K. C. Huang

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.

Competition for shared resources increases dependence on initial population size during coalescence of gut microbial communities

This study shows how initial population size and resource competition shape gut microbial community coalescence, with dose-dependent effects persisting even after many generations.

Temporal profiling of Salmonella transcriptional dynamics during macrophage infection using a comprehensive reporter library

This study uses a GFP-reporter library to profile Salmonella transcriptional dynamics during macrophage infection, revealing condition-specific regulation and novel gene activity.

Prolonged delays in human microbiota transmission after a controlled antibiotic perturbation

This study investigates gut microbiome colonization dynamics after antibiotic use, finding prolonged delays in microbial transmission and ecological barriers to colonization.

A mutant fitness compendium in Bifidobacteria reveals molecular determinants of colonization and host-microbe interactions

The paper creates a mutant fitness compendium for Bifidobacterium breve to identify molecular factors affecting colonization and host-microbe interactions.

Metabolomic rearrangement controls the intrinsic microbial response to temperature changes

The paper shows that metabolomic rearrangements, not stress responses, control bacterial temperature adaptation, with a model explaining growth dynamics under temperature shifts.

Modulation of bacterial cell size and growth rate via activation of a cell envelope stress response

This study shows that activating the Rcs phosphorelay in E. coli reduces growth rate and alters FtsZ distribution, with effects mediated through growth-rate changes rather than direct regulation.

Bacterial cell widening alters periplasmic size and activates envelope stress responses

This study shows that changes in bacterial cell width affect periplasmic thickness and activate the Rcs stress response system through RcsF.

Resource competition predicts assembly of in vitro gut bacterial communities

This study develops a framework to distinguish resource competition from other interactions in gut bacterial communities, showing it explains most pairwise interactions and predicts community assembly.

Feedback linking cell envelope stiffness, curvature, and synthesis enables robust rod-shaped bacterial growth

This study combines theory and experiment to show that E. coli uses feedback between cell-envelope curvature and expansion to maintain growth rate and cell width during osmotic stress.

Deconstructing the role of iron and heme in the structure of healthy human gut microbial communities

The paper investigates how iron and heme affect gut microbiome structure using in vitro models derived from human stool samples, showing iron deprivation reduces diversity and alters community composition.

Previously uncharacterized rectangular bacterial structures in the dolphin mouth

The paper discovers novel rectangular bacterial structures in dolphin mouths and characterizes their morphology and potential bacterial origin through multiple methods.

A gut commensal niche regulates stable association of a multispecies microbiota

The study identifies a strain-specific bacterial niche in the Drosophila foregut that stabilizes microbiota composition through spatial and competitive interactions.

Conserved and non-conserved triggers of 24-nt reproductive phasiRNAs in eudicots

The paper identifies conserved and non-conserved triggers of 24-nt phasiRNAs in eudicots, including new triggers and expanded loci in wild strawberry and validated pathways in rose.

Starvation induces shrinkage of the bacterial cytoplasm

This study shows that starvation causes E. coli to shrink its inner membrane and cytoplasm, driven by water loss, and that the Tol-Pal system is essential for recovery.

Quantifying the interplay between rapid bacterial evolution within the mouse intestine and transmission between hosts

The paper tracks bacterial evolution and transmission in mice using barcoded E. coli strains, showing rapid selection and migration effects on microbiota composition.

Entropy-driven translocation of disordered proteins through the Gram-positive bacterial cell wall

The paper shows that entropy drives disordered proteins through Gram-positive bacterial cell walls, using a physical model and experimental validation.

Environmental and physiological factors affecting high-throughput measurements of bacterial growth

The paper presents a framework for accurate bacterial growth measurements, revealing effects of culturing conditions, initial cell density, and glycerol on growth rates and fitness.

Variations of intracellular density during the cell cycle arises from tip-growth regulation in fission yeast

This study shows that intracellular density in fission yeast changes during the cell cycle due to volume growth modulation, with density decreasing in G2, increasing in mitosis, and dropping at cell birth.

Bacterial evolution in high osmolarity environments

This study evolves Escherichia coli in high osmolarity environments and finds that adaptation strategies vary by osmolyte, with specific mutations improving fitness in certain conditions.

High-throughput cultivation of stable, diverse, fecal-derived microbial communities to model the intestinal microbiota

This study develops a high-throughput method to cultivate diverse, stable fecal-derived microbial communities in vitro, demonstrating their utility for modeling the intestinal microbiota and predicting in vivo responses to antibiotics.

SiCTeC: an inexpensive, easily assembled Peltier device for rapid temperature shifting during single-cell imaging

SiCTeC enables rapid, precise temperature shifts for single-cell imaging, revealing cellular responses to temperature changes in E. coli.

Towards Mycobacterium tuberculosis detection at the point-of-care: a brighter solvatochromic probe permits the detection of mycobacteria within minutes

This paper develops a solvatochromic dye conjugate for rapid, sensitive detection of Mycobacterium tuberculosis in minutes.

Precise regulation of the relative rates of surface area and volume synthesis in dynamic environments

The paper quantifies surface area to volume ratio dynamics in bacteria under environmental changes and develops a model linking these dynamics to gene expression and growth control.

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.

Mechanically Resolved Imaging of Bacteria using Expansion Microscopy

This paper introduces expansion microscopy to distinguish bacterial species and detect phenotypic changes in dense microbial communities.

Large-scale chemical-genetics of the human gut bacterium Bacteroides thetaiotaomicron

This study systematically measures mutant phenotypes for genes in Bacteroides thetaiotaomicron to uncover gene functions and improve understanding of gut microbiota physiology.

Bacterial interspecies interactions modulate pH-mediated antibiotic tolerance in a model gut microbiota

This study shows that interspecies interactions in a fruit fly gut microbiota modulate pH and antibiotic tolerance, with Lactobacillus plantarum showing rifampin tolerance influenced by Acetobacter species.

Decoupling of rates of protein synthesis from cell expansion leads to supergrowth

The paper shows that fission yeast can accumulate biomass without expanding in volume, leading to supergrowth when volume expansion resumes.

Chiral twisting in cytoskeletal polymers regulates filament size and orientation

This study shows that left-handed twisting in MreB filaments, influenced by nucleotide and membrane binding, determines filament length and orientation in Caulobacter crescentus.