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Panera: An innovative framework for surmounting uncertainty in microbial community modeling using pan-genera
Indumathi Palanikumar1,2,3, Himanshu Sinha1,2,3, Karthik Raman1,2,3,4
1Department of Biotechnology, Bhupat Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai 600 036, India.
Iscience
|August 2, 2024
Summary
Panera models microbial communities using pan-genus metabolic models (PGMMs) to overcome 16S rRNA data limitations. This approach enhances metabolic inference and reduces errors in community modeling.
Area of Science:
- Microbial Ecology
- Metabolic Modeling
- Bioinformatics
Background:
- Constraint-based modeling of microbial communities using 16S rRNA data faces challenges due to limited species-level resolution.
- This lack of resolution hinders the accurate construction of comprehensive community metabolic models.
Purpose of the Study:
- To introduce Panera, a novel framework for microbial community modeling under uncertainty using pan-genus metabolic models (PGMMs).
- To enable robust metabolic inferences from amplicon data and characterize genus-level metabolic capabilities.
Main Methods:
- Development and application of the Panera framework utilizing pan-genus metabolic models (PGMMs).
- Construction of hybrid community models combining genome-scale metabolic models (GSMMs) and PGMMs.
- Evaluation of model predictions against standard GSMM-based community models.
Main Results:
- PGMMs effectively characterize genus-level metabolic capabilities and community models from amplicon data.
- Hybrid models combining GSMMs and PGMMs demonstrate adaptability and utility.
- Panera-based models achieved comparable predictions to GSMM-based models with a significant error reduction of nearly 46% compared to genus model-based communities.
Conclusions:
- Panera provides a potent approach for metabolic modeling with amplicon data, overcoming resolution limitations.
- The framework enables robust predictions of community metabolic potential and offers insights into genus-level metabolic landscapes.
- Panera facilitates the construction of more accurate and efficient microbial community models.
