Michael Zimmermann

Bacterial metabolism of synthetic steroids across ecosystems reveals diverse biotransformation products, reactions, and enzymes

This study maps bacterial metabolism of synthetic steroids across ecosystems, identifying transformation products, reactions, and enzymes, and reveals cooperative microbial interactions in steroid metabolism.

13C flux ratio analysis with FRAPPPE reveals differences in metabolic fluxes between gut Bacteroidota and Escherichia coli

This study uses FRAPPPE to analyze metabolic flux differences between gut Bacteroidota and E. coli, revealing distinct metabolic patterns under anaerobic conditions and in co-metabolism of nucleosides.

Lithocholic acid modulates the growth of butyrate-producing bacteria and is decreased in the feces of stunted children

This study finds that lithocholic acid levels are lower in stunted and EED children, and it modulates butyrate-producing bacteria growth while inhibiting oral taxa.

Personalized microbiotas (counter-)select for antibiotic resistant pathogens

This study identifies how personalized gut microbiotas influence the competitiveness of antibiotic-resistant pathogens through carbohydrate competition and specific genetic mutations.

Domain-Specific Agonist Binding Affinities Explain Structural and Functional Regulation of TRPM2

This study quantifies the binding affinities of TRPM2 domains for ADPR analogs and shows that MHR1/2 drives activation while NUDT9H maintains structural integrity.

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.

Metabolic specialization structures gut bacterial niches and drives colorectal cancer progression

This study identifies Leptotrichia wadei as a pro-tumorigenic bacterium in CRC by linking metabolic specialization to microbial niches and tumor progression.

Multi-omics and biophysical phosphoproteomics upon BRAF inhibition uncover functional networks of BRAFV600E-driven signaling

This study uses multi-omics and biophysical phosphoproteomics to analyze BRAFV600E signaling, identifying ETV3 as a new downstream regulator and revealing mechanisms of drug resistance.

Linking interpersonal differences in gut microbiota composition and drug biotransformation activity

The paper examines how gut microbiota composition affects drug metabolism by analyzing 271 drugs across 89 microbial communities and develops models to predict microbiota-mediated drug metabolism.

A toolkit for transposon libraries and functional genomics in intestinal Bacteroidales

The paper develops tools for transposon mutagenesis in Bacteroidales to identify essential genes and functional elements across three gut bacteria.

Cell-type specific iron content regulation revealed by single-cell iron quantification

The paper quantifies cellular iron content in immune cells using sc-ICP-MS and finds cell-type and activation state-specific iron regulation.

Establishing an in vitro pipeline for the high-throughput quantification of epithelial permeability of gut bacterial metabolites

This study develops a high-throughput in vitro pipeline to quantify epithelial permeability of gut bacterial metabolites and identifies new bacteria-drug pairs affecting permeability.

Uncovering nitroxoline activity spectrum, mode of action and resistance across Gram-negative bacteria

This study identifies nitroxoline's broad antibacterial activity against Gram-negative bacteria, its mode of action involving metal homeostasis and outer membrane disruption, and resistance mechanisms across multiple species.

Systematic analysis of gut bacterial carcinogen metabolism and its functional consequences

The paper systematically analyzes gut bacterial metabolism of carcinogens and shows bidirectional interactions with host metabolism, highlighting the microbiome's role in tumorigenesis.

Unraveling interindividual differences and functional consequences of gut microbial metabolism of immunosuppressants

This study reveals interindividual variability in gut microbial metabolism of immunosuppressive drugs mediated by specific bacterial species and enzymes.

Deep quantitative glycoproteomics reveals gut microbiome induced remodeling of the brain glycoproteome

The paper introduces a high-throughput glycoproteomics method to quantify brain glycoproteome changes induced by gut microbiome composition.

Multiomics and quantitative modelling disentangle diet, host, and microbiota contributions to the host metabolome

The paper uses multiomics and quantitative modeling to determine how diet, host, and microbiota contribute to the host metabolome in gnotobiotic mice.

Model-based integration of genomics and metabolomics reveals SNP functionality in Mycobacterium tuberculosis

The paper integrates metabolomics and genomics data to identify functional SNPs in Mycobacterium tuberculosis strains, revealing genetic basis for antibiotic sensitivity.

Two parallel pathways implement robust propionate catabolism and detoxification in mycobacteria

The paper characterizes two propionate catabolism pathways in mycobacteria, showing the methylcitrate pathway's high capacity and the methylmalonyl pathway's detoxification role.