Kyle L. Bittinger

This paper evaluates virome analysis methods using a synthetic viral community, finding that VLP enrichment improves read yields and longer sequencing cycles enhance genome assembly.

The paper shows that suppressing both COX-1 and COX-2 does not cause intestinal injury in mice unless combined with specific NSAIDs, and that gut microbiome changes amplify NSAID-induced enteropathy.

This study shows colibactin-producing E. coli promote GEAC carcinogenesis by increasing proliferation, DNA damage, and cancer pathways, while also inducing autophagy and differentiation.

This study investigates how the gut microbiome interacts with aging and dietary restriction in mice, finding that host genetics significantly influence microbiome features and that dietary restriction does not rejuvenate the microbiome.

The paper introduces a quantitative method to measure and predict microbiome responses to antibiotics using a Microbiome Response Index (MiRIx) and applies it to human microbiome data.

This study examines the impact of probiotic yogurt containing two or three bacterial strains on gut microbiome and metabolome in healthy children, finding no global diversity changes but reduced fecal metabolites in the three-strain group.

Sunbeam is a modular pipeline for metagenomic analysis that standardizes preprocessing and removes low-complexity reads, enabling reproducible and extensible workflows.