GutCyc

Advances in high-throughput sequencing are reshaping how we

    perceive microbial communities inhabiting the human body, with

    implications for therapeutic interventions. Several large-scale

    datasets derived from hundreds of human microbiome samples sourced

    from multiple studies are now publicly available. However,

    idiosyncratic data processing methods between studies introduce

    systematic differences that confound comparative analyses. To

    overcome these challenges, we developed GutCyc, a compendium of

    environmental pathway genome databases constructed from 418

    assembled human microbiome datasets using MetaPathways, enabling

    reproducible functional metagenomic annotation. We also generated

    metabolic network reconstructions for each metagenome using the

    ptools software, empowering researchers and clinicians

    interested in visualizing and interpreting metabolic pathways

    encoded by the human gut microbiome. For the first time, GutCyc

    provides consistent annotations and metabolic pathway predictions,

    making possible comparative community analyses between health and

    disease states in inflammatory bowel disease, Crohn's disease, and

    type 2 diabetes. GutCyc data products are searchable online, or

    may be downloaded and explored locally using MetaPathways and

    ptools.