Karsten Zengler

Targeting catecholate siderophore systems enables precision depletion of gut enterobacteria during colitis

This study shows that targeting catecholate siderophore systems reduces AIEC colonization in colitis by immunization, preserving gut microbiome composition.

Synthesis-driven reverse metabolomics reveals 3-hydroxy N-acyl amides as gut microbial molecules

The paper synthesizes 3-hydroxy N-acyl amides and uses reverse metabolomics to identify their presence in biological samples and link them to microbial production and metabolic disease.

Evolved microbial diversity enables combinatoric biosensing in complex environments

The paper develops a framework using evolved microbial diversity and machine learning to enable combinatoric biosensing of multiple analytes in complex environments.

Multi-omics Analyses of Facial Skin in Acne Identify Distinct Microbial and Metabolic Features at Lesional and Non-lesional Sites

This study identifies distinct microbial and metabolic features in non-lesional acne skin using multi-omics analyses, showing molecular dysbiosis extends beyond visible lesions.

Rational engineering of facultative anaerobiosis enables commensal survival in the oxygenated gut

This study engineers obligate anaerobic bacteria to tolerate oxygen, improving their survival in the gut.

An Anaerobic Pathogen Rewires Host Metabolism to Fuel Oxidative Growth in the Inflamed Gut

This study shows how ETBF reprograms host metabolism to create an oxidative niche that supports its growth in the inflamed gut.

A Multi-Omics Processing Pipeline (MOPP) for Extracting Taxonomic and Functional Insights from Metaribosome Profiling (metaRibo-Seq) data

The paper introduces MOPP, a pipeline for processing metaRibo-Seq data to improve taxonomic and functional analysis by reducing false positives through coverage breadth filtering.

Pan-repository analysis reveals a drug-activating function of microbial bile acid conjugation

The paper identifies microbial bile acid conjugation as a drug-activating function for 5-ASA, revealing its therapeutic relevance through metabolomics analysis.

A searchable metadata network graph for microbiome metabolomics

The paper introduces microbiomeMASST, a metadata network graph linking metabolites across datasets, enabling cross-study analysis of microbial metabolites and their biological context.

Proteome allocation of the microbiome reveals how diet and metabolic dysbiosis impact disease

The paper uses ME-models to predict proteome allocation in the gut microbiome and identifies taxa associated with metabolic changes in IBD patients.

Multi-laboratory Study Establishes Reproducible Methods for Plant-Microbiome Research in Fabricated Ecosystems

The paper establishes reproducible methods for plant-microbiome research using fabricated ecosystems across multiple laboratories.

Insights into the role of root exudates in bacteriophage infection dynamics

This study investigates how plant-bacteria-phage interactions affect nitrogen acquisition and exometabolite composition by comparing phage-lysed and uninfected bacterial necromass.

The microbiome diversifies N-acyl lipid pools - including short-chain fatty acid-derived compounds

The paper creates a spectral library of N-acyl lipids from metabolomics data, identifies novel compounds, and links them to health conditions like HIV and cognitive impairment.

Empirically establishing drug exposure records directly from untargeted metabolomics data

The paper develops a drug exposure resource from untargeted metabolomics data to identify medications without clinical records.

FROG Analysis Ensures the Reproducibility of Genome Scale Metabolic Models

The paper introduces FROG analysis to standardize reproducibility assessments of genome-scale metabolic models, resulting in full reproducibility of all tested models.

Spatial chemistry of citrus reveals molecules bactericidal to Candidatus Liberibacter asiaticus

This study uses spatial metabolomics to identify bactericidal compounds in citrus plants infected with Candidatus Liberibacter asiaticus, suggesting potential alternatives to antibiotics for HLB treatment.

A synthetic skin microbial community (SkinCom) enables reproducible investigations of the human skin microbiome

The paper introduces SkinCom, a synthetic skin microbial community, which enables reproducible in vitro and in vivo studies of the human skin microbiome and recapitulates 65.6% of in vitro responses in a human trial.

Pathogenic Bacteroides fragilis strains can emerge from gut-resident commensals

This study identifies genetic factors enabling Bacteroides fragilis to transition from commensal to pathogenic by analyzing 813 strains and their genomic diversity.

ChiMera: An easy to use pipeline for Bacterial Genome Based Metabolic Network Reconstruction, Evaluation and Visualization

ChiMera is a pipeline that reconstructs, evaluates, and visualizes bacterial genome-scale metabolic models using efficient tools and a user-friendly interface.