GutCyc: a Multi-Study Collection of Human Gut Microbiome Metabolic Models

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 GO_SCPCAPUTC_SCPCAPCO_SCPCAPYCC_SCPCAP, a compendium of environmental pathway genome databases constructed from 418 assembled human microbiome datasets using MO_SCPCAPETAC_SCPCAPPO_SCPCAPATHWAYSC_SCPCAP, enabling reproducible functional metagenomic annotation. We also generated metabolic network reconstructions for each metagenome using the PO_SCPCAPATHWAYC_SCPCAP TO_SCPCAPOOLSC_SCPCAP software, empowering researchers and clinicians interested in visualizing and interpreting metabolic pathways encoded by the human gut microbiome. For the first time, GO_SCPCAPUTC_SCPCAPCO_SCPCAPYCC_SCPCAP provides consistent annotations and metabolic pathway predictions, making possible comparative community analyses between health and disease states in inflammatory bowel disease, Crohns disease, and type 2 diabetes. GO_SCPCAPUTC_SCPCAPCO_SCPCAPYCC_SCPCAP data products are searchable online, or may be downloaded and explored locally using MO_SCPCAPETAC_SCPCAPPO_SCPCAPATHWAYSC_SCPCAP and PO_SCPCAPATHWAYC_SCPCAP TO_SCPCAPOOLSC_SCPCAP.