title: A geographically-diverse collection of 418 human gut microbiome pathway genome databases.
abstract: 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.
authors.affiliation: Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.|Koonkie Inc., Menlo Park, California 94025, USA.
authors.forename: Aria S
authors.initials: AS
authors.lastname: Hahn
authors.affiliation: Biomedical Informatics, Stanford University School of Medicine, Stanford, California 94305, USA.|Whole Biome, Inc., 953 Indiana Street, San Francisco, California 94107, USA.
authors.forename: Tomer
authors.identifier: 0000-0002-6521-5454
authors.initials: T
authors.lastname: Altman
authors.affiliation: Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.|Koonkie Inc., Menlo Park, California 94025, USA.|Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
authors.forename: Kishori M
authors.initials: KM
authors.lastname: Konwar
authors.affiliation: Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.
authors.forename: Niels W
authors.initials: NW
authors.lastname: Hanson
authors.affiliation: Department of Computer Science, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.
authors.forename: Dongjae
authors.initials: D
authors.lastname: Kim
authors.affiliation: Department of Microbiology and Immunology, Stanford University School of Medicine, 299 Campus Drive, Stanford, California 94305, USA.|Department of Medicine, Stanford University School of Medicine, Stanford, California 94305, USA.|Veterans Affairs Palo Alto Health Care System, Palo Alto, California 94304, USA.
authors.forename: David A
authors.initials: DA
authors.lastname: Relman
authors.affiliation: Department of Computer Science, Stanford University, Stanford, California 94305, USA.
authors.forename: David L
authors.initials: DL
authors.lastname: Dill
authors.affiliation: Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.|Koonkie Inc., Menlo Park, California 94025, USA.|Ecosystem Services, Commercialization and Entrepreneurship (ECOSCOPE), University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.
authors.forename: Steven J
authors.initials: SJ
authors.lastname: Hallam
mesh_terms: D003424:Crohn Disease / Q000382:microbiology; D030541:Databases, Genetic; D003924:Diabetes Mellitus, Type 2 / Q000382:microbiology; D000069196:Gastrointestinal Microbiome; D062306:Geography, Medical; D006801:Humans; D015212:Inflammatory Bowel Diseases / Q000382:microbiology; D053858:Metabolic Networks and Pathways; D054892:Metagenome; D056186:Metagenomics