Unveiling microbial and helminth diversity in Southern Ocean penguins: insights from amplicon metabarcoding and metagenomics

This thesis addresses several key questions aimed at understanding host-microbial and host-helminth dynamics within Southern Ocean penguin populations. The overall thesis aim is to characterise microbial and helminth diversity in the penguin gut using amplicon metabarcoding of non-invasive faecal samples, and to gain insights into the utility of shotgun metagenomics for the profiling of helminth diversity. The work is presented in three chapters: (2) Composition and Drivers of the Gut Microbiome in Southern Ocean Penguins, (3) Hunting for Helminths: A Comprehensive Evaluation of Bioinformatic Methods in Helminth Detection Using Short- and Long-Read Shotgun Metagenomics, and (4) Helminth Diversity and Transmission Pathways in Southern Ocean Penguin Gut Communities: Insights from Metabarcoding and Shotgun Metagenomics.