Nanopore full length 16S rRNA gene sequencing increases species resolution in bacterial biomarker discovery

≥0.8). Nanopore sequencing identified more specific bacterial biomarkers for colorectal cancer than those obtained with Illumina, such as Parvimonas micra, Fusobacterium nucleatum, Peptostreptococcus stomatis, Peptostreptococcus anaerobius, Gemella morbillorum, Clostridium perfringens, Bacteroides fragilis and Sutterella wadsworthensis. Prediction of colorectal cancer through manual feature selection and machine learning resulted in an AUC of 0.87 with 14 species or 0.82 with just 4 species (P. micra, F. nucleatum, B. fragilis and Agathobaculum butyriciproducens). Full 16S rRNA V1V9 sequencing through Oxford Nanopore and its new R10.4.1 chemistry achieved accurate species-level bacterial identification, facilitating the discovery of more precise disease-related biomarkers and increasing the taxonomic fidelity of future microbiome analyses.