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An integrated respiratory microbial gene catalogue to better understand the microbial aetiology of Mycoplasma pneumoniae pneumonia

BACKGROUND: The imbalanced respiratory microbiota observed in pneumonia causes high morbidity and mortality in childhood. Respiratory metagenomic analysis demands a comprehensive microbial gene catalogue, which will significantly advance our understanding of host–microorganism interactions. RESULTS:...

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Autores principales: Dai, Wenkui, Wang, Heping, Zhou, Qian, Li, Dongfang, Feng, Xin, Yang, Zhenyu, Wang, Wenjian, Qiu, Chuangzhao, Lu, Zhiwei, Xu, Ximing, Lyu, Mengxuan, Xie, Gan, Li, Yinhu, Bao, Yanmin, Liu, Yanhong, Shen, Kunling, Yao, Kaihu, Feng, Xikang, Yang, Yonghong, Zhou, Ke, Li, Shuaicheng, Zheng, Yuejie
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6669060/
https://www.ncbi.nlm.nih.gov/pubmed/31367746
http://dx.doi.org/10.1093/gigascience/giz093
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author Dai, Wenkui
Wang, Heping
Zhou, Qian
Li, Dongfang
Feng, Xin
Yang, Zhenyu
Wang, Wenjian
Qiu, Chuangzhao
Lu, Zhiwei
Xu, Ximing
Lyu, Mengxuan
Xie, Gan
Li, Yinhu
Bao, Yanmin
Liu, Yanhong
Shen, Kunling
Yao, Kaihu
Feng, Xikang
Yang, Yonghong
Zhou, Ke
Li, Shuaicheng
Zheng, Yuejie
author_facet Dai, Wenkui
Wang, Heping
Zhou, Qian
Li, Dongfang
Feng, Xin
Yang, Zhenyu
Wang, Wenjian
Qiu, Chuangzhao
Lu, Zhiwei
Xu, Ximing
Lyu, Mengxuan
Xie, Gan
Li, Yinhu
Bao, Yanmin
Liu, Yanhong
Shen, Kunling
Yao, Kaihu
Feng, Xikang
Yang, Yonghong
Zhou, Ke
Li, Shuaicheng
Zheng, Yuejie
author_sort Dai, Wenkui
collection PubMed
description BACKGROUND: The imbalanced respiratory microbiota observed in pneumonia causes high morbidity and mortality in childhood. Respiratory metagenomic analysis demands a comprehensive microbial gene catalogue, which will significantly advance our understanding of host–microorganism interactions. RESULTS: We collected 334 respiratory microbial samples from 171 healthy children and 76 children with pneumonia. The respiratory microbial gene catalogue we established comprised 2.25 million non-redundant microbial genes, covering 90.52% of prevalent genes. The major oropharyngeal microbial species found in healthy children were Prevotella and Streptococcus. In children with Mycoplasma pneumoniae pneumonia (MPP), oropharyngeal microbial diversity and associated gene numbers decreased compared with those of healthy children. The concurrence network of oropharyngeal microorganisms in patients predominantly featured Staphylococcus spp. and M. pneumoniae. Functional orthologues, which are associated with the metabolism of various lipids, membrane transport, and signal transduction, accumulated in the oropharyngeal microbiome of children with pneumonia. Several antibiotic resistance genes and virulence factor genes were identified in the genomes of M. pneumoniae and 13 other microorganisms reconstructed via metagenomic data. Although the common macrolide/β-lactam resistance genes were not identified in the assembled M. pneumoniae genome, a single-nucleotide polymorphism (A2063G) related to macrolide resistance was identified in a 23S ribosomal RNA gene. CONCLUSIONS: The results of this study will facilitate exploration of unknown microbial components and host–microorganism interactions in studies of the respiratory microbiome. They will also yield further insights into the microbial aetiology of MPP.
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spelling pubmed-66690602019-08-05 An integrated respiratory microbial gene catalogue to better understand the microbial aetiology of Mycoplasma pneumoniae pneumonia Dai, Wenkui Wang, Heping Zhou, Qian Li, Dongfang Feng, Xin Yang, Zhenyu Wang, Wenjian Qiu, Chuangzhao Lu, Zhiwei Xu, Ximing Lyu, Mengxuan Xie, Gan Li, Yinhu Bao, Yanmin Liu, Yanhong Shen, Kunling Yao, Kaihu Feng, Xikang Yang, Yonghong Zhou, Ke Li, Shuaicheng Zheng, Yuejie Gigascience Research BACKGROUND: The imbalanced respiratory microbiota observed in pneumonia causes high morbidity and mortality in childhood. Respiratory metagenomic analysis demands a comprehensive microbial gene catalogue, which will significantly advance our understanding of host–microorganism interactions. RESULTS: We collected 334 respiratory microbial samples from 171 healthy children and 76 children with pneumonia. The respiratory microbial gene catalogue we established comprised 2.25 million non-redundant microbial genes, covering 90.52% of prevalent genes. The major oropharyngeal microbial species found in healthy children were Prevotella and Streptococcus. In children with Mycoplasma pneumoniae pneumonia (MPP), oropharyngeal microbial diversity and associated gene numbers decreased compared with those of healthy children. The concurrence network of oropharyngeal microorganisms in patients predominantly featured Staphylococcus spp. and M. pneumoniae. Functional orthologues, which are associated with the metabolism of various lipids, membrane transport, and signal transduction, accumulated in the oropharyngeal microbiome of children with pneumonia. Several antibiotic resistance genes and virulence factor genes were identified in the genomes of M. pneumoniae and 13 other microorganisms reconstructed via metagenomic data. Although the common macrolide/β-lactam resistance genes were not identified in the assembled M. pneumoniae genome, a single-nucleotide polymorphism (A2063G) related to macrolide resistance was identified in a 23S ribosomal RNA gene. CONCLUSIONS: The results of this study will facilitate exploration of unknown microbial components and host–microorganism interactions in studies of the respiratory microbiome. They will also yield further insights into the microbial aetiology of MPP. Oxford University Press 2019-07-31 /pmc/articles/PMC6669060/ /pubmed/31367746 http://dx.doi.org/10.1093/gigascience/giz093 Text en © The Author(s) 2019. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research
Dai, Wenkui
Wang, Heping
Zhou, Qian
Li, Dongfang
Feng, Xin
Yang, Zhenyu
Wang, Wenjian
Qiu, Chuangzhao
Lu, Zhiwei
Xu, Ximing
Lyu, Mengxuan
Xie, Gan
Li, Yinhu
Bao, Yanmin
Liu, Yanhong
Shen, Kunling
Yao, Kaihu
Feng, Xikang
Yang, Yonghong
Zhou, Ke
Li, Shuaicheng
Zheng, Yuejie
An integrated respiratory microbial gene catalogue to better understand the microbial aetiology of Mycoplasma pneumoniae pneumonia
title An integrated respiratory microbial gene catalogue to better understand the microbial aetiology of Mycoplasma pneumoniae pneumonia
title_full An integrated respiratory microbial gene catalogue to better understand the microbial aetiology of Mycoplasma pneumoniae pneumonia
title_fullStr An integrated respiratory microbial gene catalogue to better understand the microbial aetiology of Mycoplasma pneumoniae pneumonia
title_full_unstemmed An integrated respiratory microbial gene catalogue to better understand the microbial aetiology of Mycoplasma pneumoniae pneumonia
title_short An integrated respiratory microbial gene catalogue to better understand the microbial aetiology of Mycoplasma pneumoniae pneumonia
title_sort integrated respiratory microbial gene catalogue to better understand the microbial aetiology of mycoplasma pneumoniae pneumonia
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6669060/
https://www.ncbi.nlm.nih.gov/pubmed/31367746
http://dx.doi.org/10.1093/gigascience/giz093
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