Metagenomic investigation of the faecal microbiomes of great tits and blue tits - supplementary sequences

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). Mitochondrial genomes from the host and eukaryotic pathogens that 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. Individual sample assemblies were performed on each metagenomic sample using MEGAHIT v1.2.9. The BLAST 2.16 suite of programs was downloaded from ftp.ncbi.nlm.nih.gov/blast and used to perform homology searches of the assemblies, using the makeblastdb utility to generate libraries, the blastn and tblastx utilities to search contigs with query sequences under high stringency (e value ≥1*e-200) and the blastdbcmd utility to retrieve hits from databases.

Files:

The Isospora_mitochondrial.fasta contains the fasta sequences for mitochondrial genomes of the bird pathogen Isospora sp, assembled from two faecal samples from the Great Tit (Parus major).

The Cyanistes.caeruleus_mitochondrial.fasta contains the fasta sequences for mitochondrial genomes of the host bird, assembled from two faecal samples from the blue Tit (Cyanistes caeruleus).

The Parus.major_mitochondrial.fasta contains the fasta sequences for mitochondrial genomes of the host bird, assembled from two faecal samples from the blue Tit (Cyanistes caeruleus).