通过纳米孔测序进行空气监测。

IF 5.1 Q1 ECOLOGY
ISME communications Pub Date : 2024-07-16 eCollection Date: 2024-01-01 DOI:10.1093/ismeco/ycae099
Tim Reska, Sofya Pozdniakova, Sílvia Borràs, Albert Perlas, Ela Sauerborn, Lídia Cañas, Michael Schloter, Xavier Rodó, Yuanyuan Wang, Barbro Winkler, Jörg-Peter Schnitzler, Lara Urban
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引用次数: 0

摘要

虽然空气微生物组及其多样性对人类健康和生态系统的恢复能力至关重要,但全面的空气微生物多样性监测仍然很少见,因此人们对空气微生物组的组成、分布或功能知之甚少。在这里,我们展示了基于纳米孔测序的元基因组学,结合通过液体撞击进行的主动空气采样和量身定制的计算分析,可以对空气微生物组进行强有力的评估。我们为空气微生物组分析提供了快速、便携的实验室和计算方法,并利用这些方法对受控温室环境和室外自然环境中核心空气微生物组的分类组成进行了有力评估。我们表明,尽管作为纳米孔测序输入的片段 DNA 数量较少,但长读程测序可以通过全新的元基因组组装解析物种级注释和特定生态系统功能。然后,我们以西班牙巴塞罗那为例,应用我们的管道评估了城市空气微生物组的多样性和变异性;这一随机实验首次揭示了城市边界内存在高度稳定的特定地点空气微生物组,并展示了通过自动化、快速、便携的纳米孔测序技术可以实现的强大微生物评估功能。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Air monitoring by nanopore sequencing.

While the air microbiome and its diversity are essential for human health and ecosystem resilience, comprehensive air microbial diversity monitoring has remained rare, so that little is known about the air microbiome's composition, distribution, or functionality. Here we show that nanopore sequencing-based metagenomics can robustly assess the air microbiome in combination with active air sampling through liquid impingement and tailored computational analysis. We provide fast and portable laboratory and computational approaches for air microbiome profiling, which we leverage to robustly assess the taxonomic composition of the core air microbiome of a controlled greenhouse environment and of a natural outdoor environment. We show that long-read sequencing can resolve species-level annotations and specific ecosystem functions through de novo metagenomic assemblies despite the low amount of fragmented DNA used as an input for nanopore sequencing. We then apply our pipeline to assess the diversity and variability of an urban air microbiome, using Barcelona, Spain, as an example; this randomized experiment gives first insights into the presence of highly stable location-specific air microbiomes within the city's boundaries, and showcases the robust microbial assessments that can be achieved through automatable, fast, and portable nanopore sequencing technology.

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