Kerwyn Casey Huang

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.

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

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

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

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

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

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.

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.

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

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

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.

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

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.

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

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

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.

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.

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.

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.

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

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.

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

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.

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

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