Comprehensive nemabiome assay development using sequencing data from humans and dog faecal samples. Homo sapiens and Canis lupus familiaris

Gastrointestinal nematodes (GINs) severely affect animals, including humans, by causing serious morbidity whilst also exacerbating cycles of poverty. Attempts to characterise all GIN species simultaneously, i.e. the nemabiome have been developed using next-generation sequencing (NGS). To date, these methods have relied on short-read NGS platforms that can only detect limited genera and for some taxa cannot classify to a species level. Improving upon this, we demonstrate how a nanopore sequencing approach can accurately characterise the complete nemabiome from animals and humans. This novel nemabiome assay was developed and validated using positive controls and field samples from humans and canines. Overall, long-read nanopore sequencing provides unprecedented species classification accuracy and more comprehensive characterisation of GIN communities in a way previously unachievable using older technologies.

胃肠道线虫（Gastrointestinal nematodes，简称GINs）会引发严重的发病症状，同时加剧贫困循环，对包括人类在内的多种动物造成严重危害。已有研究尝试通过下一代测序（next-generation sequencing，NGS）技术，开发可同时表征所有胃肠道线虫物种的分析方法，即线虫宏基因组（nemabiome）分析；但迄今为止，此类方法均依赖短读长NGS平台，仅能检测有限的线虫属类群，且针对部分分类单元无法完成物种水平的分类鉴定。针对上述技术局限，本研究验证了纳米孔测序（nanopore sequencing）技术可精准完成人和动物体内完整线虫宏基因组的特征解析。本研究通过人类与犬类的阳性对照样本及田间样本，开发并验证了这款新型线虫宏基因组检测方法。总体而言，长读长纳米孔测序可实现前所未有的物种分类鉴定精度，且能更全面地表征胃肠道线虫群落，这是过往技术无法达成的分析效果。