Doctoral Meeting: 'Bioinformatics procedures for the advancement of the implementation of clinical metagenomics'

Clinical metagenomics involves the comprehensive analysis of microbial and host genetic material (DNA and RNA) from patient samples. An important component in this research is the 16S rRNA gene, a highly conserved part of the prokaryotic ribosome that serves as a crucial marker for studying bacterial and archaeal phylogeny and taxonomy. In metagenomic studies, the 16S rRNA gene is amplified using polymerase chain reaction (PCR) with primers targeting its conserved regions.

In this talk, we will explore the impact of the 16S rRNA gene intragenomic redundancy, and present a gene copy number database, 16SGOSeq. We will discuss PrimerEvalPy, our bioinformatics Python package designed to analyse the coverage of primers or primer pairs against any database, i.e., the proportion of target sequences in the dataset that can be effectively amplified by the primer or primer pair. Additionally, we will discuss EPheClass, our curated pipeline for binary phenotype classification based on a count table of 16S rRNA gene amplicons, which can be applied to any microbiome, but we employed to diagnose periodontitis.

• Supervisors: María José Carreira and Inmaculada Tomás.
• Moderator: Alejandro Catalá