Kerwyn Casey Huang

Multiple non-redundant functions underlie the essentiality of lipopolysaccharide in Gram-negative bacteria

This study identifies multiple non-redundant functions of lipopolysaccharide (LPS) in Gram-negative bacteria, showing it is essential for envelope mechanics, membrane biogenesis, and efflux pump activity.

Diverse stresses converge on bacterial periplasmic expansion through distinct physiological mechanisms

This study shows that diverse stresses cause periplasmic expansion in E. coli through distinct mechanisms, but UDP-glucose synthesis is required for expansion under some conditions.

FastaLake selects compact metaproteomic databases from large sequence reservoirs by de novo peptide lookup

FastaLake constructs compact metaproteomic databases from sequence resources to improve peptide identification without requiring matched metagenomic sequencing.

Tracking gene flow in the gut microbiome reveals phage activation and host-range expansion in response to diet

The paper tracks gene flow in the gut microbiome, showing diet and community ecology influence phage activation and horizontal gene transfer.

Gut microbiome shifts in chronic systolic heart failure are associated with disease severity and clinical improvement

The paper examines gut microbiome changes in chronic systolic heart failure patients, linking microbiome alterations to disease severity and clinical improvement.

Independent tuning of outer membrane fluidity and mechanics in Gram-negative bacteria

This study shows that outer membrane fluidity and mechanics in Gram-negative bacteria can be independently controlled by altering lipid composition and crosslinking.

Mechanofiltration Enables High-Throughput Measurements of Bacterial Cell Mechanics

This paper introduces mechanofiltration, a high-throughput method to measure bacterial cell mechanics using standard lab equipment, showing it accurately detects changes in cell stiffness across genetic and environmental conditions.

Capsular polysaccharide can sensitize bacteria to non-antibiotic drugs

The paper shows that the K5 capsular polysaccharide of E. coli Nissle 1917 sensitizes it to thioridazine and related antipsychotics, revealing CPS as a vulnerability under non-antibiotic drug pressure.

Path-dependent recovery of the gut microbiome after antibiotics emerges from coupled ecological and evolutionary dynamics

This study shows that gut microbiome recovery after antibiotics is path-dependent, shaped by ecological and evolutionary dynamics including strain sweeps, genetic changes, and phage activity.

CUPID-seq enables highly multiplexed amplicon sequencing via combinatorial in-line dual indexing

CUPID-seq improves amplicon sequencing by reducing costs and increasing multiplexing through combinatorial indexing, enabling efficient use of high-throughput sequencing platforms.

Phage-based microbiome manipulation reveals ecological interactions within gut communities

This study uses phage-based manipulation to reveal ecological interactions in gut microbiomes by targeting Escherichia fergusonii and analyzing its role in community dynamics.

The network structure of cross-feeding impacts microbial community diversity under growth-inhibiting stresses

The paper models how cross-feeding network structures affect microbial community diversity under growth-inhibiting stresses, finding cyclic networks promote coexistence in narrow-spectrum inhibition but can be detrimental in broader contexts.

Eubiota: Modular Agentic AI for Autonomous Discovery in the Gut Microbiome

Eubiota enables autonomous discovery in the gut microbiome by integrating modular agents and reinforcement learning, identifying key pathways and designing therapeutic interventions.

Sensing the shape of a surface by intracellular filaments

This paper develops a biophysical model to explain how MreB filaments localize to curved surfaces in bacteria, showing that their curvature preference is governed by mean and Gaussian curvatures.

Nutrient competition predicts gut microbiome restructuring under drug perturbations

The paper shows that nutrient competition drives changes in gut microbiome composition under drug perturbations, with implications for predicting and mitigating drug side effects.

A load-bearing function for the cytoplasmic membrane of Escherichia coli

This study shows that MreB couples the cell wall to the cytoplasmic membrane in E. coli, increasing resistance to bending and preventing membrane detachment under stress.

Gut microbe-derived lactic acid optimizes host energy metabolism during starvation

This study identifies lactic acid from gut microbes as a key factor improving Drosophila survival during starvation by enhancing oxidative phosphorylation.

Abundance measurements reveal the balance between lysis and lysogeny in the human gut microbiome

The paper estimates phage population dynamics and lifestyle in the human gut using integrated data, finding a low lysis rate and high genome-to-genome ratio suggesting temperate phage dominance.

Comprehensive double-mutant analysis of the Bacillus subtilis envelope using double-CRISPRi

The paper uses double-CRISPRi to systematically analyze genetic interactions in Bacillus subtilis, identifying over 1000 interactions and revealing roles of paralogous genes in cell division.

Improved mouse models of the small intestine microbiota using region-specific sampling from humans

The paper develops improved mouse models of the small intestine microbiota using region-specific human intestinal sampling and in vitro culturing, showing increased diversity and reproducibility in colonization.

Challenges in quantifying functional redundancy and selection in microbial communities

The paper challenges the assumption that reduced functional variability in microbial communities indicates selection, showing that apparent functional selection can be artifacts of statistical averaging and functional bias.

Adversarial domain translation networks for fast and accurate integration of large-scale atlas-level single-cell datasets

Portal integrates large-scale single-cell datasets efficiently and accurately by preserving biological variation across samples, platforms, and species.

Molecular hallmarks of heterochronic parabiosis at single cell resolution

This study uses single-cell RNA-sequencing to analyze cell type-specific responses to young or aged blood in heterochronic parabiosis, identifying mitochondrial function as a key factor in rejuvenation.

Extracting the phylogenetic dimension of coevolution reveals hidden functional signal

This paper introduces a method to extract the phylogenetic dimension of coevolution, revealing hidden functional signals in proteins and improving structural-contact prediction.

Rapid ordering of barcoded transposon insertion libraries of anaerobic bacteria

This paper develops a fast, cheap protocol for assembling ordered transposon insertion libraries in anaerobic bacteria, using cell sorting and barcoded transposons to improve accuracy and efficiency.

Chemical-genetic interrogation of RNA polymerase mutants reveals structure-function relationships and physiological tradeoffs

The paper uses chemical-genetic analysis of RNA polymerase mutants to uncover structure-function relationships and physiological trade-offs in Escherichia coli.

The inner membrane protein YhdP modulates the rate of anterograde phospholipid flow in Escherichia coli

The paper identifies YhdP as a modulator of phospholipid transport rate in Escherichia coli, showing its role in controlling inner membrane shrinkage and outer membrane rupture during mlaA* mutation.

Limits and constraints on mechanisms of cell-cycle regulation imposed by cell size-homeostasis measurements

The paper develops a general model to explore how cell-cycle regulation mechanisms are constrained by cell-size homeostasis measurements across different organisms.

Bellymount enables longitudinal, intravital imaging of abdominal organs and the gut microbiota in adult Drosophila

Bellymount allows long-term, non-invasive imaging of Drosophila abdominal organs and gut microbiota, enabling tracking of cellular and microbial dynamics over multiple days.