Eric J. Alm

This study examines gut microbiome diversity and structure across different lifestyles in Thailand, finding variations in microbial composition and associations with lifestyle factors.

This study identifies Blautia wexlerae's role in converting dietary fats into bioactive metabolites that enhance gut hormone secretion and improve metabolic health in mice and humans.

The paper identifies new phosphorothioate DNA modification systems in the human gut microbiome using genomic and mass spectrometric analysis.

The paper compares host transcriptional responses to urban and rural gut microbiomes, finding urban microbiomes affect innate immune pathways and high-diversity microbiomes trigger stronger host responses.

This study examines how gut bacteria genomes adapt to industrialization, finding convergent genomic responses in stress response, cell envelope remodeling, and central metabolism across different populations.

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.

The paper identifies a novel subspecies of Bifidobacterium longum, BL. nexti, in infant gut microbiomes, showing its association with formula feeding and vertical transmission.

The paper examines microbial community diversity in a uranium-contaminated aquifer, finding reduced taxonomic and phylogenetic diversity but stable functional diversity.

The paper characterizes phosphorothioate (PT) modifications in the human gut microbiome using metagenomics and mass spectrometry, revealing temporal dynamics and species-specific patterns.

The paper shows that individuals vary in their gut microbiota's ability to ferment dietary fibers, leading to different SCFA production, and suggests personalized fiber supplementation as a therapeutic strategy.

The paper identifies gut microbiome biomarkers associated with T2D progression in a Mexican cohort and shows metformin treatment reverses these changes.

This paper introduces MicrobiomeCensus, an algorithm to estimate human population size from sewage samples using microbial taxon abundance distributions, showing it outperforms generic algorithms in simulations and field data.

The paper introduces StrainTrack, a method to track bacterial strains in metagenomes and identifies shared strains between twins.

The paper uses longitudinal wastewater sampling to analyze metabolite temporal dynamics across buildings, revealing distinct feature temporal dynamics and enabling building classification.

This study analyzes 24-hour residential sewage using untargeted genomics and metabolomics to identify human-derived biomarkers and inform public health.

This paper benchmarks classic and modern false discovery rate methods in computational biology, finding modern methods with informative covariates offer modest power gains without sacrificing FDR control.

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

The paper shows that random DNA sequences can rapidly evolve into functional promoters in E. coli with minimal mutations, highlighting the accessibility of promoter recognition machinery.

The paper characterizes mobile genetic elements in the gut microbiome, revealing phylum-level adaptive gene pools and their role in horizontal gene transfer.

The paper develops a Bayesian allocation strategy to improve statistical power in FMT trials by accounting for donor stool efficacy differences.