L. de Nies

The gut microbiome-linked long chain fatty acid stearate suppresses colorectal cancer

This study shows that the ketogenic diet reduces colorectal tumors in mice by altering the gut microbiome to increase stearic acid, which suppresses cancer cell growth and immune responses.

Altered infective competence of the human gut microbiome in COVID-19

This study identifies increased virulence factors and antimicrobial resistance genes in the gut microbiome of COVID-19 patients, suggesting heightened infective competence.

Glacier-fed stream biofilms harbour diverse resistomes and biosynthetic gene clusters

This study examines AMR and BGCs in glacier-fed stream biofilms, finding diverse resistance genes and biosynthetic clusters across bacteria and eukaryotes.

Mobilome-driven segregation of the resistome in biological wastewater treatment

The paper analyzes meta-omic data from a wastewater treatment plant to show how different antimicrobial resistance genes are disseminated via plasmids or phages, with some categories showing exclusive or primary dissemination routes.

Genomic and metabolic adaptations of biofilms to ecological windows of opportunities in glacier-fed streams

This study identifies genomic and metabolic adaptations of biofilms in glacier-fed streams that enable them to exploit ecological windows of opportunity under harsh conditions.

Synergistic effect of short- and long-read sequencing on functional meta-omics

The paper evaluates short-read, long-read, and hybrid metagenomic assembly methods on complex samples and proposes a reference-independent approach using multi-omic integration for microbiome analysis.

PathoFact: A pipeline for the prediction of virulence factors and antimicrobial resistance genes in metagenomic data

PathoFact predicts virulence factors and antimicrobial resistance genes in metagenomic data with high accuracy and specificity, and identifies signature genes differentiating disease and control groups.