J. L. Sonnenburg

MiFoDB, a workflow for microbial food metagenomic characterization, enables high-resolution analysis of fermented food microbial dynamics

MiFoDB is a metagenomics workflow that identifies microbes in fermented foods with high taxonomic resolution, enabling strain tracking and functional analysis.

High-resolution lineage tracking of within-host evolution and strain transmission in a human gut symbiont across ecological scales

The paper tracks lineage evolution and transmission of Bacteroides thetaiotaomicron across hosts and ecological scales using genomic barcoding and whole-genome sequencing.

Metagenomic Immunoglobulin Sequencing (MIG-Seq) Exposes Patterns of IgA Antibody Binding in the Healthy Human Gut Microbiome

The paper introduces MIG-Seq to analyze IgA binding to gut microbiome strains and finds that microbial genes, especially mucus degradation genes, predict IgA binding levels.

Hadza Prevotella Require Diet-derived Microbiota Accessible Carbohydrates to Persist in Mice.

The paper shows that Prevotella copri requires plant-derived microbiota-accessible carbohydrates for persistence in mice, unlike Bacteroides thetaiotaomicron.

Metabolic diversity in commensal protists regulates intestinal immunity and trans-kingdom competition

The paper identifies metabolic diversity in commensal protists and shows how it influences intestinal immunity and trans-kingdom competition with bacteria.

Butyrate differentiates permissiveness to Clostridioides difficile infection and influences growth of diverse C. difficile isolates

This study shows butyrate reduces C. difficile fitness in mice and humans, and inhibits growth of diverse C. difficile isolates, suggesting dietary interventions could help prevent CDI.

Fermented foods restructure gut microbiota and promote immune regulation via microbial metabolites

This study shows fermented foods reshape gut microbiota and enhance immune regulation through microbial metabolites, independent of live microbes.

Robust Variation in Infant Gut Microbiome Assembly Across a Spectrum of Lifestyles

This study compares infant gut microbiome assembly in Hadza hunter-gatherers and industrialized infants, finding distinct microbial trajectories and functional differences.

Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Microbes

The paper uses ultra-deep metagenomic sequencing to analyze the gut microbiome of Hadza hunter-gatherers, revealing many microbes absent from existing datasets and highlighting differences in microbial dynamics compared to industrialized populations.

In vivo augmentation of a complex gut bacterial community

The paper improves a synthetic gut microbiota community by adding strains that persist after fecal challenge and removing those that do not, resulting in a more stable model of the human gut microbiome.

A metabolomics pipeline enables mechanistic interrogation of the gut microbiome

The paper develops a metabolomics pipeline to identify microbiota-dependent metabolites and explores their links to host phenotypes using machine learning and comparative genomics.

High-throughput cultivation of stable, diverse, fecal-derived microbial communities to model the intestinal microbiota

This study develops a high-throughput method to cultivate diverse, stable fecal-derived microbial communities in vitro, demonstrating their utility for modeling the intestinal microbiota and predicting in vivo responses to antibiotics.

Multiple phase-variable mechanisms, including capsular polysaccharides, modify bacteriophage susceptibility in Bacteroides thetaiotaomicron

This study shows that capsular polysaccharides and other phase-variable cell surface structures in Bacteroides thetaiotaomicron influence bacteriophage susceptibility, enabling bacterial persistence through phase variation.

Bacteroides thetaiotaomicron-infecting bacteriophage isolates inform sequence-based host range prediction

The paper isolates and analyzes 27 bacteriophages infecting Bacteroides thetaiotaomicron, identifies phage structural gene alleles linked to infectivity, and highlights unexplored phage diversity in the human gut.

Electron transfer proteins in gut bacteria yield metabolites that circulate in the host

The paper shows that gut bacteria use reductive amino acid metabolism to produce metabolites that circulate in the host, linked to energy capture via the Rnf complex.

The clinical drug candidate ebselen attenuates inflammation and promotes microbiome recovery after antibiotic treatment for Clostridium difficile infection

This study shows ebselen reduces CDI recurrence and colitis in hamsters and promotes microbiome recovery without altering diversity in mice.

Long-term dietary intervention reveals resilience of the gut microbiota despite changes in diet and weight

This study tracks gut microbiota changes over 12 months in response to low-carbohydrate or low-fat diets, finding initial shifts followed by resilience to long-term perturbation.

Recovery of the gut microbiota after antibiotics depends on host diet and environmental reservoirs

The paper investigates how gut microbiota recovers after antibiotics, showing diet and environmental factors influence resilience and recovery patterns.

A metabolic pathway for glucosinolate activation by the human gut symbiont Bacteroides thetaiotaomicron

This study identifies a metabolic pathway in Bacteroides thetaiotaomicron for glucosinolate activation into isothiocyanates, showing its role in processing dietary nutrients.

Links between environment, diet, and the hunter-gatherer microbiome

The paper examines the microbiome of Hadza hunter-gatherers, finding seasonal changes and unique bacterial families compared to industrialized populations.

Microbiota Accessible Carbohydrates Suppress Clostridium difficile in a Murine Model

The paper shows that microbiota accessible carbohydrates (MACs) reduce Clostridium difficile infection in mice by suppressing bacterial burdens.