采用宏基因组学分析肺结核患者与健康人群呼吸道微生物菌群的特征

doi:10.3969/j.issn.1000-6621.2020.10.016

摘要/Abstract

摘要：

目的明确肺结核患者和健康人群的呼吸道微生物菌群组成的变化情况。方法时间限定为2010年1月至2019年12月,在英文数据库(PubMed、Embase and Ovid、Web of Science、Google Scholar、Cochrane Library)和中文数据库(中国知网、万方、中国生物医学文献服务系统与维普)检索所有包含结核和呼吸道菌群的文献,按照文献检索流程筛选文献并最终纳入。收集所有可用的下一代测序数据,统一处理参数,进行数据预处理和系统的宏基因组学分析及统计学处理。结果共纳入9篇英文文献。物种分析结果提示肺结核组和健康对照组在门水平相对丰度排在前10位的共有菌群有:厚壁菌门、OD1菌门、变形菌门、拟杆菌门、放线菌门、梭杆菌门、蓝菌门。但两组呼吸道菌群群落结构组成差异有统计学意义,α多样性分析显示,肺结核组观测到的可操作分类单元(operational taxonomic units,OTU)数目(286.60±22.82)、Faith 谱系多样性(phylogenetic diversity,PD)指数(Faith PD指数)(13.57±2.58)、Shannon指数(7.17±0.24)明显高于健康对照组(分别为42.88±2.49、6.52±0.22、4.42±0.07),差异均具有统计学意义(P值分别为0.00016、0.00056、0.00016)。肺结核组Chao1指数高于健康对照组(266.50±92.71 和38.44±2.86),但差异无统计学意义(P>0.05)。门水平上两组丰度有差异的物种有6种,其中5种在健康对照组聚集,为厚壁菌门、放线菌门、拟杆菌门、梭杆菌门、变形菌门,另有OD1门在肺结核组聚集。F16科、丙型变形菌纲、梭杆菌门梭杆菌目、厚壁菌门下的明串珠菌科和芽孢杆菌科是肺结核特有的菌群种类。结论肺结核患者与健康人群比较,呼吸道菌群的多样性及物种组成均发生了较大变化,并具有特有的菌群种类。

关键词: 结核, 肺, 呼吸道黏膜, 微生物学, 宏基因组, 数据说明, 统计

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

邱倩, 刘东鑫, 刘春法, 邱捷, 严晓峰, 赵雁林. 采用宏基因组学分析肺结核患者与健康人群呼吸道微生物菌群的特征[J]. 中国防痨杂志, 2020, 42(10): 1100-1108. doi: 10.3969/j.issn.1000-6621.2020.10.016

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

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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