Marco Fondi

This study develops a microbial community to study plasmid-mediated AMR spread, showing plasmids protect the community from antibiotics and that HGT dynamics can be controlled.

MErlin integrates bacterial methylome data with other omics data to produce gene-level evidence and reports, using a modular toolkit and LLM interface.

The paper investigates the relationship between microbiome composition in guppies and sperm motility traits, finding that skin microbiome diversity correlates with sperm velocity.

This study cures the pMEGA plasmid from PhTAC125 using PTasRNA technology, resulting in a strain with enhanced oxidative stress resistance and reduced biofilm formation.

This paper develops a genome-scale metabolic model for Umbelopsis sp. WA50703 to identify genes and reactions important for polyunsaturated fatty acid production.

This study shows that acquiring additional quorum sensing modules reduces population size variability in Burkholderia by buffering noise in growth dynamics.

The paper analyzes DNA methylation patterns across 21 Sinorhizobium meliloti strains, revealing epigenomic diversity linked to genome structure and phenotypic variation.

The paper investigates metabolic robustness and transcriptomic reprogramming in a cold-adapted bacterium at different temperatures, revealing key intermediates and pathway cross-talk involved in adaptation.

The paper argues that DNA replication and cell division coupling introduces a selective force driving metabolic gene clustering, which is a preliminary step in operon formation.

The paper investigates how antimicrobial exposure affects bacterial metabolism using transcriptomics and computational modeling, finding that experimental conditions influence metabolic networks more than antimicrobial type, but common metabolic strategies exist.

The paper introduces MeStudio, a tool for analyzing DNA methylation from SMRT sequencing data, and demonstrates its application on bacterial genomes.

The paper models growth interactions in a diatom-bacterium co-culture using experimental data to create a mathematical model that explains observed dynamics.

The paper models the metabolic burden of producing hCDKL5 in bacteria and identifies targets for optimized production.

The paper models how additional regulatory modules in bacterial quorum sensing improve response speed and control.

The paper models the inter-kingdom metabolic integration during symbiotic nitrogen fixation in Medicago truncatula and Sinorhizobium meliloti using in silico reconstruction and flux balance analysis.

The paper shows that diauxic growth and co-utilization of multiple substrates can coexist in complex environments, with nutrient uptake order determined by biomass yield and growth rate.

The paper presents a high-resolution chromosome-assigned genome of the Komodo dragon, identifying adaptations in cardiovascular, muscular, and chemosensory systems through comparative genomics.

This study develops a metabolic model of Pectobacterium parmentieri SCC3193 to predict its adaptation to soil and rhizosphere niches and identify core essential genes for growth in these environments.

The paper develops a synthetic microbial ecosystem to model metabolic interactions between a diatom and a heterotrophic bacterium, showing oscillatory behavior and stochastic extinction effects.

Tn-Core integrates Tn-seq data with metabolic models to generate context-specific core reconstructions and supports functional model generation and model curation.

The paper creates a genomically hybrid strain of Sinorhizobium meliloti by transferring a secondary replicon and characterizes its phenotypes and metabolic properties.

The paper investigates how extrachromosomal replicons in Sinorhizobium meliloti influence gene function and metabolism using Tn-seq and metabolic modeling, revealing widespread genetic interactions and functional dependencies.

The paper uses constraint-based modeling and gene expression data to identify new potential drug targets against colistin-resistant A. baumannii.