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Advances in high-throughput sequencing are reshaping how we perceive microbial communities inhabiting the human body with implications for prevention and therapeutic intervention. 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 431 assembled human microbiome datasets using the open-source MetaPathways that enable 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 the MetaPathways graphical user interface and ptools.

Advances in high-throughput sequencing are reshaping how we perceive microbial communities inhabiting the human body with implications for prevention and therapeutic intervention. 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 431 assembled human microbiome datasets using the open-source MetaPathways that enable 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 the MetaPathways graphical user interface and ptools.