Posted on 2016-07-31 - 22:43 authored by Aria S Hahn
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


Hahn, Aria S; Altman, Tomer; Konwar, Kishori M; Hanson, Niels W; Kim, Dongjae; A Relman, David; et al. (2016): GutCyc. figshare. Collection.
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Tomer Altman
Kishori M Konwar
Niels W Hanson
Dongjae Kim
David A Relman
David L Dill
Steven J Hallam


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