Predicted Functional Annotations, Biosynthetic Gene Clusters, and Peptides for Fermented Food Microbial Isolates from the BacDive Database

This repository contains results and raw files from running the MicrocosmFoods/bac-mining workflow on ~250 bacterial isolate genomes that were sourced from the BacDive database and originally from diverse fermented foods. Specifically, functional annotations were predicted using the Kofam KEGG HMMs, biosynthetic gene clusters (BGCs) were predicted using antiSMASH and two different peptide types - small ORFs (smORFs) and cleavage peptides were predicted on these set of genomes. This repository contains the following files: 

• curated_bacdive_genomes.tar.gz - Compressed archive of FASTA files of the ~250 bacterial BacDive genomes that were downloaded from NCBI
• 2024-12-06-bacdive-accessions-curated-metadata.tsv - Associated metadata for the ~250 bacterial BacDive genomes
• all_molecule_counts.tsv - This is the main summary file that summarizes for each genome the count of each type of molecule such as certain types of BGCs, smorfs, and cleavage peptides
• combined_kofamscan_results.tsv - All Kofam KEGG HMM annotation results
• all_smorfinder_results.tsv - All combined results output from smorfinder
• all_deeppeptide_results.tsv - All combined results from DeepPeptide for predicting cleavage peptides
• 2025-02-24-bacdive-antismash-predictions.zip - All predicted antiSMASH results for each of the ~250 bacterial genomes. The decompressed archive is split by genome, so for example each subdirectory for a genome contains: 
  • genome_name.json - The json summary file of all identified BGCs
  • genome_name.log - The logfile from the antiSMASH run
  • genome_name*.gbk - Each biosynthetic gene cluster identified in GBK format