software
Mentions: We first analyzed the applicability of the WGA method for characterizing oropharyngeal microbial DNA samples. We compared the DGGE profiles between WGA-amplified DNA (Fig. 1a, lanes A1, B1, C1, and D1) and the original DNA (Fig. 1a, lanes A0, B0, C0, and D0) and found that the WGA-positive samples comprised more bands than those of WGA-negative samples, suggesting that the WGA method was capable of enriching oropharyngeal microbial DNA samples for DGGE analysis.Fig. 1

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