Comprehensive nemabiome assay development using sequencing data from humans and dog faecal samples

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.