D. Segre

Biophysical metabolic modeling of complex bacterial colony morphology

The paper models bacterial colony morphology by integrating metabolic reactions and biomass propagation, showing realistic colony shapes and metabolic ring formation.

Diversity in the Utilization of Different Molecular Classes of Dissolved Organic Matter by Heterotrophic Marine Bacteria

This study investigates how different molecular classes of dissolved organic matter (DOM) are utilized by heterotrophic marine bacteria in the Eastern Mediterranean Sea, revealing diverse utilization patterns among bacterial clades.

Metabolic complexity drives divergence in microbial communities

This study shows that microbial communities become more divergent as environmental metabolic complexity increases, driven by community diversity and specialist taxa.

Growth instabilities shape morphology and genetic diversity of cellular aggregates

This study links environmental conditions, colony morphology, and evolution by showing how growth instabilities affect genetic diversity in microbial colonies.

Metabolic phenotyping of marine heterotrophs on refactored media reveals diverse metabolic adaptations and lifestyle strategies

The paper characterizes the carbon source utilization preferences of marine heterotrophic bacteria across multiple synthetic media to reveal metabolic adaptations and lifestyle strategies.

A co-culture microplate for real-time measurement of microbial interactions

The paper introduces a microplate device for real-time measurement of microbial interactions and applies it to study both natural and engineered microbial relationships.

Inferring microbial co-occurrence networks from amplicon data: a systematic evaluation

This study evaluates how different tools and parameters affect microbial co-occurrence network inference from 16S amplicon data and develops a standardized pipeline.

Dynamic allocation of carbon storage and nutrient-dependent exudation in a revised genome-scale model of Prochlorococcus

This paper extends a genome-scale metabolic model of Prochlorococcus to study carbon storage and exudation dynamics under nutrient limitation.

The effects of environmental complexity on microbial community yield and structure

The paper investigates how environmental complexity affects microbial community yield and diversity, finding that yield remains constant while diversity is lower than expected.

Comparative whole-genome approach to identify bacterial traits for microbial interactions

The paper identifies bacterial traits for microbial interactions using a whole-genome approach across 473 marine bacterial genomes, revealing functional clusters and interaction patterns.

Emergent Simplicity in Microbial Community Assembly

The paper shows that microbial communities re-assemble into predictable, stable communities through non-specific metabolic cross-feeding, even when grown in minimal environments.