CBA_DREAMM (CBA Data Repository of Expression, Amplicon, Metagenomic, Metabolites)

CBA_DREAMM (CBA Data Repository of Expression, Amplicon, Metagenomic, Metabolites) is a fecal CBA-specific microbiome resource that spans diet, time, and pathogen gradients. This resource includes amplicon, metagenomic, and metatranscriptomic sequencing, and metabolomics, to unveil microbial functionalities. More descriptive info about CBA-DREAMM resource can be found in the CBA-DREAM- a diet and time-resolved multi-omics CBA gut microbiome resource.pdf document and file descriptions are written below.

-              CBA_DREAM_metadata.txt: Sample overview for all sequencing data with accession numbers and sample metadata (round, cage, mouse, day, treatment, diet, mouse_id). Here we include analyzed data, with all raw data deposited under PRJNA348350 Bioproject in NCBI.

-              16S rRNA amplicon data for 1754 samples

o   Amplicon_taxonomy_silva.txt: ASV taxonomy file generated using SILVA release 132 SSU Ref NR 99

o   Amplicon_featuretable.csv: feature table of ASVs per sample

-              Metagenomic data for 17 samples

o   CBA_DREAM_metaG_seq_info.txt: metagenomic sequencing information (number of reads, Gbp, sequencer, library type)

o   CBA_DREAM_drep_MAG_info.txt: description of 160 dereplicated metagenome assembled genomes (MAGs) including taxonomy (vContact2), quality, and sample information

o   CBAJDB_v1.2_MQHQ_drepped_MAGs.tar.gz: contains all drepped 160 MAGs

o   All_609vMAGs.fasta: contains fasta of 609 drepped vMAGs

o  CBA_DREAM_drep_vMAG_info.xlsx: description of 609 depreplicated vMAGs including quality, taxonomy, vMAG annotations from DRAM, read mapping to metaG for abundances, host-viral linkages, and MAG AMG hits. 

o   DRAM_annotations_files.zip: contains DRAM annotations for 160 dereplicated MAGs, genes.faa, genes.gff, genes.fna, rrna, tsv, scaffolds.fna, and trna.tsv

o   DRAMvMAGs_annotations_files.zip: contains DRAM annotations for 609 dereplicated vMAGs, genes.faa, genes.gff, genes.fna, rrna, tsv, scaffolds.fna, and trna.tsv

-              Metatranscriptomics for 43 samples

o   CBA_DREAM_metaT_seq_info.txt: metatranscriptomic sequencing information (number of reads, Gbp, sequencer, library type)

o   counts_scaffoldmapCBAJDB1.2_97.txt: counts mapped at 97% identity to dereplicated genes of CBAJ-DB version 1.2 across chow fed mice metatranscriptomes **It is advisable that counts are normalized via geTMM, TMM, FPKM, or other metatranscriptome normalization methods

o   counts_scaffoldmapCBAJDB1.2_95.txt counts mapped at 95% identity to dereplicated genes of CBAJ-DB version 1.2 across chow fed mice **It is advisable that counts are normalized via geTMM, TMM, FPKM, or other metatranscriptome normalization methods metatranscriptomes

o   counts_genemap_salmonella_pangenome_97.xlsx: counts mapped at 97% identity to a salmonella pangenome across chow fed and high-fat diet fed mice metatranscriptomes **It is advisable that counts are normalized via geTMM, TMM, FPKM, or other metatranscriptome normalization methods

o   getmm_genemap_salmonella_pangenome_97.csv: geTMM normalize counts mapped at 97% identity to a salmonella pangenome across chow fed and high-fat diet fed mice metatranscriptomes

-              Metabolomics for 40 samples- analyzed data included here

o   SCFA_concentrations.txt: short chain fatty acid concentrations (acetate, propionate, and butyrate) obtained from fecal samples (13 samples) of mice fed a fibrous chow diet without Salmonella, a high-fat diet without Salmonella or a high-fat diet with Salmonella at day 7.

o   annotation_normabundance_metabolomics.xlsx: normalized metabolite abundance obtained across 27 fecal samples.

Scripts and more information can be found here:

            https://github.com/Kokkinias/HFDtimeseries

            https://github.com/ileleiwi/Salmonella-Multiomics-Paper

            https://zenodo.org/records/8395759