We describe the technical feasibility of metagenomic water quality analysis using only portable equipment, for example mini-vacuum pumps and filtration units, mini-centrifuges, mini-PCR machines and the memory-stick sized MinION of Oxford Nanopore Technologies, for the library preparation and sequencing of 16S rRNA gene amplicons. Using this portable toolbox on site, we successfully characterized the microbiome of water samples collected from Birtley Sewage Treatment Plant, UK, and its environs. We also demonstrated the applicability of the portable metagenomics toolbox in a low-income country by surveying water samples from the Akaki River around Addis Ababa, Ethiopia. The 16S rRNA gene sequencing workflow, including DNA extraction, PCR amplification, sequencing library preparation, and sequencing was accomplished within one working day. The metagenomic data became available within 24–72 h, depending on internet speed. Metagenomic analysis clearly distinguished the microbiome of pristine samples from sewage influenced water samples. Metagenomic analysis identified the potential role of two bacterial genera not conventionally monitored, Arcobacter and Aeromonas, as predominant faecal pollution indicators/waterborne hazards. Subsequent quantitative PCR analysis validated the high Arcobacter butzleri abundances observed in the urban influenced Akaki River water samples by portable next generation sequencing with the MinION device. Overall, our field deployable metagenomics toolbox advances the capability of scientists to comprehensively monitor microbiomes anywhere in the world, including in the water, food and drinks industries, the health services, agriculture and beyond.

我们描述了仅使用便携式设备进行宏基因组水质分析的技术可行性，例如微型真空泵和过滤装置、微型离心机、微型 PCR 机和 Oxford Nanopore Technologies 的记忆棒大小的 MinION，用于文库制备和16S rRNA 基因扩增子的测序。在现场使用这个便携式工具箱，我们成功地表征了从英国伯特利污水处理厂及其周边地区收集的水样的微生物组。我们还通过调查埃塞俄比亚亚的斯亚贝巴周围阿卡基河的水样，展示了便携式宏基因组学工具箱在低收入国家的适用性。16S rRNA基因测序工作流程，包括DNA提取、PCR扩增、测序文库制备、测序在一个工作日内完成。宏基因组数据在 24-72 小时内可用，具体取决于互联网速度。宏基因组分析清楚地区分了原始样品的微生物组与受污水影响的水样。宏基因组分析确定了两个未按常规监测的细菌属的潜在作用，弓形杆菌和气单胞菌，作为主要的粪便污染指标/水传播危害。随后的定量 PCR 分析通过使用 MinION 设备进行便携式下一代测序，验证了在受城市影响的 Akaki 河水样中观察到的高丰度布氏弓杆菌。总的来说，我们可现场部署的宏基因组学工具箱提高了科学家全面监测世界各地微生物组的能力，包括水、食品和饮料行业、卫生服务、农业等。