Viral catalogue from faecal microbiomes of great tits and blue tits

Overview:

The vertebrate gut microbiome plays crucial roles in host health and disease. However, there is limited data on the microbiomes of wild birds, most of which is restricted to barcode sequences. We therefore explored the use of shotgun metagenomics on the faecal microbiomes of two wild bird species widely used as model organisms in ecological studies: the great tit (Parus major) and the Eurasian blue tit (Cyanistes caeruleus). High and Medium quality Metagenome Assembled Genomes (MAGs) were assembled from these metagenomes and are made available as a catalogue in this archive.

Methods:

Metagenomic reads were trimmed, and quality controlled using FastP configured to a minimum phred score of 20 and minimum length of 50 bp. The potential viral and plasmidic sequences were retrieved from the assembled contigs using GeNomad v1.8.0 (Camargo et al. 2023) and the quality of these viral sequences was then assessed using CheckV v 1.0.3 (Nayfach et al. 2021) using the checkV database v 1.5. Putative viral sequences longer than 1000bp carrying at least one hallmark viral gene or no detectable cellular genes were considered in this analysis. The viral sequences were clustered into species-level vOTU clusters using mmseqs2 v2.13 using an identity threshold of 95% over 75% of the longest sequence. For viral species identified as Caudoviral, the potential host was inferred using iPhop v1.3.3 (Roux et al 2023).

Files:

• The vOTU_characteristics.csv table contains the sequence characteristics from CheckV and the viral taxonomy determined by GeNomad
• The vOTU_PredictedHost.csv table contains the viral sequence inferred host from iPhop
• The vOTU_representatives.fasta file contains the fasta sequence of the vOTU representatives