Sean M. Gibbons

The microbial soy metabolite S-equol mitigates cadmium neurotoxicity in mice

This study shows that S-equol, a microbial metabolite, reduces cadmium-induced neurotoxicity in mice by restoring neural gene expression and is associated with lower levels in humans carrying the apolipoprotein E4 allele.

Phenotypic heterogeneity in the human gut microbiome revealed by subspecies-resolution single-cell transcriptomics

The paper develops metaSPLiT, a single-cell RNA sequencing method, to reveal sub-species functional specialization in the human gut microbiome.

Non-invasive Vagal Nerve Stimulation as a Potential Treatment for Repetitive Blast Trauma

This study investigates non-invasive vagus nerve stimulation as a treatment for repetitive blast trauma in mice, finding reduced inflammation and behavioral changes but not all effects.

A data-driven modeling framework for mapping genotypes to synthetic microbial community functions

This paper introduces a data-driven model to predict synthetic microbial community functions from genetic features, enabling predictions for new species not included in training data.

If you give a mouse a poopsicle: a novel fecal microbiota transplant method for exploring the role of the gut microbiome in stress-related outcomes in mice

This paper introduces a novel fecal microbiota transplant method using 'poopsicles' to reduce stress in mice, showing lower corticosterone levels and better microbial similarity compared to traditional gavage.

MICOMWeb: a website for microbial community metabolic modeling of the human gut

MICOMWeb provides a user-friendly platform for microbial community metabolic modeling of the human gut, addressing challenges in computational infrastructure and user expertise.

Industrialization drives convergent microbial and physiological shifts in the human metaorganism

The paper investigates how industrialization affects microbial and physiological traits in the human gut across diverse populations, finding homogenized microbiomes, reduced diversity, and impaired disease prediction accuracy in less industrialized groups.

Metagenomic estimation of absolute bacterial biomass in the mammalian gut through host-derived read normalization.

This paper estimates absolute bacterial biomass in the gut using host-derived read normalization from metagenomic data, showing it tracks antibiotic treatment response in mice and humans.

Metagenomic estimation of dietary intake from human stool

This paper introduces MEDI, a method to estimate dietary intake from stool metagenomes by analyzing food-derived DNA, showing accurate detection of food items and prediction of dietary patterns.

Understanding disease-associated metabolic changes in human colon epithelial cells using iColonEpithelium metabolic reconstruction

The paper develops a cell-type-specific genome-scale metabolic model of human colonic epithelial cells to identify metabolic signatures associated with inflammatory bowel disease.

APOE Genotype and Biological Age Impact Inter-Omic Associations Related to Bioenergetics

The paper identifies APOE genotype-related metabolite associations with biological age and bioenergetics in humans, showing counterintuitive patterns in {varepsilon}2 and {varepsilon}4 carriers.

Elucidating human gut microbiota interactions that robustly inhibit diverse Clostridioides difficile strains across different nutrient landscapes

This study identifies gut microbiota interactions that inhibit C. difficile strains across nutrient environments, highlighting strain variability and nutrient context as key factors.

Long-term NMN treatment increases lifespan and healthspan in mice in a sex dependent manner

This study shows that long-term NMN treatment improves healthspan and extends lifespan in female mice but not males, with sex-specific effects on metabolism and microbiome.

Personalized Clostridioides difficile engraftment risk prediction and probiotic therapy assessment in the human gut.

The paper uses microbial community-scale metabolic models to predict C. difficile engraftment risk and assess probiotic therapy efficacy in the human gut.

Generally-healthy individuals with aberrant bowel movement frequencies show enrichment for microbially-derived blood metabolites associated with reduced kidney function.

The paper examines the link between bowel movement frequency and blood metabolites in healthy individuals, finding associations with kidney function and chronic disease risk.

Microbial community-scale metabolic modeling predicts personalized short chain fatty acid production profiles in the human gut.

This paper uses microbial community-scale metabolic modeling to predict individual-specific short chain fatty acid production profiles in the human gut and links these predictions to clinical health markers.

Genome-microbiome interplay provides insight into the determinants of the human blood metabolome

The paper analyzes the genetic and microbiome contributions to blood metabolite variation across 2,049 individuals, finding that over 60% of metabolites are associated with either genetics or the microbiome, with some showing interaction effects.

Non-responder phenotype reveals microbiome-wide antibiotic resistance in the murine gut

The paper identifies a non-responder phenotype in the murine gut microbiome that exhibits resistance to cefoperazone, showing upregulated antimicrobial resistance genes and reduced central metabolism during antibiotic treatment.

Gut Microbiome Pattern Reflects Healthy Aging and Predicts Extended Survival in Humans

The paper shows that gut microbiome uniqueness increases with age and predicts survival in humans.

MICOM: metagenome-scale modeling to infer metabolicinteractions in the microbiota.

MICOM models gut microbiota metabolism to predict individual-specific short chain fatty acid production and interactions, showing differences between healthy and diabetic subjects.

Blood metabolome signature predicts gut microbiome α-diversity in health and disease

The paper identifies a blood metabolome signature that robustly predicts gut microbiome α-diversity across health and disease conditions.

Correcting for batch effects in case-control microbiome studies

This paper compares batch correction methods for microbiome case-control studies, showing percentile-normalization improves sensitivity in meta-analyses.