P. Wilmes

Fetal programming by the parental microbiome of offspring behavior, and DNA methylation and gene expression within the hippocampus

This study shows that the maternal microbiome influences offspring behavior, body weight, and hippocampal DNA methylation and gene expression.

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.

Functional prediction of proteins from the human gut archaeome

The paper predicts and characterizes protein functions in Methanobrevibacter smithii using sequence and structure data, identifying gut-specific proteins and potential horizontal gene transfer events.

Cross-domain interactions induce community stability to benthic biofilms in proglacial streams

The paper examines cross-domain interactions in proglacial stream biofilms, showing that specific taxa contribute to community stability despite environmental gradients.

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.

Forecasting of a complex microbial community using meta-omics

The paper forecasts microbial community dynamics in a wastewater treatment plant using longitudinal meta-omics data and temporal signals, achieving accurate predictions of gene abundance and expression.

Multi-omics analysis of mouse fecal microbiome reveals supplier-dependent functional differences and novel metagenome-assembled genomes

This study compares the fecal microbiome of mice from two U.S. suppliers using multi-omics approaches, revealing supplier-specific functional differences and novel metagenome-assembled genomes.

Alterations of oral microbiota and impact on the gut microbiome in type 1 diabetes mellitus revealed by multi-omic analysis

This study identifies oral microbiota changes in T1DM linked to gut microbiome alterations through multi-omic analysis of saliva and stool samples.

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.

Critical Assessment of Metaproteome Investigation (CAMPI): a Multi-Lab Comparison of Established Workflows

CAMPI evaluates metaproteomic workflows across labs, finding sample processing drives peptide variability while workflows yield similar functional profiles.

Homogeneous selection promotes microdiversity in the glacier-fed stream microbiome

The paper shows that homogeneous selection drives microdiversity in glacier-fed stream microbiomes, with implications for microbial diversity under climate change.

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.

Extensive Transmission of Microbes along the Gastrointestinal Tract

The paper shows oral microbes commonly colonize the large intestine in healthy individuals and more so in disease states like colorectal cancer and rheumatoid arthritis.