F. B. Yu

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.

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.

ENPP1 is an innate immune checkpoint of the anticancer cGAMP-STING pathway

This study identifies ENPP1 as an innate immune checkpoint that suppresses the cGAMP-STING pathway, promoting tumor growth and metastasis, and shows that inhibiting its cGAMP hydrolase activity enhances cancer immunity.

Assembly of gut-derived bacterial communities follows "early-bird" resource utilization dynamics

This study shows that gut microbiota assembly follows 'early-bird' dynamics where fast-growing species dominate nutrient sources, and develops a predictive model for community composition based on nutrient inputs.

Microcosm cultures of a complex synthetic community reveal ecology and genetics of gut microbial organization

The paper uses synthetic microbial communities in mucin microcosms to study gut microbial spatial organization and identifies genes associated with mucosal versus lumen enrichment.

Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Microbes

The paper uses ultra-deep metagenomic sequencing to analyze the gut microbiome of Hadza hunter-gatherers, revealing many microbes absent from existing datasets and highlighting differences in microbial dynamics compared to industrialized populations.

Construction and characterization of a genome-scale ordered mutant collection of Bacteroides thetaiotaomicron

The paper constructs an ordered mutant collection of Bacteroides thetaiotaomicron using transposon-insertion and barcode sequencing, identifies factors limiting coverage, and demonstrates phenotypic screening for growth defects and cell shape changes.

Phage-delivered CRISPR-Cas9 for strain-specific depletion and genomic deletions in the gut microbiome

This study uses phage-delivered CRISPR-Cas9 to deplete specific E. coli strains and induce genomic deletions in the gut microbiome of mice.

Impact of a 7-day homogeneous diet on interpersonal variation in human gut microbiomes and metabolomes

A 7-day homogeneous diet did not reduce interindividual variation in uremic microbiome-derived metabolites, indicating limited dietary impact and suggesting the need for microbial interventions.

Gut Microbiota-Targeted Diets Modulate Human Immune Status

This study examines how plant-based fiber and fermented food diets affect the gut microbiome and immune system in healthy adults over 17 weeks.

Genetic and behavioral adaptation of Candida parapsilosis to the microbiome of hospitalized infants revealed by in situ genomics, transcriptomics and proteomics

This study identifies genetic and behavioral adaptations of C. parapsilosis in the gut microbiome of hospitalized infants using in situ genomics, transcriptomics, and proteomics.

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.

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.

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.

Hydrogenotrophic methanogenesis in archaeal phylum Verstraetearchaeota reveals the shared ancestry of all methanogens

The paper discovers a hydrogenotrophic methanogenesis pathway in Verstraetearchaeota and the Wood-Ljungdahl pathway in Desulfurococcales, suggesting an ancient origin of hydrogenotrophic methanogenesis and a later adaptation to methylotrophic methanogenesis.