Gut Mycobiota: the CHILD Health Project
We developed a published, peer-reviewed predictive model to predict the development of allergies and asthma in children based on their gut fungi.
The Fungus Inside Us
Researchers had limited knowledge of the gut fungi, or mycobiota, and its influence on the developing immune system of young children. With our collaborators, we discovered dynamic changes in children’s mycobiota during their first year of life and offered a tool for predicting the likelihood of a child developing environmental allergies by their 5th birthday.
With advanced bioinformatics techniques and data collected from the stool samples of 343 infants from the CHILD (Canadian Healthy Infant Longitudinal Development) cohort, we discovered the identities of these little-known fungal communities. We assessed the relationships between fungal community composition and environmental factors like where infants live, their diets, and seasons of birth. Potential links between infant gut mycobiota and the development of allergies in childhood were also investigated. Using a set of early-life environmental factors in combination with fungal community composition at 1 year of age, we developed a predictive model for the tendency to develop diseases such as allergies and asthma.
This work highlights the important role of infant gut mycobiota in immune system development, and shows the promise of modifying gut mycobiota as a viable therapeutic intervention when faced with early risk factors for asthma and environmental allergies.
Read more here: https://journals.asm.org/doi/full/10.1128/mbio.03396-20
A Tool for Better Breast Cancer Screening
As an Illumina certified and preferred bioinformatics provider, we created a diagnostic tool for a Canadian hospital to run a cancer detection pipeline.
Creating a Diagnostic Tool for Breast Cancer Biomarkers
Medical researchers are getting closer to understanding the complex biomarkers that can help catch cancer early and save lives. As an Illumina certified and preferred bioinformatics provider, we used Illumina’s Connected Analytics platform to create a secure and HIPPA-compliant web-based tool for a Canadian hospital to run their cancer detection pipeline.
Advancing Health Research with the Microbiome
This nature-published genomics tool enables breakthroughs in disease prevention and intervention for several significant human diseases.
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