S. K. Higginbottom

Gut microbiota gate host exposure to cholinesterase inhibitors from dietary Solanums

The paper investigates how gut microbiota modify steroidal alkaloids from Solanum plants, affecting host exposure and physiological effects.

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.

A mutant fitness compendium in Bifidobacteria reveals molecular determinants of colonization and host-microbe interactions

The paper creates a mutant fitness compendium for Bifidobacterium breve to identify molecular factors affecting colonization and host-microbe interactions.

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.

Strain dropouts reveal interactions that govern the metabolic output of the gut microbiome

The paper investigates how strain dropouts in the gut microbiome affect community metabolism and host physiology, finding that functionally redundant strains can have significant impacts outside their niche.

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.

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.

Quantifying the interplay between rapid bacterial evolution within the mouse intestine and transmission between hosts

The paper tracks bacterial evolution and transmission in mice using barcoded E. coli strains, showing rapid selection and migration effects on microbiota composition.

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.

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.

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.