Simone Zuffa

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.

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.

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-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.

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.

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.

Environmental and Maternal Imprints on Infant Gut Metabolic Programming

The paper examines how environmental and maternal factors influence infant gut metabolism through microbiome and metabolome profiling in Bangladeshi mother-infant pairs.

Influence of perinatal ampicillin exposure on maternal fecal microbial and metabolic profiles

This study examines how maternal ampicillin exposure during pregnancy and postpartum affects fecal microbiome and metabolic profiles, linking these changes to increased offspring weight gain.

A Multi-Organ Murine Metabolomics Atlas Reveals Molecular Dysregulations in Alzheimer's Disease

The paper presents a multi-organ metabolomics atlas in AD mouse models, identifying dysregulated metabolites and microbiome associations linked to oxidative stress and cognitive impairment.

Fecal Microbial and Metabolic Signatures in VEO-IBD: Implications for Unique Pathophysiology

This study identifies distinct microbial and metabolic signatures in VEO-IBD compared to healthy controls, linking microbiome changes to metabolic dysregulation.

MS/MS Mass Spectrometry Filtering Tree for Bile Acid Isomer Annotation.

This paper introduces a mass spectrometry filtering tree to distinguish bile acid isomers in LC-MS/MS data and identifies a novel deoxycholyl-2-aminophenol amidate linked to whole grain consumption.

Gut Microbiota and Derived Metabolites Mediate Obstructive Sleep Apnea Induced Atherosclerosis

This study shows that gut microbiota and their metabolites contribute to OSA-induced atherosclerosis, particularly in the aorta, through specific bacterial imbalances and bile acid dysregulation.

Human untargeted metabolomics in the gut microbiome era: ethanol vs methanol

The paper compares ethanol and methanol extraction methods for fecal metabolomics, showing ethanol is safer for off-site collection and preserves metabolic profiles.

To impute or not to impute in untargeted metabolomics - that is the compositional question

This study evaluates imputation methods for untargeted metabolomics data, finding that kNN and RF imputation perform poorly with missing data, especially MNAR, and that missing data proportion significantly affects accuracy.

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.

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.

plantMASST - Community-driven chemotaxonomic digitization of plants

The paper curates LC-MS/MS data from plant extracts to create a taxonomically focused database for exploring plant-derived molecules.