Francisco Zorrilla

The paper shows that many soil bacteria depend on metabolite supplementation from other community members, revealing widespread cross-feeding in soil microbial communities.

CarveMe-GutMicrobes reconstructs genome-scale metabolic models for gut microbes from genomic data, showing high accuracy in predicting gene essentiality and metabolite secretion.

The paper introduces FROG analysis to standardize reproducibility assessments of genome-scale metabolic models, resulting in full reproducibility of all tested models.

The paper identifies key microbial interactions and metabolic pathways that confer resistance to C. difficile invasion using synthetic and clinical communities.

The paper assesses the global potential of microorganisms to degrade plastics by analyzing metagenomes and correlates enzyme abundance with pollution trends.

metaGEM reconstructs genome-scale metabolic models directly from metagenomes, demonstrating comparable metabolic representation to reference-based models and capturing intraspecies diversity in gut microbiomes.

This paper demonstrates the reconstruction of a genome-scale metabolic model for Hansenula polymorpha using the RAVEN toolbox through a homology-based approach.