Metagenomic analysis of respiratory tract microbial flora distribution characteristics in pulmonary tuberculosis patients

doi:10.3969/j.issn.1000-6621.2020.10.016

Abstract

Abstract:

Objective To investigate changes in respiratory microbial flora composition in pulmonary tuberculosis patients and healthy individuals. Methods Multiple Chinese and English databases were searched with keywords “tuberculosis” and “respiratory tract flora”. Publications between 2010 and 2019 were selected according to literature screening procedure and then included. All available next-generation sequencing data were collected, parameters unified, data pre-processed and then used for metagenomic analysis and statistical processing. Results Nine English literatures were included. Species analysis suggested that the top 10 most abundant bacterial groups in both tuberculosis group and healthy control group were: Firmicutes, OD1, Proteobacteria, Bacteroidetes, Actinobacteria, and Fusobacteria, Cyanobacteria. However, there were significant differences in the composition of respiratory bacterial flora between the two groups. α diversity analysis showed that the number of OTUs (286.60±22.82), Faith ‘s PD index (13.57±2.58), and Shannon index (7.17±0.24) observed in tuberculosis group were significantly higher than those of healthy control group (42.88±2.49, 6.52±0.22, 4.42±0.07, respectively), which was statistically significant (P=0.00016,0.00056,0.00016). Chao1 index of tuberculosis group was higher than healthy control group (266.50±92.71 vs. 38.44±2.86), without statistical significance (P>0.05). Six phyla were found to have different abundance in the two groups, 5 of which were clustered in healthy controls: Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria and Fusobacteria, the other one-OD1 clustered in tuberculosis group. F16 family, Gammaproteobacteria, Firmicutes phylum, Leuconostocaceae family and Bacilillaceae family were found to be tuberculosis-specific. Conclusion Compared with healthy people, there are significant changes in respiratory tract flora diversity and species composition in tuberculosis patients, with presence of unique flora.

Key words: Tuberculosis, pulmonary, Respiratory mucosa, Microbiology, Metagenome, Data interpretation, statistical

QIU Qian, LIU Dong-xin, LIU Chun-fa, QIU Jie, YAN Xiao-feng, ZHAO Yan-lin. Metagenomic analysis of respiratory tract microbial flora distribution characteristics in pulmonary tuberculosis patients[J]. Chinese Journal of Antituberculosis, 2020, 42(10): 1100-1108. doi: 10.3969/j.issn.1000-6621.2020.10.016

Figures/Tables 12

References 23

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研究作者及文献	发表年份	国家	检测方法	16S rRNA 测序区域	测序平台	健康对照组		肺结核组
研究作者及文献	发表年份	国家	检测方法	16S rRNA 测序区域	测序平台	样本数	样本类型	样本数	样本类型
Cui等^[6]	2012	中国	16S rRNA测序	V3	Roche/454	24	唾液,咽部分泌物	31	痰液
Cheung等^[7]	2013	中国	16S rRNA测序	V1-V2	Roche/454	14	痰液	22	痰液
Wu等^[8]	2013	中国	16S rRNA测序	V1-V2	Roche/454	20	咽拭子	75	痰液
Botero等^[9]	2014	哥伦比亚	16S rRNA测序	V1-V2	Roche/454	6	鼻腔,口咽分泌物	6	鼻腔,口咽分泌物,痰液
Zhou等^[10]	2015	中国	16S rRNA测序	V3	Roche/454	24	唾液,咽部分泌物	32	BALF
Bassis等^[11]	2015	美国	16S rRNA测序	V1-V2	Roche/454	72	口腔冲洗液, 鼻拭子,BALF	N/A	N/A
Dube等^[12]	2016	南非	Multiplex RT PCR	N/A	N/A	N/A	N/A	34	鼻咽分泌物
Krishna等^[13]	2016	印度	16S rRNA测序	V6-V7	Ion Torrent	16	痰液	25	痰液
Vázquez-Pérez等^[5]	2020	墨西哥	16S rRNA测序	全部可变区域	Illumina	10	BALF	6	BALF

物种分类(门水平)	W值	P值	物种分类(属水平)	W值	P值
OD1门	17	<0.05	OD1门下的属	279	<0.05
厚壁菌门(Firmicutes)	16	<0.05	链球菌属(Streptococcus)	267	<0.05
放线菌门(Actinobacteria)	15	<0.05	普氏菌属(Prevotella)	252	<0.05
拟杆菌门(Bacteroidetes)	15	<0.05
梭杆菌门(Fusobacteria)	14	<0.05
变形菌门(Proteobacteria)	14	<0.05