Whole Genome Sequencing (WGS) relies on the availability of high-quality reference genomes. Many of them are now being sequenced by multiple genomics consortia such as the Vertebrate Genomes Project.
SNP profiles based on WGS provide the highest resolution to both identify genomic structure of species and populations and establish associations between genomic and microbial metagenomic traits.
Acknowledging the structure of wild animal populations enables estimating population sizes, connectivity across populations and other relevant factors to understand the impact of host-microbiota interactions.
Overlapping patterns of DNA sequences recovered from oral and anal swabs and faeces are used to generate long DNA sequences that are used to characterise microbial genomes.
Bacterial genomes are reconstructed based on genetic properties and abundance patterns of DNA sequences characterised from metagenomic samples.
The use of reference-free approaches enables detecting and characterising hidden diversity not still represented in public databases.
We are currently trialing a standardised homemade preservation buffer which will reduce costs, commercial dependence and increase longevity of the Initiative. Samples will be registered using the QR codes of the tubes, and linked to the metadata provided by the field researchers. Biological samples will be stored in the sample storage facility of the EHI at -20ºC until DNA extraction is carried out.
We are using robots to fill and label tubes included in the Sampling kits, as well as to extract DNA and prepare sequencing libraries. In doing so, we ensure rapid reaction to collaborators' needs for sampling material and high-throughput processing of biological samples.
We multiplex libraries derived from multiple samples and taxa to sequence animal genomes and microbial metagenomes at the lowest fares and fastest throughput, using the most advanced sequencing technologies.
Relevant metadata of the sampling events, sampled animals, processed samples and generated data are stored in the central EHI database.
Genomic and metagenomic data belonging to each animal individual, as well as assemblies and bacterial MAGs derived from them, are stored at the European Nucleotide Archive (ENA), and are available to all researchers.
Results are disseminated via publishing articles under open access license, and participating in international conferences.