The mOTUs online database provides web-accessible genomic context to taxonomic profiling of microbial communities - Supplementary Tables

Supplementary Table 1:

A map between each of the genomes in mOTUs-db (3’747’151), the associated study and its metagenomic sample (in case of MAGs).

Columns:

    GENOME             → Unique mOTUs-db name of the genome    STUDY              → Unique mOTUs-db name of the study    IS_MAG             → True if genome is a MAG, otherwise False     METAGENOMIC_SAMPLE → Unique name of the metagenomic sample or NA in case of non-MAG genome

Example:

    GENOME                                     STUDY        IS_MAG    METAGENOMIC_SAMPLE    ---------------------------------------------------------------------------------------------    ACIN21-1_SAMN05421555_MAG_00000001         ACIN21-1     True      ACIN21-1_SAMN05421555_METAG    RSGB23-1_GCA-006096615-V1_GENO_10000001    RSGB23-1     False     NA

Supplementary Table 2:

A map between all non-MAG genomes (919’090) and their source (e.g. Refseq or JGI).

Columns:

    GENOME             → Unique mOTUs-db name of the genome    SOURCE_SAMPLE_LINK → Link to the original location of this genome

Example:

    #GENOME                                     SOURCE_SAMPLE_LINK    --------------------------------------------------------------------------------------------------------    JGIG23-1_GA0055041_GENO_10000001            https://gold.jgi.doe.gov/analysis_project?id=Ga0055041    RSGB23-1_GCA-006717865-V1_GENO_10000001     https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_006717865.1

Supplementary Table 3:

A list of all metagenomic studies processed for the mOTUs-db, their number of samples, the number of reconstructed MAGs and the associated publication.

Columns:

    STUDY       --> Unique mOTUs-db study identifier    BIOPROJECT  --> Public identifier (NCBI/JGI) of metagenomic sequencing project    SAMPLES     --> Number of metagenomic samples    MAGs        --> Number of reconstructed MAGs    PUBLICATION --> Link to publication

Example:

    STUDY        BIOPROJECT    SAMPLES    MAGs     PUBLICATION    -------------------------------------------------------------------------------------------------    ACIN21-1     PRJEB44456    58         1,110    https://www.nature.com/articles/s42003-021-02112-2

Supplementary Table 4:

Mapping between mOTUs-db sample identifier, the associated biosample and the environment.

Columns:

    SAMPLE             --> Unique mOTUS-db sample identifier    BIOSAMPLE          --> Public identifier (NCBI/JGI) of metagenomic sample    STUDY              --> Unique mOTUs-db study identifier    ENVIRONMENT        --> Environment of metagenomic sample    SOURCE_SAMPLE_LINK --> Link to the original location of this sample

Example:

    #SAMPLE                      BIOSAMPLE     STUDY    ENVIRONMENT  SOURCE_SAMPLE_LINK    ---------------------------------------------------------------------------------------------------------------------    ACIN21-1_SAMN05421555_METAG  SAMN05421555  ACIN21-1 marine       https://www.ncbi.nlm.nih.gov/biosample/SAMN05421555/

Supplementary Table 5:

A list of environments covered in the mOTUs-db mapped to the respective NCBI taxonomy (if possible)

Columns:

    TERM             --> Unique environment name    NCBI TAXONOMY ID --> Link to the NCBI taxonomy

Example:

    TERM                          NCBI TAXONOMY ID    ----------------------------------------------    activated sludge metagenome   NCBI:txid942017    air metagenome                NCBI:txid655179