Data for "Gut microbial genes are associated with neurocognition and brain development in healthy children"

Datasets accompanying Gut microbial genes are associated with neurocognition and brain development in healthy children, submitted to Nature Microbiology.

Contents:

•  fecal_samples_master.csv
  • Metadata for all fecal samples processed by the Klepac-Ceraj Lab at Wellesley College
• filemakerdb.csv
  • Initial export and parsing (long form) of deidentified patient metadata from internal filemnaker pro database
• gbm.txt
  • Info about potentially neuroactive gene sets
  • This was acquired as Supplementary Dataset 1 from https://doi.org/10.1038/s41564-018-0337-x
• batchXXX_analysis_noknead.tar.gz
  • Sequencing batches 001-012 (see fecal_samples_master.csv for metadata about samples contained in each batch)
  • Each tarball contains:
    • cluster.yaml: configuration file for snakemake pipeline (repo link)
    • config.yaml: run configuration for snakemake pipeline
    • .snakemake/: metadata about snakemake pipeline runs on engaging cluster at MIT
    • output/: outputs from metaphlan2 and humann2 analysis runs. Note: kneaddata sequence files were not included, but will be uploaded to SRA (link to come)
• All uniprot searches were performed 2019-09-19
  • uniprot-abxr.tsv
    • search term: "keyword:\"Antibiotic resistance [KW-0046]\" AND reviewed:yes"
  • uniprot-carbohydrate.tsv
    • search term: "keyword:\"Carbohydrate metabolism [KW-0119]\" AND reviewed:yes"
  • uniprot-fa.tsv
    • search term: (keyword:\"Fatty acid biosynthesis [KW-0275]\" OR keyword:\"Fatty acid metabolism [KW-0276]\") AND reviewed:yes"