Community Highlight: Aimee Kessell
Aimee Kessell (AK) earned her PhD in Complex Biosystems at the University of Nebraska – Lincoln. Aimee grew up on St. Lucia, a small island in the Caribbean and came to the United States for her undergraduate education. She has a Bachelor of Science in Biotechnology and a Master of Science in Mathematics from the University of Nebraska – Omaha.
Part of Aimee’s dissertation research focused on the role of soil microbes in nutrient cycling, specifically chitin degradation. Chitin is the second most abundant biopolymer in soil – a known component of fungi cell walls and insect exoskeletons. More importantly, chitin is a source of nitrogen. Microbial degradation of chitin allows for carbon- and nitrogen-cycling observed in soil. Aimee is interested in how these nutrients are efficiently used by microbial communities and individual microbes.
How has using KBase supported your research project?
(AK) My project involves building and using metabolic networks of chitin-degrading microbial communities and their isolates. Through a collaboration with Pacific Northwest National Laboratory (PNNL), I’ve built individual and community models of a model soil consortium used for chitin degradation. KBase was necessary in building these metabolic models and performing initial flux balance analysis using experimental phenotypic growth data.
How have you benefited from working with KBase?
Aimee Kessell (second from left) and fellow participants from the training event at Argonne. Photo credit: Joon Yoon Lee.
(AK) I’ve benefited greatly through my collaboration with KBase. I had the opportunity to spend three days with KBase team members – Chris Henry, Janaka Edirisinghe, and Felipe Liu – at Argonne National Laboratory (ANL). I learned how to register and run applications within the KBase Narrative interface and developed a better understanding of programming with Python. This work also led to further collaboration between my group in the Song Lab, PNNL, and KBase. Our efforts helped improve gap filling by the inclusion of OMEGGA (OMics-Enable Global GApfilling) which can be found in the ModelSEED2 Build and Gapfilling (Metabolic Model Reconstruction) applications.
What is your favorite part about using KBase?
(AK) I love the open science aspects of the KBase Narrative. I can build a Narrative that includes all my data and applications to share with fellow scientists. The markdown cells allow for detailed explanations so others can follow along and use my Narratives as a starting point for their own work. I like that I can simply include a URL in an article and it will always be available.
What role do you see KBase having in open science principles?
(AK) KBase makes building metabolic models much quicker through pipelines for model building. By using open science principles, we can make these models public for future improvements.
What is one “behind the scenes” thing you want to share about your project?
(AK) Building my microbial metabolic models taught me the challenges of model reconstruction. Sequential gapfilling approaches require manual iterations that take time. This was a driver behind our decision to find new ways of gapfilling, including a global technique (OMEGGA).
Links
(AK) Please check out MS2 – Improved Gapfill Metabolic Models with OMEGGA App and the tutorial Narrative using this application (link here: https://narrative.kbase.us/narrative/175924)!
There is a lot of great collaborative work seen in this Narrative that really helps with building and gapfilling metabolic models.
Learn more about the collaborative efforts between PNNL, the Song Lab, and KBase through the Soil Microbiome Science Focus Area.
