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Front Cell Infect Microbiol. 2019 May 21;9:149. doi: 10.3389/fcimb.2019.00149. eCollection 2019.

Alterations to the Lung Microbiome in Idiopathic Pulmonary Fibrosis Patients.

Tong X1, Su F2, Xu X1, Xu H3, Yang T4,5, Xu Q6, Dai H4,5, Huang K7, Zou L8, Zhang W1, Pei S9, Xiao F2,8, Li Y1, Wang C4,5,10.

Author information

1
Department of Respiratory and Critical Care Medicine, National Center of Gerontology, Beijing Hospital, Beijing, China.
2
Clinical Biobank, National Center of Gerontology, Beijing Hospital, Beijing, China.
3
Department of Laboratory Medicine, Beijing Hospital, Beijing, China.
4
National Clinical Research Center for Respiratory Diseases, Center for Respiratory Diseases, China-Japan Friendship Hospital, Peking University Health Science Center, Beijing, China.
5
Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Peking University Health Science Center, Beijing, China.
6
Department of Respiratory and Critical Care Medicine, Bengbu University Affiliated Hospital, Bengbu, China.
7
Department of Respiratory and Critical Care Medicine, Beijing Chao-Yang Hospital, Capital Medical University and Beijing Institute of Respiratory Medicine, Beijing, China.
8
The Key Laboratory of Geriatrics, National Center of Gerontology, Beijing Hospital, Beijing, China.
9
Annoroad Gene Technology (Beijing) Co., Ltd., Beijing, China.
10
National Clinical Research Center for Respiratory Diseases, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.

Abstract

Lung microbiome ecosystem homeostasis in idiopathic pulmonary fibrosis (IPF) remains uncharacterized. The aims of this study were to identify unique microbial signatures of the lung microbiome and analyze microbial gene function in IPF patients. DNA isolated from BALF samples was obtained for high-throughput gene sequencing. Microbial metagenomic data were used for principal component analysis (PCA) and analyzed at different taxonomic levels. Shotgun metagenomic data were annotated using the KEGG database and were analyzed for functional and metabolic pathways. In this study, 17 IPF patients and 38 healthy subjects (smokers and non-smokers) were recruited. For the PCA, the first and the second principal component explained 16.3 and 13.4% of the overall variability, respectively. The β diversity of microbiome was reduced in the IPF group. Signature of IPF's microbes was enriched of Streptococcus, Pseudobutyrivibrio, and Anaerorhabdus. The translocation of lung microbiome was shown that 32.84% of them were from oral. After analysis of gene function, ABC transporter systems, biofilm formation, and two-component regulatory system were enriched in IPF patients' microbiome. Here we shown the microbiology characteristics in IPF patients. The microbiome may participate in altering internal conditions and involving in generating antibiotic resistance in IPF patients.

KEYWORDS:

antibiotic resistant gene; bronchoalveolar lavage fluid; idiopathic pulmonary fibrosis; microbiota; virulence factor

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