Jacopo Grilli

Environmental history can counteract nutrient quality in shaping the evolution of bacterial growth rates

This study shows that environmental history influences bacterial growth rates through proteome allocation, often opposing expectations based on nutrient quality.

Leveraging rDNA and rRNA dynamics to investigate the link between ecology and physiology in a freshwater microbial community

This study uses rRNA and rDNA dynamics to model microbial physiology in a freshwater community, finding that rRNA:rDNA ratios reflect growth rates and respond more strongly to environmental changes than rDNA alone.

Population growth is primarily inhibited by processes other than resource depletion, leaving a sublinear signature across species

The paper shows that population growth slows sublinearly with density in most species, challenging the resource-depletion model and suggesting other inhibitory processes are at play.

The macroecological dynamics of sojourn trajectories in the human gut microbiome

This study characterizes the macroecological dynamics of sojourn trajectories in the human gut microbiome using theoretical models and empirical data.

A balance between environmental filtering and competitive exclusion modulates the macroecology of alternative stable states in microbial communities

The paper shows that microbial community structure is shaped by state-dependent competitive exclusion, leading to alternative stable states and reciprocal prevalence patterns among phylogenetically close relatives.

Resource ratio fluctuations drive the evolution of microbial metabolic strategies

The paper shows that resource ratio fluctuations drive the evolution of microbial metabolic strategies, with balanced environments favoring specialists and imbalanced ones favoring generalists.

Label invariance: a guiding principle for ecological models

This paper introduces label invariance as a principle for ecological models, showing it ensures consistency in dynamics across population groupings and aids in model selection and evaluation.

Longitudinal dynamics of ethanol-resistant microbes and sporulation in the human gut

This study examines ethanol-resistant gut bacteria and their sporulation dynamics in humans over six months, finding that resistance correlates with persistence and inter-individual transmission.

Incoherent feedback from coupled amino acids and ribosome pools generates damped oscillations in growing E. coli

The paper develops a mechanistic model of bacterial growth that incorporates amino acid pools, ppGpp sensing, and transcriptional regulation, showing oscillatory dynamics during environmental changes.

Protein degradation sets the fraction of active ribosomes at vanishing growth

The paper shows that protein degradation balances ribosome allocation at slow growth, maintaining active ribosomes even as growth rate diminishes.

Transcriptome dynamics predict thermotolerance in Caenorhabditis elegans

The paper measures transcriptional resilience to heat stress in C. elegans and finds it predicts long-term thermotolerance.

Temporal dynamics of gene expression in heat-stressed Caenorhabditis elegans

This study examines gene expression changes in C. elegans during heat stress, identifying a critical time window where gene expression shifts and phenotypic damage becomes irreversible.