Alterations to the Lung Microbiome in Idiopathic Pulmonary Fibrosis Patients.

Xunliang Tong,Fei Xiao,Huaping Dai,Huaping Dai,Hongtao Xu,Surui Pei,Wenna Zhang,Lihui Zou,Yanming Li,Qixia Xu,Kewu Huang,Kewu Huang,Ting Yang,Ting Yang,Chen Wang,Chen Wang,Chen Wang,Xiaomao Xu,Fei Su

doi:10.3389/fcimb.2019.00149

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.

Highlights

Idiopathic pulmonary fibrosis (IPF) is a progressive, fatal disease without a known cause (Molyneaux et al, 2014)
Bacteria and virus microbial genes discriminated between idiopathic pulmonary fibrosis (IPF) patient Bronchoalveolar lavage fluid (BALF) and the BALF of healthy individuals with a high specificity; for example, Acinetobacter and Neisseria were identified at the genus level
The same results had been reported with an increased bacterial load and decreased microbial diversity in bronchoalveolar lavage (BAL) samples from IPF patients (Morris et al, 2014)

Summary

Introduction

Idiopathic pulmonary fibrosis (IPF) is a progressive, fatal disease without a known cause (Molyneaux et al, 2014). Lung Microbiome may disturb the internal environment of the lower airway and cause lung damage, it is crucial to determine the precise composition of the lung microbiota and predict associated gene functions to understand IPF (Han et al, 2014; O’dwyer et al, 2016). Culture-independent approaches, primarily based on gene sequencing, better describe the wide diversity of the microbial inhabitants of the lung microbiota and are able to identify significant differences between healthy subjects and patients with various respiratory diseases (Turnbaugh et al, 2007; Huse et al, 2012; Dickson and Huffnagle, 2015; O’dwyer et al, 2016). Few studies have examined differences in the microbiomes of the lower respiratory tract in smokers vs nonsmokers (Garmendia et al, 2012; Morris et al, 2013)

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