A. M. Eren

Closest relatives of poxviruses replicate in the digestive system of humans and animals worldwide

The paper discovers a new group of DNA viruses, egoviruses, found in the digestive systems of humans and animals, closely related to poxviruses and suggesting an evolutionary link between gut-infecting viruses and animal pathogens.

Untangling the Role of Pathobionts from Bacteroides Species in Inflammatory Bowel Diseases

This study shows that Bacteroides fragilis from UC patients promotes colitis in genetically susceptible mice, suggesting a role for pathobionts in IBD.

Two-million-year-old microbial communities from the Kap Kobenhavn Formation in North Greenland

This paper reconstructs microbial communities from 2-million-year-old permafrost in Greenland, finding similarities to modern thawing permafrost microbes and suggesting microbial communities may signal climate change impacts before plants and animals.

Bile acid fitness determinants of a Bacteroides fragilis isolate from a human pouchitis patient

This study identifies genes and pathways in B. fragilis that affect its fitness in bile acids, using a barcoded mutant library and transcriptomic analysis.

Microbes with higher metabolic independence are enriched in human gut microbiomes under stress

The paper identifies high metabolic independence as a marker of gut microbiome changes in IBD, using a software framework to analyze metagenomic data from healthy and IBD patients.

A highly conserved and globally prevalent cryptic plasmid is among the most numerous mobile genetic elements in the human gut

The paper identifies a highly prevalent cryptic plasmid in the human gut that is more numerous than crAssphage and has potential applications in detecting fecal contamination and inflammatory states.

Dietary- and host-derived metabolites are used by diverse gut bacteria for anaerobic respiration

The paper identifies gut bacteria that use dietary and host-derived metabolites as electron acceptors in anaerobic respiration, revealing new metabolic pathways and reductase evolution.

pWCP is a widely distributed and highly conserved Wolbachia plasmid in Culex mosquitoes worldwide

The paper investigates the global distribution and conservation of the Wolbachia plasmid pWCP in Culex mosquitoes across diverse geographic regions and laboratory strains.

A comprehensive update to the Mycobacterium tuberculosis H37Rv reference genome

The paper updates the M. tuberculosis H37Rv reference genome using Bact-Builder, revealing 6.4 kb of new sequence and ten new regions in widely used strains.

Structure-informed microbial population genetics elucidate selective pressures that shape protein evolution

The paper uses structure-informed metagenomic analysis to study evolutionary pressures in a marine microbial population, revealing links between protein structure, selective pressures, and environmental factors.

The mosquito microbiome includes habitat-specific but rare symbionts

This study identifies habitat-specific rare symbionts in mosquito microbiomes using high-resolution oligotyping, revealing microdiversity and co-occurring bacterial variants.

Early-life microbial intervention reduces colitis risk promoted by antibiotic-induced gut dysbiosis

The paper shows that adding a specific Bacteroides strain early in life reduces colitis risk in genetically susceptible mice with antibiotic-induced gut dysbiosis.

AGNOSTOS-DB: a resource to unlock the uncharted regions of the coding sequence space

AGNOSTOS-DB is a database that integrates known and unknown coding sequences from genomes and metagenomes to enhance understanding of genes of unknown function.

Heterotrophic bacterial diazotrophs are more abundant than their cyanobacterial counterparts in metagenomes covering most of the sunlit ocean

The paper identifies heterotrophic bacterial diazotrophs as more abundant than cyanobacterial diazotrophs in ocean metagenomes, expanding the known diversity of marine nitrogen fixers.

High molecular weight DNA extraction strategies for long-read sequencing of complex metagenomes

The paper benchmarks HMW DNA extraction methods for long-read sequencing of metagenomes, finding non-phenol-chloroform methods may yield better results.

Metabolic independence drives gut microbialcolonization and resilience in health and disease

This study investigates how metabolic independence influences gut microbial colonization and resilience in health and disease using fecal microbiota transplantation.

Functional repertoire convergence of distantly related eukaryotic plankton lineages revealed by genome-resolved metagenomics

The paper uses Tara Oceans metagenomic data to reconstruct and analyze eukaryotic genomes, revealing functional convergence among distantly related plankton lineages.

Colwellia and Marinobacter metapangenomes reveal species-specific responses to oil and dispersant exposure in deepsea microbial communities

The paper examines how dispersants affect microbial communities in oil spills by analyzing metapangenomes of Colwellia and Marinobacter, showing species-specific metabolic responses to oil and dispersant exposure.

Unifying the known and unknown microbial coding sequence space

The paper presents a framework and workflow to integrate genes of unknown function into genomic analysis, quantifying their diversity and relevance across biomes and providing a resource for studying Cand. Patescibacteria.

Metapangenomics of the oral microbiome provides insights into habitat adaptation and cultivar diversity

The paper uses metapangenomics to analyze oral microbiome diversity, revealing habitat-specific genomic groups and highlighting limitations in cultivated organisms' representation.

Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome

The paper analyzes oral microbiome metagenomes to identify niche partitioning among TM7 taxa, revealing distinct ecological and genetic patterns between plaque and tongue-associated TM7.

Disinfection exhibits systematic impacts on the drinking water microbiome.

This study compares the impact of disinfection and nutrient limitation on drinking water microbiomes, finding that disinfection reduces diversity and selects for microorganisms using decay products.

Accurate and Complete Genomes from Metagenomes

The paper improves metagenome-assembled genomes (MAGs) by curating them to achieve complete, circularized genomes (CMAGs) using cumulative GC skew and other metrics.

High-throughput isolation and sorting of gut microbes reduce biases of traditional cultivation strategies

This study develops a microfluidic platform to isolate and sort gut microbes, increasing richness and rare taxa representation compared to traditional methods.

Disinfectant residuals in drinking water systems select for mycobacterial populations with intrinsic antimicrobial resistance.

This study shows that disinfectant residuals in drinking water systems are linked to higher prevalence of antimicrobial resistance genes in nontuberculous mycobacteria.

The global biogeography of amino acid variants within a single SAR11 population is governed by natural selection

The paper analyzes amino acid variants in a SAR11 population to show natural selection drives genomic diversity across oceanic regions.

Nitrogen-Fixing Populations Of Planctomycetes And Proteobacteria Are Abundant In The Surface Ocean

The paper identifies abundant non-cyanobacterial nitrogen-fixing bacteria in surface ocean waters, challenging previous assumptions about nitrogen sources.

High-resolution tracking of microbial colonization in Fecal Microbiota Transplantation experiments via metagenome-assembled genomes

This study tracks microbial colonization in FMT experiments using metagenome-assembled genomes to identify colonization patterns and factors influencing success.