Kin selection explains the evolution of cooperation in the gut microbiota, by Simonet & McNally, 2020, Dataset S1 and codes for statistical analysis and figures production

Dataset S1 contains all raw and processed material referred to in the published article "Kin selection explains the evolution of cooperation in the gut microbiota". R codes files provide all codes to replicate the analysis. Please refer to the README file for a description of all code files. The manifest files are those obtained by accessing the HMP portal on April 2020 under Project > HMP, Body Site > feces, Studies>WGS-PP1, File Type > WGS raw sequences set, File format > FASTQ.

We also provide access to these data and codes at our GitHub (https://github.com/CamilleAnna/HamiltonRuleMicrobiome gitRepos.git) which can be cloned to directly re-run this analysis. 

Legends for Dataset S1:

Sheet 1: Metagenomic samples used and access links.

Sheet 2: Reference on bacterial cooperation retrieved from Web of Science search: TI¯((microb* OR bacter* OR microorganis* OR micro-organis*) AND (coop* OR social*)

Sheet 3: Retained bacteria cooperation keywords

Sheet 4: GOs identified by annotating all MIDAS database genomes (5944 genomes) with PANNZER2.

Sheet 5: Full list of potential bacterial cooperation GO terms and description of manual curation decisions.

Sheet 6: Final list of bacterial cooperation GO used for the analysis

Sheet 7: Genomic diversity of the bacterial population within and across host. Computed from MIDAS snp_diversity.py pipeline.

Sheet 8: final dataset for statistical analysis.

Sheet 9: per-gene annotation of cooperation.