Dirk Haller

Microbial Invasion and Immunosuppression Drives Adenoma Progression in Early Colorectal Cancer Development

The paper shows bacterial invasion and neutrophil immunosuppression drive adenoma progression in a porcine FAP model using single-cell RNA sequencing and spatial transcriptomics.

Distinct colorectal cancer genotypes shape microbial ecosystems and reveal stage-specific microbiota dependencies

This study shows that different colorectal cancer genotypes create distinct microbial ecosystems and that microbiota dependence decreases as tumors progress.

A transient CD87-centred axis enhances the Th17 potential of cDC2 in neonates

The paper identifies a CD87-dependent coagulation pathway that enhances Th17 potential in neonatal cDC2, with implications for early-life immunity.

Probiotic formula intervention in infants leads to colonization and competitive strain displacement independent of IgA binding

The paper investigates how probiotic interventions in infants affect bacterial strain dynamics and immune responses, finding that specific strains are displaced regardless of IgA binding.

Periweaning diet-induced activation of an IFNγ-mediated regulatory circuit promotes the homeostasis of cytotoxic CD8+ T Cells

The paper shows that periweaning diet activates an IFNγ-mediated circuit in cDC1 that promotes effector memory CD8 T cell homeostasis through immunogenic maturation.

Gut microbiota within-host evolution enforces colonization resistance against enteric infection

The paper shows that E. faecalis evolves to metabolize fructoselysine, reducing S. Typhimurium colonization by limiting a key nutrient.

Extensive genomic diversity in Desulfovibrio species reveals species-specific functional traits associated with disease

The paper compiles 2,658 Desulfovibrio genomes from 90 diseases and 32 countries to identify species-specific functional traits linked to inflammatory diseases.

A microbial metabolite protects against graft-versus-host disease via mTORC1 and STING-dependent intestinal regeneration

This study identifies desaminotyrosine (DAT) as a microbial metabolite that protects against graft-versus-host disease by promoting intestinal regeneration and modulating immune responses.

Reduced intestinal GLP-1+ cell numbers are associated with an inflammation-related epithelial metabolic signature

The paper shows reduced GLP-1+ cell numbers in inflamed intestinal tissues of mice and CD patients, linked to an inflammatory metabolic signature affecting epithelial differentiation.

Ultra-sensitivity metaproteomics redefines the gut dark metaproteome, uncovering host-microbiome interactions and drug targets in intestinal inflammatory diseases.

The paper introduces uMetaP, an ultra-sensitive metaproteomic method that enhances detection of the gut dark metaproteome and identifies drug targets in intestinal inflammatory diseases.

Susceptibility to inflammatory bowel diseases promotes invasive carcinomas in a murine model of ATF6-driven colon cancer

This study shows that IBD susceptibility increases the risk of ATF6-driven tumorigenesis in a murine model.

Microbiota metabolized Bile Acids accelerate Gastroesophageal Adenocarcinoma via FXR inhibition

This study shows that high-fat diets promote GEAC by altering the microbiota-Bile Acid axis and inhibiting FXR, with FXR agonists like OCA slowing disease progression.

On the limits of 16S rRNA gene-based metagenome prediction and functional profiling

This study evaluates 16S rRNA gene-based functional prediction tools using simulated and metagenomic data, finding they lack sensitivity to detect health-related microbiome functional changes.

The Intestinal Clock Regulates Host Metabolism through the Fiber-Dependent Microbiome and Macronutrient Transcriptome.

This study shows that the intestinal clock influences microbiome oscillations and host metabolism, with dietary fiber playing a key role in linking circadian rhythms to metabolic health.

Namco: A microbiome explorer

Namco provides a user-friendly R Shiny application for comprehensive microbiome analysis, covering data processing to complex tasks like machine learning and network analysis.

A randomization-based causal inference framework for uncovering environmental exposure effects on human gut microbiota

The paper introduces a causal inference framework to assess environmental exposure effects on the gut microbiome using observational data from the KORA cohort.