The Challenge
Despite decades of research into the human microbiome, we haven’t been able to harness the microorganisms living in human bodies for widespread disease prevention and therapeutic interventions. While a promising field of research, a major barrier to breakthroughs in this area are data analysis and interpretation issues faced by medical researchers.
The most densely populated area of the human microbiome is the lowest region of the gut, home to microorganisms that play critical roles in nutrition, detoxification, and immune system conditioning. Large scale datasets about the metabolic activity of these organisms are available, but differences in how that data was originally processed make comparative analyses difficult.
Being able to understand and use these data will help advance research on significant human diseases such as inflammatory bowel disease, Crohn's disease, type 2 diabetes, and others.
Koonkie’s Approach
To help overcome this data compatibility barrier and enable new discoveries, we created GutCyc, a software pipeline and a collection of pathway genome databases. GutCyc transforms this data into a format that both domain experts and machines can understand. GutCyc provides the consistent annotations and metabolic pathway predictions needed to analyze differences in microbial communities between health and disease states.
Visit the GutCyc website here: http://www.gutcyc.org/
Read our paper in Scientific Data: https://www.nature.com/articles/sdata201735
