DataSheet_1_The Lung Microbiome of Three Young Brazilian Patients With Cystic Fibrosis Colonized by Fungi.xlsx

Microbial communities infiltrate the respiratory tract of cystic fibrosis patients, where chronic colonization and infection lead to clinical decline. This report aims to provide an overview of the diversity of bacterial and fungal species from the airway secretion of three young CF patients with severe pulmonary disease. The bacterial and fungal microbiomes were investigated by culture isolation, metataxonomics, and metagenomics shotgun. Virulence factors and antibiotic resistance genes were also explored. A. fumigatus was isolated from cultures and identified in high incidence from patient sputum samples. Candida albicans, Penicillium sp., Hanseniaspora sp., Torulaspora delbrueckii, and Talaromyces amestolkiae were isolated sporadically. Metataxonomics and metagenomics detected fungal reads (Saccharomyces cerevisiae, A. fumigatus, and Schizophyllum sp.) in one sputum sample. The main pathogenic bacteria identified were Staphylococcus aureus, Pseudomonas aeruginosa, Burkholderia cepacia complex, and Achromobacter xylosoxidans. The canonical core CF microbiome is composed of species from the genera Streptococcus, Neisseria, Rothia, Prevotella, and Haemophilus. Thus, the airways of the three young CF patients presented dominant bacterial genera and interindividual variability in microbial community composition and diversity. Additionally, a wide diversity of virulence factors and antibiotic resistance genes were identified in the CF lung microbiomes, which may be linked to the clinical condition of the CF patients. Understanding the microbial community is crucial to improve therapy because it may have the opposite effect, restructuring the pathogenic microbiota. Future studies focusing on the influence of fungi on bacterial diversity and microbial interactions in CF microbiomes will be welcome to fulfill this huge gap of fungal influence on CF physiopathology.微生物群落可侵袭囊性纤维化（cystic fibrosis, CF）患者的呼吸道，慢性定植与感染会导致患者临床状况恶化。本研究旨在概述3例伴有重度肺部疾病的年轻CF患者气道分泌物中细菌与真菌物种的多样性。研究通过培养分离法、宏分类组学（metataxonomics）以及鸟枪法宏基因组学（metagenomics shotgun）对细菌与真菌微生物组进行了分析，同时还对毒力因子与抗生素抗性基因进行了探究。研究通过培养分离法从患者痰液样本中检出了高发生率的烟曲霉（Aspergillus fumigatus, A. fumigatus），此外还偶见分离到白假丝酵母（Candida albicans）、青霉属（Penicillium sp.）、汉逊酵母属（Hanseniaspora sp.）、德尔布克托鲁酵母（Torulaspora delbrueckii）以及阿默斯特篮状菌（Talaromyces amestolkiae）。宏分类组学与鸟枪法宏基因组学在1份痰液样本中检出了真菌序列读段（reads），包括酿酒酵母（Saccharomyces cerevisiae）、烟曲霉以及裂褶菌属（Schizophyllum sp.）。本次鉴定出的主要致病菌包括金黄色葡萄球菌（Staphylococcus aureus）、铜绿假单胞菌（Pseudomonas aeruginosa）、洋葱伯克霍尔德菌复合群（Burkholderia cepacia complex）以及木糖氧化无色杆菌（Achromobacter xylosoxidans）。经典的CF核心微生物组由链球菌属（Streptococcus）、奈瑟菌属（Neisseria）、罗氏菌属（Rothia）、普雷沃菌属（Prevotella）以及嗜血杆菌属（Haemophilus）的物种构成。由此可见，3例年轻CF患者的气道内存在优势细菌属，且微生物群落组成与多样性存在个体间差异。此外，本研究在CF肺部微生物组中鉴定出了丰富多样的毒力因子与抗生素抗性基因，这些因子可能与CF患者的临床状况相关。解析该微生物群落对于优化治疗方案至关重要，因为不当的治疗可能产生相反效果，反而会重塑致病微生物群落。未来若能聚焦真菌对CF微生物组中细菌多样性与微生物互作的影响，将有助于填补真菌在CF病理生理学中作用的研究空白。