Pathogen Identification In Norway Rat (Rattus norvegicus) Faeces Using Long-Read Sequencing Of Bacterial Communities

This study aims to assess the taxonomic resolution of the 16S rRNA V4 region, the full-length 16S rRNA, and the 16S-ITS-23S operon in identifying pathogenic bacterial species in Norway rat droppings. In silico analysis was performed on 168 bacterial genomes from foodborne pathogen genera. Additionally, DNA was extracted from 64 rat droppings collected from various locations across the United Kingdom. Oxford Nanopore Technologies’ (ONT) new R10.4.1 chemistry was employed to sequence the full-length 16S rRNA and 16S-ITS-23S operon, while Illumina technology was used for the 16S rRNA V4 region. Preliminary results suggest that sequencing longer regions (full-length 16S rRNA and 16S-ITS-23S operon) with ONT’s improved R10.4.1 chemistry provides superior species-level resolution, enabling more accurate identification of potential pathogens and comprehensive microbiota profiling.