Analyzing protein digestibility by integrating food proteomics and human serum metabolomics

Proteins are essential nutrients that we need to ingest in a daily basis for our health. However, not all proteins are equally digestible, and not all individuals can digest proteins equivalently. In this project, we perform integrative data analysis by combining food proteomics and human serum metabolomics data to understand sequence-level protein digestibility and the variation of protein digestibility among individuals.

Results

Our derived digestibility scores accurately captured the general trends of animal proteins being more digestible than plant proteins (Digestibility score = 0.58 ± 0.13 vs. 0.48 ± 0.10; p-value = 4.1 x 10^-3). However, this heatmap also revealed that certain individuals digested plant-based proteins more efficiently than animal-based proteins. Another interesting finding was that although animal proteins, in general, were more digestible, some specific sequences were less digestible, such as actin.

Directories

data: Contains the raw data files. outputs: Contains the output files. src: Contains the source code files. scripts: Contains the scripts for running the code.

Getting Started

The code has been tested in the following environment:

• Ubuntu: 20.04.4 LTS
• Python: 3.10.8

Clones this repository to your local machine.

git clone https://github.com/IBPA/PTFIFoodomics
cd PTFIFoodomics

Create an Anaconda environment.

conda create -n foodomics python=3.10.8
conda activate foodomics

Install the required packages.

pip install - requierments.txt

Run the code.

• Step 1: Unpack the zipped FASTA file.

cd data
unzip combined_v3.fasta.zip
cd ..

• Step 2: Two main analysis repositories can be found in src directory: variability and digestibility. You will be able to run any of the Python files, e.g., ones without leading underscore. For example:

python -m src.variability.plot_auc

Authors

Repository Contributors

• Fangzhou Li^1,2,3: Graduate Student Researcher
• Ilias Tagkopoulos, Ph.D.^1,2,3: Principal Investigator

Project Contributors

• Mariana Barboza, Ph.D.^2,11*
• Fangzhou Li^1,2,3*
• Cheng-Yu Weng, Ph.D.^6*
• Shawn Ehlers Cheang⁶
• Antoine Abrieux, Ph.D.¹¹
• Emelie Strandberg, Ph.D.⁹
• Karin Schaal⁹
• Nikita Bacalzo Jr., Ph.D.⁶
• Efrain Vasquez Santos⁹
• Ryan Caster²
• Visakan Vairavamoorthy¹¹
• Bruce German, Ph.D.⁷
• Selena Ahmed, Ph.D.^4,8
• John de la Parra, Ph.D.^10,12
• Keith Baar, Ph.D.⁹
• Ilias Tagkopoulos, Ph.D.^1,2,3
• Carlito Lebrilla, Ph.D.^5,6
• Justin Siegel, Ph.D.^2,5,6,11

1. Department of Computer Science, University of California, Davis
2. Genome Center, University of California at Davis
3. USDA/NSF AI Institute for Next Generation Food Systems (AIFS)
4. American Heart Association
5. Department of Biochemistry and Molecular Medicine, University of California, Davis
6. Department of Chemistry, University of California, Davis
7. Department of Food Science and Technology, University of California, Davis
8. Department of Health and Human Development, Montana Stata University
9. Department of Physiology and Membrane Biology, School of Medicine, University of California, Davis
10. Harvard University
11. Innovation Institute for Food and Health, University of California, Davis
12. The Rockefeller Foundation

*. These authors contributed equally

Contact

For any questions regarding the code, you can contact Fangzhou Li (fzli@ucdavis.edu) or Prof. Ilias Tagkopoulos (itagkopoulos@ucdavis.edu).

Citation

The work is currently under review. Please check back later for the citation!

License

This project is licensed under the Apache-2.0 License. Please see the LICENSE file for details.

Acknowledgments

Special thanks to all the collaborators of this work: Dr. Antoine Abrieux, Dr. Mariana Barboza, Dr. Justin B. Siegel, and Visakan Vairavamoorthy from the Innovation Institute for Food and Health, Dr. Nikita Bacalzo, Shawn E. Cheang, Carlito B. Lebrilla, and Cheng-Yu Weng from the Department of Chemistry at UC Davis, Dr., Keith Baar, Efrain V. Santos, Karin Schaal, and Dr. Emelie K. Strandberg from the Department of Physiology and Membrane Biology, School of Medicine at UC Davis, Ryan Caster from Genome Center at UC Davis, Dr. Bruce German from the Department of Food Science and Technology at UC Davis, Dr. Selena Ahmed from American Heart Association, and Dr John de la Parra from the Rockefeller Foundation.

Funding

Funding was provided by the Rockefeller Foundation and the American Heart Association.