Panera: An innovative framework for surmounting uncertainty in microbial community modeling using pan-genera metabolic models

Abstract

Summary: Utilization of 16S rRNA data in constraint-based modeling to characterize microbial communities confronts a major hurdle of lack of species-level resolution, impeding the construction of community models. We introduce “Panera,” an innovative framework designed to model communities under this uncertainty and yet perform metabolic inferences using pan-genus metabolic models (PGMMs). We demonstrated PGMMs’ utility for comprehending the metabolic capabilities of a genus and in characterizing community models using amplicon data. The unique, adaptable nature of PGMMs unlocks their potential in building hybrid communities, combining genome-scale metabolic models (GSMMs) and PGMMs. Notably, these models provide predictions comparable to the standard GSMM-based community models, while achieving a nearly 46% reduction in error compared to the genus model-based communities. In essence, “Panera” presents a potent and effective approach to aid in metabolic modeling by enabling robust predictions of community metabolic potential when dealing with amplicon data, and offers insights into genus-level metabolic landscapes.

Keywords

• Microbiology
• Bioinformatics
• Computational bioinformatics
• Systems biology