Ghosh Abhirupa, Saha Sudipto
Division of Bioinformatics, Bose Institute, Kolkata - 700091, India.
J Med Microbiol. 2022 Dec;72(12). doi: 10.1099/jmm.0.001617.
Studying taxonomic and functional signatures of respiratory microbiomes provide a better understanding of airway diseases.. Several human airway metagenomics studies have identified taxonomic and functional features restricted to a single disease condition and the findings are not comparable across airway diseases due to use of different samples, NGS platforms, and bioinformatics databases and tools. To study the microbial taxonomic and functional components of sputum microbiome across airway diseases and healthy smokers. Here, 57 whole metagenome shotgun sequencing (WMSS) runs coming from the sputum of five airway diseases: asthma, bronchiectasis, chronic obstructive pulmonary diseases (COPD), cystic fibrosis (CF), tuberculosis (TB), and healthy smokers as the control were reanalysed using a common WMSS analysis pipeline. Shannon's index (alpha diversity) of the healthy smoker group was the highest among all. The beta diversity showed that the sputum microbiome is distinct in major airway diseases such as asthma, COPD and cystic fibrosis. The microbial composition based on differential analysis showed that there are specific markers for each airway disease like as a marker for COPD and as a marker cystic fibrosis. Pathways and metabolites identified from the sputum microbiome of these five diseases and healthy smokers also show specific markers. 'ppGpp biosynthesis' and 'purine ribonucleosides degradation' pathways were identified as differential markers for bronchiectasis and COPD. In this meta-analysis, besides bacteria kingdom, was detected in asthma and COPD, and Roseolovirus human betaherpesvirus 7 was detected in COPD. Our analysis showed that the majority of the gene families specific to the drug-resistant associated genes were detected from opportunistic pathogens across all the groups. In summary, the specific species in the sputum of airway diseases along with the microbial features like specific gene families, pathways, and metabolites were identified which can be explored for better diagnosis and therapy.
研究呼吸道微生物群的分类学和功能特征有助于更好地理解气道疾病。多项人类气道宏基因组学研究已确定了仅限于单一疾病状态的分类学和功能特征，由于使用了不同的样本、二代测序平台以及生物信息学数据库和工具，这些研究结果在不同气道疾病之间无法进行比较。为了研究跨气道疾病和健康吸烟者痰液微生物群的微生物分类学和功能成分。在此，我们使用通用的全基因组鸟枪法测序（WMSS）分析流程，重新分析了来自五种气道疾病（哮喘、支气管扩张症、慢性阻塞性肺疾病（COPD）、囊性纤维化（CF）、肺结核（TB））患者痰液的57次全基因组鸟枪法测序数据，以及作为对照的健康吸烟者的痰液数据。健康吸烟者组的香农指数（α多样性）在所有组中最高。β多样性分析表明，痰液微生物群在哮喘、COPD和囊性纤维化等主要气道疾病中存在差异。基于差异分析的微生物组成显示，每种气道疾病都有特定的标志物；例如， 作为COPD的标志物， 作为囊性纤维化的标志物。从这五种疾病和健康吸烟者的痰液微生物群中鉴定出的通路和代谢物也显示出特定的标志物。“鸟苷四磷酸（ppGpp）生物合成”和“嘌呤核糖核苷降解”通路被确定为支气管扩张症和COPD的差异标志物。在这项荟萃分析中，除细菌域外，在哮喘和COPD中检测到了 ，在COPD中检测到了玫瑰疹病毒人类β疱疹病毒7。我们的分析表明，所有组中大多数与耐药相关基因特异的基因家族都来自机会性病原体。总之，我们确定了气道疾病痰液中的特定物种以及特定基因家族、通路和代谢物等微生物特征，这些可用于探索更好的诊断和治疗方法。
