Pieter C. Dorrestein

Mapping bacterial bile amidation across the bile salt hydrolase family

The paper maps bacterial bile amidation by analyzing BSH transaminase activities and identifying BBAs in human samples.

Genomic detection of domoic acid biosynthesis uncovers expanded toxigenic diversity across Pseudo-nitzschia diatoms

The paper identifies genomic features of domoic acid biosynthesis in Pseudo-nitzschia diatoms, revealing expanded toxigenic diversity and environmental expression patterns.

The Evolving Bileome: A Pan-Repository Landscape of Expanded Bile Acid and Related Steroidal Signatures

The paper expands a bile acid and steroidal MS/MS spectral library across three repositories, capturing diverse structures and providing a resource for classifying unknown spectra.

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.

Serum metabolomics reveals signatures associated with physical resilience trajectories from middle to older age

The paper identifies metabolomic signatures associated with physical resilience trajectories from middle to older age using long-term serum data.

Widespread detection of Polyethylene glycol reveals chronic human exposure through pharmaceutical drugs

Polyethylene glycol in human biofluids can mark drug exposure rather than contamination; it is oxidized to acid metabolites and appears in 2.3% of public metabolomics files.

The caddisfly gut microbiome contributes to the consumption of riparian leaf litter within rivers

This study shows that caddisfly gut microbiomes help decompose non-local plant litter, while dietary plant secondary metabolites inhibit consumption regardless of microbiome state.

The Everything Bagel Feature Finder: Ultra-fast automated feature finding for untargeted metabolomics

The Everything Bagel feature finder automates metabolomics data processing, achieving comparable or better performance than existing methods with significantly reduced computational time.

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.

Effect of Perinatal Ampicillin or Amoxicillin/Clavulanate Exposure on Maternal and Infant Gut Microbiome, Metabolome, and Infant Responses to the 20-valent Pneumococcal Conjugate Vaccine

This study examines how maternal exposure to ampicillin or amoxicillin/clavulanate affects neonatal gut microbiome, metabolome, and vaccine responses to PCV20.

Agentic AI for Structural Elucidation and Discovery of Drug Metabolites from Mass Spectrometry Data

The paper develops an agentic AI system using LLMs and domain tools to hypothesize and validate structures of unknown drug metabolites from mass spectrometry data.

Among-population variation in the threespine stickleback ( Gasterosteus aculeatus ) liver metabolome: effects of ancestry and environment

This study examines metabolome variation in threespine stickleback across populations, showing both genetic and environmental influences on liver metabolites.

Early life gut microbial and metabolic shifts reflected in stool consistency- a gut transit time proxy

This study links gut transit time, inferred from stool consistency, to microbial metabolites and microbiota in infants, showing associations with breastfeeding, bile acid metabolism, and short-chain fatty acids.

Ordering molecular diversity in untargeted metabolomics via molecular community networking

This paper introduces molecular community networking to organize metabolite data, revealing hidden connections and discovering novel dipeptide-conjugated bile acids.

TIMS-Bench: Towards community standards for benchmarking untargeted trapped ion mobility metabolomics tools and datasets

TIMS-Bench evaluates three TIMS feature-finding tools using public and benchmark datasets, identifying strengths and weaknesses in feature detection and annotation.

Alkamines reveal a hidden layer of steroid and drug metabolism

The paper identifies alkamines as a previously hidden class of metabolites formed via reductive amination, revealing significant gaps in metabolomics and drug metabolism understanding.

Antibiotic Exposure Through Human Milk Influences the Infant Gut Microbiome

This study examines how maternal antibiotic use during breastfeeding affects the infant gut microbiome and metabolome, finding altered microbial profiles and increased BMI in some infants.

Serum metabolic signatures of cognitive resilience in a longitudinal aging cohort

The paper identifies serum metabolic signatures associated with cognitive resilience in a longitudinal aging cohort using untargeted LC-MS/MS profiling.

Farnesoid X receptor-dependent microbiome-bile acid signaling mediates obstructive sleep apnea-induced atherosclerosis

This study shows that FXR deficiency prevents IHC-induced atherosclerosis by disrupting microbiome-bile acid signaling in ApoE-/- mice.

Pan-Metabolomics Repository Mapping of the Carnitine Landscape

The paper systematically extracts and catalogs acylcarnitine metabolites from multiple repositories, identifying previously unknown carnitines and providing a resource for further metabolic research.

Ecological Interactions Drive Metabolomic Diversification in Amazonian Pseudonocardia Symbionts

This study examines metabolomic diversity in Amazonian Pseudonocardia bacteria, showing that ecological interactions and local adaptation drive chemical variation rather than phylogeny.

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.

Early seed priming with closely related Bacillus strains induces divergent physiological and defense responses in melon

This study shows that melon seeds primed with two closely related Bacillus strains trigger different physiological and defense responses based on microbial identity and inoculum dose.

Navigating the conjugated metabolome

This study maps conjugated metabolites by analyzing MS/MS spectra from public repositories, identifying potential conjugation events and providing a resource for structural discovery.

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.

Community Curation of Microbial Metabolites Enables Biological Insights of Metabolomics Data

The paper introduces a collaborative platform for curating microbial metabolite knowledge to enhance metabolomics data interpretation.

ChemEmbed: A deep learning framework for metabolite identification using enhanced MS/MS data and multidimensional molecular embeddings

ChemEmbed improves metabolite identification by combining enhanced MS/MS data with multidimensional molecular embeddings, achieving high accuracy in benchmark tests.

Unlocking the Bile Acid Universe: Advanced Workflows and a Multidimensional Library of 280 Unique Species

The paper develops a multidimensional bile acid reference library and evaluates workflows for accurate bile acid measurement in biological samples.

A metabolic atlas of mouse aging

This study maps metabolic changes in 12 organs of male and female mice across 5 ages, identifying sex-specific patterns and a metabolic aging clock.

Charting the undiscovered metabolome with synthetic multiplexing implicates ibuprofen-carnitine in myotoxicity

The paper uses synthetic multiplexing to annotate uncharacterized metabolites, identifying ibuprofen-carnitine as a metabolite linked to muscle toxicity.