Pangenome reconstruction of Lactobacillaceae metabolism predicts species-specific metabolic traits

作者：Omid Ardalani, Patrick V. Phaneuf, Omkar S. Mohite, Lars Keld Nielsen, Bernhard Ørn Palsson · 发表于：mSystems · 年份：2024 · DOI：10.1128/msystems.00156-24 · 被引用次数：26 · 研究领域：Microbial Metabolic Engineering and Bioproduction、Probiotics and Fermented Foods、Microbial Metabolites in Food Biotechnology

ABSTRACT Strains across the Lactobacillaceae family form the basis for a trillion-dollar industry. Our understanding of the genomic basis for their key traits is fragmented, however, including the metabolism that is foundational to their industrial uses. Pangenome analysis of publicly available Lactobacillaceae genomes allowed us to generate genome-scale metabolic network reconstructions for 26 species of industrial importance. Their manual curation led to more than 75,000 gene-protein-reaction associations that were deployed to generate 2,446 genome-scale metabolic models. Cross-referencing genomes and known metabolic traits allowed for manual metabolic network curation and validation of the metabolic models. As a result, we provide the first pangenomic basis for metabolism in the Lactobacillaceae family and a collection of predictive computational metabolic models that enable a variety of practical uses. IMPORTANCE Lactobacillaceae , a bacterial family foundational to a trillion-dollar industry, is increasingly relevant to biosustainability initiatives. Our study, leveraging approximately 2,400 genome sequences, provides a pangenomic analysis of Lactobacillaceae metabolism, creating over 2,400 curated and validated genome-scale models (GEMs). These GEMs successfully predict (i) unique, species-specific metabolic reactions; (ii) niche-enriched reactions that increase organism fitness; (iii) essential media components, offering insights into the global amino acid essentiality...