M. R. Olm

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.

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.

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.

Using strain-resolved analysis to identify contamination in metagenomics data

This study identifies contamination in metagenomics data using strain-resolved analysis, finding that contamination is more common in low-biomass samples and adjacent extraction plate positions.

Genetic and behavioral adaptation of Candida parapsilosis to the microbiome of hospitalized infants revealed by in situ genomics, transcriptomics and proteomics

This study identifies genetic and behavioral adaptations of C. parapsilosis in the gut microbiome of hospitalized infants using in situ genomics, transcriptomics, and proteomics.

Meanders as a scaling motif for understanding of floodplain soil microbiome and biogeochemical potential at the watershed scale

The paper investigates microbial metabolic potential in floodplain soils along a river corridor, finding that meander-bound regions predict biogeochemical capacities at the watershed scale.

Infant gut strain persistence is associated with maternal origin, phylogeny, and functional potential including surface adhesion and iron acquisition

The paper investigates factors influencing gut microbiome strain persistence in infants, finding maternal origin and specific genetic functions are associated with strain survival.

InStrain enables population genomic analysis from metagenomic data and rigorous detection of identical microbial strains

InStrain analyzes metagenomic data to detect microbial strain diversity and finds siblings share more strains than unrelated infants, but identical twins do not share more than fraternal siblings.

Consistent metagenome-derived metrics verify and define bacterial species boundaries

The paper evaluates metagenome-derived metrics to define bacterial species boundaries and finds ribosomal proteins are more effective than 16S rRNA genes for species discrimination.

Clades of huge phage from across Earth’s ecosystems

The paper identifies major clades of large phage genomes across diverse ecosystems and highlights their expanded genetic repertoires and potential functional roles.

Necrotizing enterocolitis is preceded by increased gut bacterial replication, Klebsiella, and fimbriae-encoding bacteria that may stimulate TLR4 receptors

The paper identifies microbial features predictive of necrotizing enterocolitis (NEC) in premature infants using metagenomic analysis and machine learning.

Functional potential of bacterial strains in the premature infant gut microbiome is associated with gestational age

This study investigates how gestational age affects the functional potential and species richness of the gut microbiome in premature infants using genome-resolved metagenomics.

Shifts in microbial transcription patterns prior to onset of Necrotizing enterocolitis may indicate low oxygen levels in the gut

The paper identifies shifts in microbial transcription patterns in preterm infants prior to NEC onset, suggesting hypoxic conditions in the gut.

Megaphage infect Prevotella and variants are widespread in gut microbiomes

The paper identifies large phage (Lak phage) in gut microbiomes that infect Prevotella and are widespread, especially in developing-world individuals.

Strain-level overlap between infant and hospital fungal microbiomes revealed through de novo assembly of eukaryotic genomes from metagenomes

The paper analyzes metagenomic data from premature infants and NICUs to identify fungal strains and their genetic diversity, revealing high similarity between infant and hospital-associated fungi.

The developing premature infant gut microbiome is a major factor shaping the microbiome of neonatal intensive care unit rooms

The paper investigates how the gut microbiome of premature infants shapes the microbial composition of NICU rooms over time.

Hospitalized premature infants are colonized by related bacterial strains with distinct proteomic profiles

This study examines microbial colonization in premature infants, finding distinct proteomic profiles among related bacterial strains and correlations with NEC development.

Machine learning leveraging genomes from metagenomes identifies influential antibiotic resistance genes in the infant gut microbiome

The paper uses machine learning on genome-resolved metagenomics data to identify antibiotic resistance genes in the infant gut microbiome that influence bacterial survival and response to antibiotics.