This work package focuses on the analysis of sequencing data from the rumen, colon, and milk microbiomes, provided by the groups contributing to Work Packages 3 and 6.

Work package 4 is divided into three main steps:

1. Impact of algae feeding on the composition of cow microbiomes

To assess how feeding Baltic Sea algae and their extracts influences the bacterial composition of the rumen, colon, and raw milk microbiomes, 16S rRNA-based analyses will be conducted.These analyses enable the characterization of microbial diversity and community composition, and facilitate the identification of potentially beneficial bacterial species that may contribute to improved animal health and reduced methane emissions.

2. Metagenomic analysis of rumen microbiomes

Selected rumen samples will undergo comprehensive metagenomic sequencing using PacBio HiFi technology to analyze the complete genetic repertoire of the rumen microbial community beyond basic compositional data. State-of-the-art bioinformatic pipelines will be applied to reconstruct metagenome-assembled genomes (MAGs) from both prokaryotic and eukaryotic sequences. These MAGs will be taxonomically classified and structurally annotated to generate predicted protein sequences with preliminary functional annotations.

3. Identification of polysaccharide-degrading organisms and enzymes

The metagenomic data will form the foundation for downstream proteomic analysis (Work Package 6) and provide crucial insights into (uncultivated) key organisms capable of degrading algal polysaccharides. Using advanced bioinformatics pipelines, prokaryotic and eukaryotic sequences will be separated, and specific protein-coding genes identified. This integrative analysis will support the functional characterization of carbohydrate-active enzymes (CAZymes) and their potential use in biotechnology.