Next-generation sequencing (NGS) and advances in microbiota knowledge are opening new perspectives for environmental microbiology and public health. Massive parallel sequencing of bacterial DNA is providing new insights to unravel microbial dissemination in different matrices, including air. Here, we have assessed the air biodiversity in several indoor environments by NGS-based metagenomics and compared results with respect to classical approaches. Environmental sampling was achieved in three exemplificative indoor locations: offices, recreational facilities and public restrooms. Sampling was performed by active (surface air system and high-volume aerosol collection system) and passive (index of microbial air contamination and novel tissue-based passive sampling) techniques. Collected samples were tested by traditional microbiology and DNA-based methods. Biodiversity indices were computed using EstimateS software. Statistical analysis by SPSS and R was applied to determine the variability of bacteria groups after comparing sampling and analysis protocols. In each point ( n = 6), air was sampled in duplicate by four methods and tested in parallel by culture-based and DNA-based approaches. A total of over 30 ± 10 isolates for each point were identified at species level. A total of 3,207,415 sequence reads were generated by NGS analysis, leading to the identification of over 170 OTUs. NGS analyses of air biodiversity were more informative when using active sampling methods (0.729, p < 0.05) and less by passive methods (− 0.897, p < 0.05). NGS allowed a comprehensive and reproducible evaluation of air microbiota and the definition of microbial signatures. Air can be assayed by NGS using different strategies, representing a promising tool for evaluating microbial load and biodiversity. Although NGS requires sophisticated equipment, bioinformatics tools and trained personnel, we propose a model for the evaluation of indoor air quality in occupational and public health settings.

中文翻译：

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空气微生物群能否成为公共卫生的新标志物？来自不同环境的采样模型和初步数据

新一代测序 (NGS) 和微生物群知识的进步为环境微生物学和公共卫生开辟了新的视角。细菌 DNA 的大规模平行测序为解开微生物在不同基质（包括空气）中的传播提供了新的见解。在这里，我们通过基于 NGS 的宏基因组学评估了几种室内环境中的空气生物多样性，并将结果与​​经典方法进行了比较。环境采样是在三个典型的室内位置实现的：办公室、娱乐设施和公共厕所。采样是通过主动（表面空气系统和大容量气溶胶收集系统）和被动（微生物空气污染指数和新型基于组织的被动采样）技术进行的。收集的样本通过传统的微生物学和基于 DNA 的方法进行测试。使用 EstimateS 软件计算生物多样性指数。在比较采样和分析方案后，应用 SPSS 和 R 的统计分析来确定细菌群的变异性。在每个点 (n = 6)，通过四种方法对空气进行一式两份采样，并通过基于培养和基于 DNA 的方法进行平行测试。在物种水平上确定了每个点总共超过 30 ± 10 个分离株。NGS 分析共生成了 3,207,415 个序列读数，从而鉴定了 170 多个 OTU。使用主动采样方法 (0.729, p < 0.05) 和被动方法 (- 0.897, p < 0.05) 时，NGS 对空气生物多样性的分析提供更多信息。NGS 允许对空气微生物群和微生物特征的定义进行全面和可重复的评估。NGS 可以使用不同的策略对空气进行检测，这是评估微生物负荷和生物多样性的一种很有前景的工具。尽管 NGS 需要精密的设备、生物信息学工具和训练有素的人员，但我们提出了一种评估职业和公共卫生环境中室内空气质量的模型。