iamm-collection

This repo is used to consolidate various metadata related to a large portion of the Segrè lab's microbial strains. The majority of this work originated from the HFSP collaboration Interactions Among Marine Microbes (IAMM).

The result is a master metadata file which should be used as primary point of information on any of the strains covered.

Master Metadata File Column Structure

• ds_strain_id: This is the unique strain identifier across projects. It stands for "Daniel Segrè lab strain identifier" This ID must be used for all work related to these strains for consistencies.
• phylum, class, ..., strain_designation: Names of Strain at various taxonomic levels
• source, source_catalog_number: Where we got the strain from.
• id_...: Project-specific identifiers. See below for specific labels. This value together with the value of column ds_strain_id can serve to map between different projects. In addition, presence of a value in these columns indicates that this strain is being used in a particular project.
• RES_..., LIB_..., ZOC_...: Project-specific metadata, included for convenience. See below for specific labels.

Involved Projects

The following projects have in some way dealt with (some) of the strains:

• re-sequencing/RES: Re-sequencing of bacteria retrieved from various sources to investigate genome variation.
• marine_library/LIB: The Segrè lab library of marine microbial strains covering a wide range of (potential interaction) traits based on in silico analysis by Zoccerato et al. (ZOC). This is a physical strain library which is in our -80 °C.
• forchielli22/FOR: Phenotyping of marine bacteria on single carbon sources. DOI: https://doi.org/10.1128/msystems.00070-22
• zoccarato22/ZOC: An in silicon study across 473 to identify genome functional clusters (GFCs) grouping strains with similar traits (potentially involved in microbial interactions). DOI: https://doi.org/10.1038/s42003-022-03184-4

Consolidation Process

• Used metadata_merge.R to merge and unify strain metadata of RES and FOR projects.
  • This used the following metadata files as input:
    • metafile.csv: initial metafile of the RES project
    • forchielli2022-....xlsx: FOR metadata
  • This created master_metadata_file.tsv
• The metadata from projects FOR and RES in file master_metadata_file.tsv where manually combined, curated and integrated resulting in 20231026-master_metadata_file-curated.xlsx.
• Used consolidation_euler.R to integrate the curated metadata with LIB and ZOC project's:
  • This used the following metadata files as input:
    • 20231026-master_metadata_file-curated.xlsx
    • 20240122-strain_lib.tsv: LIB metafile of the marine strain library
      • created initially by Konrad, 2022-11-01 using 20221101-metadata_merge.R, curated by hand 2023-12-13 and 2024-01-22
    • zoccarato2022-....xlsx: ZOC metadata
    • 20231205-map-metadata_zoccarrato22.tsv: file used for manual mapping to ZOC metadata after using heuristics (mapping by Species, Reference-file, Source ID)
  • This creates a dated version of IAMM_metadata_file.tsv and the Euler diagram below.
• Since IAMM_metadata_file.tsv was initially copied/renamed from its dated version produced by the above process and also put under version control. Further changes need to be carefully curated and committed.