Q. R. Ducarmon

Long-term fasting remodels gut microbial metabolism and host metabolism

This study shows that long-term fasting changes gut microbial composition and function, as well as the serum metabolome, with significant shifts in microbial species and metabolite levels.

Large-scale computational analyses of gut microbial CAZyme repertoires enabled by Cayman

The paper develops Cayman, a CAZyme profiler, to analyze gut microbial CAZyme repertoires and finds differences in substrate preferences between Western and non-Western metagenomes and CRC patients.

Machine learning-based meta-analysis reveals gut microbiome alterations associated with Parkinson's disease

This study uses machine learning to meta-analyze gut microbiome data from Parkinson's disease patients, identifying microbial pathways linked to disease and potential diagnostic applications.

Clostridioides difficile PCR ribotype 151 is polyphyletic and includes pathogenic isolates from cryptic clade C-II with mono-toxin pathogenicity loci that can escape routine diagnostics

The paper identifies that PCR ribotype 151 of Clostridioides difficile is polyphyletic, includes both non-toxigenic and toxigenic isolates, and contains pathogenic variants that evade routine diagnostics.

Carriage of three plasmids in a single human clinical isolate of Clostridioides difficile

The paper describes a C. difficile clinical isolate carrying three compatible plasmids and identifies functional replicons in two of them.

Impacts of dietary exposure to pesticides on faecal microbiome metabolism in adult twins

This study links pesticide exposure to changes in gut microbiome composition and function in adult twins using urinary biomarkers and metagenomic/metabolomic analyses.

Asymptomatic gut colonization by extended-spectrum beta-lactamase-producing Escherichia coli is not associated with an altered gut microbiome or metabolome in Dutch adults

This study finds that asymptomatic gut colonization by ESBL-producing E. coli in Dutch adults is not linked to changes in microbiome or metabolome composition.

Multi-omics phenotyping of the gut-liver axis allows health risk predictability from in vivo subchronic toxicity tests of a low-dose pesticide mixture

The paper uses multi-omics analysis on pesticide-exposed rats to show metabolic and epigenetic changes in the gut-liver axis that predict health risks not detected by standard tests.

Shotgun metagenomics and metabolomics reveal glyphosate alters the gut microbiome of Sprague-Dawley rats by inhibiting the shikimate pathway

This study shows glyphosate inhibits the shikimate pathway in rat gut microbiota, altering microbial communities and metabolites, with potential health implications.

Toward standards in clinical microbiome studies: comparison of three DNA extraction methods and two bioinformatic pipelines

This study compares three DNA extraction methods and two bioinformatic pipelines for microbiome analysis, finding that methods vary in accuracy and that negative controls are critical for low-biomass samples.