R. K. Weersma

Diversity and ecology of Caudoviricetes phages with genome terminal repeats in fecal metagenomes from four Dutch cohorts

The paper identifies and characterizes Caudoviricetes phages with genome terminal repeats in fecal metagenomes, finding 1,899 species-level units and 34 associations between phages and human phenotypes.

The faecal metabolome and its determinants in inflammatory bowel disease

This study identifies metabolic alterations in IBD patients by analyzing faecal metabolites, metagenomics, host genetics, and clinical data, finding over 300 differentially abundant molecules and associations with microbiota and diet.

Mucosal host-microbe interactions associate with clinical phenotypes in inflammatory bowel disease

This study identifies host-microbe interactions in IBD by analyzing transcriptomic and microbial data from intestinal biopsies, linking specific bacteria to gene pathways and clinical phenotypes.

HIV-linked gut dysbiosis associates with cytokine production capacity in viral-suppressed people living with HIV

This study links HIV-associated gut dysbiosis to cytokine production capacity in ART-suppressed PLHIV, identifying specific microbial strains associated with immune markers.

In-depth characterization of the serum antibody epitope repertoire in inflammatory bowel disease using phage-displayed immunoprecipitation sequencing

This study identifies distinct antibody epitope repertoires in IBD patients using PhIP-seq, revealing differentially abundant antibodies associated with disease subtypes and features.

Genetic, environmental and intrinsic determinants of the human antibody epitope repertoire

This study uses PhIP-Seq to analyze antibody repertoires in 1,443 individuals, showing genetic and environmental factors influence antibody diversity and phenotype associations.

Discovery, diversity and functional associations of crAss-like phages in human gut metagenomes from four Dutch cohorts

The paper discovers new crAss-like phage species and explores their diversity, genomic features, host associations, and links to human health phenotypes in Dutch gut metagenomes.

The Dutch Microbiome Project defines factors that shape the healthy gut microbiome

This study identifies environmental and lifestyle factors shaping the gut microbiome in a large Dutch cohort, finding that most microbiome variation is due to environment rather than genetics.