ABSTRACT

The lung microbiome plays an important role in the pathophysiological processes associated with pulmonary tuberculosis (PTB). However, only a few studies using 16S rDNA amplicon sequencing have been reported, and the interactions between Mycobacterium tuberculosis (MTB) and the lung microbiome remain poorly understood. Patients with respiratory symptoms and imaging abnormalities compatible with tuberculosis (TB) were enrolled. We analyzed the lung microbiome in bronchoalveolar lavage (BAL) samples from 30 MTB-positive (MTB+) subjects and 30 MTB negative (MTB-) subjects by shotgun metagenomic sequencing. Alpha diversity tended to be lower in the MTB+ group than in the MTB- group. There was a significant difference in beta diversity between the MTB+ and MTB- subjects. MTB+ lung samples were dominated by MTB, while MTB- samples were enriched with Streptococcus, Prevotella, Nesseria, Selenomonas and Bifidobacterium, which more closely resemble the microbial composition of a healthy lung. Network analysis suggested that MTB could greatly impact the microbial community structure. MTB+ and MTB- communities showed distinct functional signatures. Fungal communities were also found to be associated with the presence or absence of MTB. Furthermore, it was confirmed that 16S rDNA amplicon sequencing underrepresents Mycobacterium. This pilot study is the first to explore the interplay between MTB and the host microbiome by using metagenomic sequencing. MTB dominates the lung microbiome of MTB+ subjects, while MTB- subjects have a Streptococcus-enriched microbiome. The 16S approach underrepresents Mycobacterium and is not the best way to study the TB-associated microbiome.

摘要

肺微生物组在与肺结核（PTB）相关的病理生理过程中起着重要作用。然而，仅报道了使用16S rDNA扩增子测序的几项研究，而结核分枝杆菌（MTB）与肺微生物组之间的相互作用仍然知之甚少。招募有呼吸道症状和影像学异常与结核病（TB）相容的患者。我们通过散弹枪宏基因组测序对来自30名MTB阳性（MTB +）受试者和30名MTB阴性（MTB-）受试者的支气管肺泡灌洗（BAL）样品中的肺微生物组进行了分析。MTB +组的Alpha多样性往往低于MTB-组。Beta有显着差异MTB +和MTB-主题之间的多样性。MTB +肺样品通过MTB为主，而MTB-样品用富集链球菌，普雷沃，Nesseria，月形和双歧杆菌，它更接近类似于健康肺的微生物组合物。网络分析表明，MTB可能会极大地影响微生物群落结构。MTB +和MTB-社区显示出不同的功能特征。还发现真菌群落与MTB的存在与否有关。此外，已证实16S rDNA扩增子测序不足代表分枝杆菌。该初步研究是第一个使用宏基因组测序探索MTB与宿主微生物组之间相互作用的研究。MTB在MTB +受试者的肺微生物组中占主导地位，而MTB-受试者具有链球菌富集的微生物组。16S方法不足以代表分枝杆菌，也不是研究结核病相关微生物组的最佳方法。