Indoor microbiome exposure is important for asthma development, but current studies characterize the microbiome at the genus or above levels due to technical limitations. We aim to profile bacterial and fungal composition and concentration at the species level and assess its potential health effects. Four hundred sixty-three students from 8 junior high schools in Terengganu, Malaysia, were surveyed for asthma symptoms. Full-length PacBio amplicon sequencing and qPCR were conducted to quantify the absolute microbial concentration in the vacuum dust of the selected classroom. In total, 1358 bacterial and 358 fungal species were characterized, and drastic compositional variation was observed among classrooms. Three-level linear regression analyses revealed that taxa richness in Cyanobacteria were negatively associated with asthma (FDR < 0.001). The absolute concentration of Nocardioides exalbidus was protectively associated with asthma, and four bacteria species were positively associated with asthma (FDR < 0.1). Interestingly, all five species were recently isolated and characterized in Asian countries and never reported to associate with asthma. Indoor NO₂ and formaldehyde concentration were associated with the overall bacterial community variation and fungal richness, respectively (p < 0.05). No environmental characteristics were directly associated with asthma, but indoor relative humidity, CO₂ concentration, and weight of vacuum dust were associated with the asthma-related species (p < 0.05), suggesting a potential indirect health effect on students. This is the first study to characterize indoor microbiome and asthma-associated microorganisms at the species level, representing a region-specific microbiome exposure pattern in a tropical Asian country.

室内微生物组暴露对哮喘的发展很重要，但由于技术限制，目前的研究将微生物组定性为属或以上水平。我们的目标是在物种水平上分析细菌和真菌的组成和浓度，并评估其潜在的健康影响。来自马来西亚登嘉楼 8 所初中的 463 名学生接受了哮喘症状调查。进行全长 PacBio 扩增子测序和 qPCR 以量化所选教室真空灰尘中的绝对微生物浓度。总共对 1358 种细菌和 358 种真菌进行了表征，并且在教室之间观察到了剧烈的组成变化。三级线性回归分析显示，蓝藻中丰富的分类群与哮喘呈负相关（FDR < 0.001）。Nocardioides exalbidus与哮喘呈保护性相关，四种细菌与哮喘呈正相关（FDR < 0.1）。有趣的是，所有五个物种最近都在亚洲国家被分离出来并进行了表征，并且从未报告过与哮喘有关。室内NO ₂和甲醛浓度分别与总体细菌群落变异和真菌丰富度相关（p  < 0.05）。没有环境特征与哮喘直接相关，但室内相对湿度、CO ₂浓度和真空粉尘重量与哮喘相关物种有关（p < 0.05)，表明对学生有潜在的间接健康影响。这是第一项在物种水平上表征室内微生物组和哮喘相关微生物的研究，代表了热带亚洲国家特定区域的微生物组暴露模式。