C. Tropini

High-resolution lineage tracking of within-host evolution and strain transmission in a human gut symbiont across ecological scales

The paper tracks lineage evolution and transmission of Bacteroides thetaiotaomicron across hosts and ecological scales using genomic barcoding and whole-genome sequencing.

PUPpy: a primer design pipeline for substrain-level microbial detection and absolute quantification.

PUPpy designs taxon-specific primers for substrain-level microbial detection and absolute quantification, outperforming 16S rRNA and shotgun sequencing in defined communities.

Phenotypic plasticity shapes biofilm's structure and fluid transport enhancing resilience

The paper investigates how phenotypic plasticity in Bacillus subtilis biofilms enhances resilience through spatial organization and fluid transport properties.

Gut commensal Enterocloster species host inoviruses that are secreted in vitro and in vivo.

This study identifies and characterizes inoviruses secreted by gut commensal Enterocloster species in vitro and in vivo, showing osmotic regulation of secretion.

An impedance-based chemiresistor for the real-time detection of gut microbiota-generated short-chain fatty acids

This paper develops an impedance-based sensor for real-time, direct detection of SCFAs in liquid samples without sample preparation, showing its ability to measure SCFAs in mixtures and screen bacterial isolates.

Single-strain behavior predicts responses to environmental pH and osmolality in the gut microbiota.

This study predicts microbiota responses to environmental pH and osmolality by analyzing bacterial growth under controlled conditions and identifying predictive genes and pathways.

Recovery of the gut microbiota after antibiotics depends on host diet and environmental reservoirs

The paper investigates how gut microbiota recovers after antibiotics, showing diet and environmental factors influence resilience and recovery patterns.