Bioinformatics Seminar
Time: 11AM
Venue: Online
22 August 2023
High taxonomic resolution of bacterial microbiomes using full 23S and full 16S amplicons from nanopore sequencing
Chris WoodruffWEHI Bioinformatics
An assessment was undertaken of the feasibility of strain-level identification and quantification of bacterial organisms in an amplicon-based, nanopore-sequenced microbiome sample. A dataset from a metagenomic shotgun-sequenced mock microbiome (Sereika et al., 2019) was used to derive in-silico 16S and 23S amplicons. The sequencing used an Oxford Nanopore Technology's R10.4.1 GridION system. Based on denoising using Kumar et al.'s Robust Amplicon Denoiser (RAD) code (2019),and a custom-built, operon-based reference database, it is shown that, with a low level of ambiguity, strain-level identification is achieved. This is despite some of the alternative strains in the reference database for the species present in the mock microbiome differing little from the true strains. Abundance estimation is described, and results indicating promising results presented. The importance, and also limitations, of operon-level considerations when identification at better than species level is sought are illustrated.