This repository contains the dataset used in the publication "Turnover of strain-level diversity modulates functional traits in the honeybee gut microbiome between nurses and foragers," which is currently under revision. A pre-print can be found here. The database is based on previously published work to create a genomic database of honeybee gut microbes by Kirsten Ellegaard (2021), found here. The zipped folder deposited here after unzipping, should contain the following files and directories: honeybee_genome.fasta : fasta file containing the host (Apis mellifera) genome sequence beebiome_db : fasta file of 198 concatenated genomes with one genome per entry (multi-line fasta) where the headers represent the genome identifier beebiome_red_db : fasta file of 39 species representative genomes with one genome per entry (multi-line fasta) where the headers represent the genome identifier to be used for the analysis of intra-specific variation fna_files : directory containing genome sequence files and concatenated files where the concatenated files contain one fasta entry renamed to the genome identifier and all contigs concatenated into one entry ffn_files : directory containing one file per genome listing the nucleotide sequence of all the predicted genes faa_files : directory containing one file per genome listing the amino acid sequence of all the predicted genes bed_files : directory containing bed files where the location of each of the predicted genes are indicated based on their position in the concatenated genome file single_ortho : directory containing one file per phylotype listing all the single-copy orthogroups (OGs) identified by orthofinder where each line represents an OG id followed by a list of genes from each of the genomes of that phylotype that belong to that OG and the corresponding sequences of these genes can be found in the ffn file belonging to the respective genome red_bed_files : directory containing bed files for species representative genomes that only list the positions genes that belong to the core orthogroups of their phylotype Further information about how this genome database was used to analyze strain-level diversity can be found in the publication and accompanying code repository.