Xiandong Meng

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.

Microbiota- and diet-specific T cells become Tregs by default

The paper shows that T cells specific for microbiota and diet antigens predominantly become regulatory T cells (iTregs) in the gut, with effector responses emerging only under specific inflammatory and genetic conditions.

Gut microbial composition modulates food-specific CD4+ T cells in food allergy

This study shows that gut microbial composition affects food allergen-specific CD4+ T cells, leading to differences in food allergy severity between mouse strains.

Ecology and engineering to modify the bile acid output of a defined microbial community

The paper shows that modifying microbial community composition, specifically overexpressing bile acid metabolic genes in Lactobacillus strains, can alter bile acid pool size and composition in mice.

A single-strain dropout screen reveals mechanistic links between microbial ecology and metabolism

The paper uses a single-strain dropout screen in a defined microbial community to show how removing specific strains affects community composition and metabolic output.

Gut microbiota gate host exposure to cholinesterase inhibitors from dietary Solanums

The paper investigates how gut microbiota modify steroidal alkaloids from Solanum plants, affecting host exposure and physiological effects.

SpaRC: Scalable Sequence Clustering using Apache Spark

SpaRC clusters large-scale sequence data using Apache Spark, achieving scalability and performance across transcriptomics and metagenomics datasets.

Widespread polycistronic transcripts in mushroom-forming fungi revealed by single-molecule long-read mRNA sequencing

The paper identifies widespread polycistronic transcripts in mushroom-forming fungi using long-read sequencing and shows short-read assembly is inadequate for isoform discovery.