361 research outputs found

    A geographically-diverse collection of 418 human gut microbiome pathway genome databases

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    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 (ePGDBs) 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 Pathway Tools 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 Pathway Tools.Alexander Graham Bell Canada (Graduate Scholarships-Doctoral Program (CGS D))Tula FoundationUniversity of British Columbia. Faculty of Graduate and Postdoctoral StudiesStanford University. School of Medicine (Dean's Funds)National Institutes of Health (U.S.) (Biotechnology Training Grant, grant number 5T32 GM008412)King Abdullah University of Science and Technology (research grant under the KAUST Stanford Academic Excellence Alliance program)National Institutes of Health (U.S.) (NIH/NIGMS 5R01GM099534)Thomas C. and Joan M. Merigan Endowmen

    O2_UC_4.zip

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    <p>This sample is part of the GutCyc Collection (<a href="http://www.gutcyc.org/" target="_blank">www.gutcyc.org</a>), a compendium of environmental pathway / genome databases. GutCyc was constructed from 418 human microbiome assemblies using the open-source MetaPathways pipeline, that enables reproducible metagenomic annotation.</p

    V1_CD_1.zip

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    <p>This sample is part of the GutCyc Collection (<a href="http://www.gutcyc.org/" target="_blank">www.gutcyc.org</a>), a compendium of environmental pathway / genome databases. GutCyc was constructed from 418 human microbiome assemblies using the open-source MetaPathways pipeline, that enables reproducible metagenomic annotation.</p

    SRS014979_scaffolds.zip

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    <p>This sample is part of the GutCyc Collection (<a href="http://www.gutcyc.org/" target="_blank">www.gutcyc.org</a>), a compendium of environmental pathway / genome databases. GutCyc was constructed from 418 human microbiome assemblies using the open-source MetaPathways pipeline, that enables reproducible metagenomic annotation.</p

    SRS014313.zip

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    <p>This sample is part of the GutCyc Collection (<a href="http://www.gutcyc.org/" target="_blank">www.gutcyc.org</a>), a compendium of environmental pathway / genome databases. GutCyc was constructed from 418 human microbiome assemblies using the open-source MetaPathways pipeline, that enables reproducible metagenomic annotation.</p

    SRS016267.zip

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    <p>This sample is part of the GutCyc Collection (<a href="http://www.gutcyc.org/" target="_blank">www.gutcyc.org</a>), a compendium of environmental pathway / genome databases. GutCyc was constructed from 418 human microbiome assemblies using the open-source MetaPathways pipeline, that enables reproducible metagenomic annotation.</p

    SRS022137.zip

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    <p>This sample is part of the GutCyc Collection (<a href="http://www.gutcyc.org/" target="_blank">www.gutcyc.org</a>), a compendium of environmental pathway / genome databases. GutCyc was constructed from 418 human microbiome assemblies using the open-source MetaPathways pipeline, that enables reproducible metagenomic annotation.</p

    SRS058723.zip

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    <p>This sample is part of the GutCyc Collection (<a href="http://www.gutcyc.org/" target="_blank">www.gutcyc.org</a>), a compendium of environmental pathway / genome databases. GutCyc was constructed from 418 human microbiome assemblies using the open-source MetaPathways pipeline, that enables reproducible metagenomic annotation.</p

    O2_UC_11.zip

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    <p>This sample is part of the GutCyc Collection (<a href="http://www.gutcyc.org/" target="_blank">www.gutcyc.org</a>), a compendium of environmental pathway / genome databases. GutCyc was constructed from 418 human microbiome assemblies using the open-source MetaPathways pipeline, that enables reproducible metagenomic annotation.</p

    NOM017.zip

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    <p>This sample is part of the GutCyc Collection (<a href="http://www.gutcyc.org/" target="_blank">www.gutcyc.org</a>), a compendium of environmental pathway / genome databases. GutCyc was constructed from 418 human microbiome assemblies using the open-source MetaPathways pipeline, that enables reproducible metagenomic annotation.</p
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