B-G.19: Improved 16S rRNA-focused computational methods for bacterial strain identification from long read datasets
Jo Dicks
UKHSA
Katharina Huber
UEA
Keywords
Bacterial genomics, rDNA variation, computational pipeline
[sponser-meet-now-chat][/sponser-meet-now-chat]
The 16S region of the ribosomal DNA (rDNA) has for decades served as a vital resource in the identification and classification of bacterial species, first in taxonomic and phylogenetic studies and more recently in metagenomic analysis. However, bacterial genomes contain between 1 and ~15 copies of the 16S, with unquantified levels of sequence variation between them. This poses several questions. How much 16S variation exists within a genome? Do the 16S sequences of distinct species overlap? Can intra-genome 16S variation alter identification outcomes?
We used long PacBio reads from UKHSA's NCTC3000 dataset, which have the capacity to span the 16S gene and beyond the rDNA operon, to assess sequence variation between distinct 16S sequence copies in Escherichia coli, Escherichia marmotae and Shigella genomes. We developed a computational pipeline to extract operon copy-specific reads and create consensus sequences for each rDNA operon. Extensive analysis was then conducted to provide insight into the breadth of 16S alleles and variants within and between both strains and species.
Extensive 16S variation was observed between copies, with 168 distinct 16S alleles amongst the 53 genomes analysed. Despite this high level of variation, almost all alleles were found within a single species, with only three 16S sequences shared between E. coli and Shigella genomes and no overlap between the other genome pairs. This remarkable finding suggests our new pipeline could enable rapid, enhanced bacterial identification capable of discriminating between phylogenetically similar but distinct bacterial species using a multi-allelic 16S method facilitated by long read analysis.
Co-authors: Jo Dicks, Katharina T. Huber
Contact Attendee
Warning: Attempt to read property "user_email" on string in /home/1276969.cloudwaysapps.com/ydbgzhdjeq/public_html/wp-content/plugins/my-conference-now/functions.php on line 2826