Ruth E. Ley

Micro-Cm: restrictase-free microbiome-wide chromosome conformation profiling

The paper introduces Micro-Cm, a restrictase-free method for microbiome-wide chromosome conformation profiling, showing improved plasmid-host association detection in simulated and real gut microbiome samples.

Human gut flagellome profiling using FlaPro reveals TLR5-related phenotype-specific alterations in IBD

The paper introduces FlaPro, a tool to profile the human gut flagellome, revealing TLR5-related changes in IBD patients.

Extensive genomic diversity in Desulfovibrio species reveals species-specific functional traits associated with disease

The paper compiles 2,658 Desulfovibrio genomes from 90 diseases and 32 countries to identify species-specific functional traits linked to inflammatory diseases.

Co-targeting an AMPK--MAPK axis reprograms CAFs and suppresses PDAC

This study shows that targeting the AMPK-MAPK axis in cancer-associated fibroblasts suppresses PDAC growth in fly and mouse models by restoring AMPK activity and inhibiting fibroblast activation.

StrainVis: interactive visual strain-level analysis of microbiome data

StrainVis integrates ANI and APSS-based strain tracking tools to enable interactive, unified analysis of microbiome strain-level diversity without programming.

Fidelity in co-diversified symbiosis

This study shows that non-native symbionts can colonize a novel host but with outcomes dependent on genetic relatedness to the native symbiont.

MMonitor: Software for Real-Time Monitoring of Microbial Communities Using Long Reads

MMonitor provides real-time analysis and visualization of metagenomic data, enabling dynamic microbiome research through automated pipelines and interactive dashboards.

Infection with gut parasites correlates with gut microbiome diversity across human populations in Africa

This study shows that gut microbiome diversity correlates with infection by multiple soil-transmitted helminths in African populations, using metagenomic sequencing for parasite detection.

D- and L-lactate consumers in the human gut are taxonomically, biochemically, and energetically different

This study compares D- and L-lactate consumption by gut microbes, finding distinct microbial communities and metabolic pathways for each isomer.

Human gut metagenomes and assembled microbial genomes from an urban cohort from Colombia, South America

The paper reports shotgun gut metagenomes and assembled microbial genomes from an urban Colombian cohort, complementing existing 16S rRNA gene and host data.

Carbohydrates and the oxidative branch of the pentose phosphate pathway modify Bacteroides thetaiotaomicron phage resistance by phase variable S-layers

This study shows that specific carbohydrates modulate phage resistance in Bacteroides thetaiotaomicron through phase variable S-layers and the pentose phosphate pathway.

Characterization and description of Clostridium filamentum ETTB, a novel gut bacterium with TLR5 modulating properties

This study isolates and characterizes a novel Clostridium species, C. filamentum ETTB, which modulates the TLR5 pathway in host cells and has distinct genomic features compared to related species.

Flagellin in the human gut microbiome is a diet-adjustable adjuvant for vaccination

This study shows that gut microbiome flagellin affects vaccine reactogenicity and can be influenced by diet.

Selection and transmission of the gut microbiome alone shifts mammalian behavior

Serial transfer of low-activity mice gut microbiomes to germ-free mice reduced locomotor activity, showing microbiome transmission can influence host traits independently of genetic changes.

Medication Use is Associated with Distinct Microbial Features in Anxiety and Depression

This study links medication use to distinct gut microbial features in anxiety and depression, showing antidepressants have a larger effect on microbiota than diagnoses.

Kinetic and structure-based comparisons of silent and stimulatory flagellin interactions with TLR5

The paper compares the binding kinetics and structural features of silent and stimulatory flagellin variants with TLR5, identifying structural differences that explain their distinct immune responses.

ResMiCo: increasing the quality of metagenome-assembled genomes with deep learning

ResMiCo improves metagenome assembly quality by accurately identifying misassembled contigs using deep learning, achieving better performance than existing methods.

Interpreting tree ensemble machine learning models with endoR

endoR interprets tree ensemble models in microbiome data by extracting feature importance and interactions, confirming known associations and revealing new microbial network insights.

Incorporating genome-based phylogeny and functional similarity into diversity assessments helps to resolve a global collection of human gut metagenomes

The paper evaluates tree-based and tree-agnostic diversity measures in human gut metagenomes, finding tree-based measures better explain phenotypic variation and improve predictive models.

Struo2: efficient metagenome profiling database construction for ever-expanding microbial genome datasets

Struo2 constructs and updates metagenome reference databases efficiently, improving speed and scalability for large microbial genome datasets.

The microbiome affects liver sphingolipids and plasma fatty acids in a murine model of the Western diet based on soybean oil

This study shows that microbial colonization affects liver sphingolipids but not plasma fatty acids in mice fed a high-soybean-oil diet.

High-resolution QTL mapping with Diversity Outbred mice identifies genetic variants that impact gut microbiome composition

This study uses 16S rRNA gene sequencing in Diversity Outbred mice to identify genetic variants affecting gut microbiome composition, finding significant heritability and novel QTLs related to immune and metabolic pathways.

DeepMAsED: Evaluating the quality of metagenomic assemblies

DeepMAsED evaluates metagenomic assembly quality using deep learning, identifying misassembled contigs without references and showing high accuracy on large assemblies.

Struo: a pipeline for building custom databases for common metagenome profilers

Struo builds custom databases for metagenome profilers by integrating new genomes, improving read mappability in synthetic and real datasets.

Human salivary amylase gene copy number impacts oral and gut microbiomes

The paper shows that human AMY1 gene copy number affects oral and gut microbiome composition and function, with low-AMY1 associated with enhanced complex carbohydrate breakdown and high-AMY1 linked to resistant starch fermentation and higher adiposity.

GeNet: Deep Representations for Metagenomics

GeNet provides deep representations for metagenomics classification, achieving competitive precision and recall with lower memory use and enabling effective downstream tasks.