Handuo Shi

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.

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.

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.

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 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.