S. Roux

A functional microbiome catalog crowdsourced from North American rivers

The paper creates GROWdb, a microbiome database from North American rivers, revealing microbial community structures and functional traits across watersheds.

Population ecology and potential biogeochemical impacts of ssDNA and dsDNA soil viruses along a permafrost thaw gradient

The paper analyzes ssDNA and dsDNA soil viruses along a permafrost thaw gradient to assess their ecological roles and biogeochemical impacts on carbon processing.

Virus diversity and activity is driven by snowmelt and host dynamics in a high-altitude watershed soil ecosystem

This study examines viral diversity and activity in a high-altitude watershed soil ecosystem, revealing seasonal shifts in phage activity and virus-host dynamics linked to environmental and host factors.

Long-term CRISPR array dynamics and stable host-virus co-existence in subsurface fractured shales

The paper studies long-term host-virus dynamics in subsurface fractured shales, finding that CRISPR arrays shrink over time as microbial communities stabilize.

A standardized quantitative analysis strategy for stable isotope probing metagenomics

This paper introduces a standardized analysis framework and R package for quantifying isotopic enrichment in SIP metagenomics to identify active microbial genomes.

Highly diverse and unknown viruses may enhance Antarctic endoliths' adaptability

The paper analyzes viral diversity in Antarctic rocks using metagenomics, revealing highly diverse and spatially structured virus communities that may influence bacterial adaptation and biogeochemistry.

From motor protein to toxin: Mutations in the zonula occludens toxin (Zot) of Vibrio cholerae phage CTXΦ suggest a loss of phage assembly function

The paper investigates mutations in the Zot toxin of Vibrio cholerae phage CTXΦ, showing that these mutations impair phage assembly and suggest a shift in Zot's function to an auxiliary toxin.

iPHoP: an integrated machine-learning framework to maximize host prediction for metagenome-assembled virus genomes

iPHoP integrates multiple methods to predict viral hosts from metagenome-derived genomes with low false discovery rate.

A vast world of viroid-like circular RNAs revealed by mining metatranscriptomes

The paper identifies 11,420 viroid-like circular RNAs across 5,131 metatranscriptomes and 1,344 plant transcriptomes, revealing a five-fold increase in known viroid-like agents and novel ribozyme combinations.

New Microviridae isolated from Sulfitobacter reveals two cosmopolitan subfamilies of ssDNA phages infecting marine and terrestrial Alphaproteobacteria

The paper isolates a new Microviridae phage and identifies two new subfamilies of ssDNA phages infecting Alphaproteobacteria, showing their cosmopolitan distribution.

Community-wide epigenetics provides novel perspectives on the ecology and evolution of marine microbiome

The paper analyzes DNA methylation patterns in marine microbiomes to explore ecological and evolutionary relationships among microbes and viruses.

Ecogenomics of groundwater viruses suggests niche differentiation linked to specific environmental tolerance

The paper identifies 41 viral clusters in groundwater plasmidomes, links them to bacterial hosts, and detects novel phage genera and host-specific genes.

Virus-host interactions and genetic diversity of Antarctic sea ice bacteriophages

The paper studies four Antarctic sea ice bacteriophages, revealing their genetic diversity, infectivity under varied conditions, and potential ecological significance.

Diversity, taxonomy and evolution of archaeal viruses of the class Caudoviricetes

The paper presents 37 new genomes of haloarchaeal tailed viruses, expands their classification into 14 families, and explores their evolution and ecological distribution.

Ecology and molecular targets of hypermutation in the global microbiome.

The paper analyzes metagenome-derived DGRs to show their evolutionary origin, mutation bias, ecological niches, and role in microbial community dynamics.

Metagenomes from the Loxahatchee wildlife refuge in the Florida Everglades

The paper analyzes metagenomes from sediment samples in the Florida Everglades to characterize microbial and viral communities, their taxonomic composition, and functional potential, revealing correlations between environmental factors and gene frequencies.

Virus-associated organosulfur metabolism in human and environmental systems

This study identifies 39 viral gene families involved in organosulfur metabolism across diverse ecosystems, showing their role in sulfide production and viral fitness.

Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems

The paper analyzes plankton genomic distribution across oceans to show how large-scale currents shape biogeography, revealing size-dependent patterns and basin-scale transport effects.

Isolation of potential plant growth-promoting bacteria from nodules of legumes grown in arid Botswana soil

The paper isolates plant growth-promoting bacteria from legume nodules in Botswana soils, identifying drought-tolerant species and noting differences in microbial composition between soil and nodule microbiomes.

Ecology of inorganic sulfur auxiliary metabolism in widespread bacteriophages

The paper identifies 227 auxiliary metabolic genes in 191 phages from twelve environments, showing their role in sulfur and thiosulfate oxidation and ecological impact on biogeochemistry.

DRAM for distilling microbial metabolism to automate the curation of microbiome function

DRAM automates microbiome function curation by translating genomic data into microbial traits, accurately assigning metabolic roles in soil and gut communities.

Metagenome-assembled genomes of phytoplankton communities across the Arctic Circle

This study assembles metagenome-assembled genomes (MAGs) from Arctic and non-polar phytoplankton communities to compare their genetic diversity and functional differences.

Role of Diversity-Generating Retroelements for Regulatory Pathway Tuning in Cyanobacteria

This study identifies DGRs in cyanobacteria and shows they diversify regulatory proteins involved in signal response, particularly in colonial and filamentous strains.

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.

Host population diversity as a driver of viral infection cycle in wild populations of green sulfur bacteria with long standing virus-host interactions

This study examines viral infection dynamics in green sulfur bacteria, finding that multiple viruses, including lysogenic ones, co-infect host populations and that host diversity may influence the lytic/lysogenic switch.

Diversity and Distribution of a Novel Genus of Hyperthermophilic Aquificae Viruses Encoding a Proof-reading Family-A DNA Polymerase

The paper describes novel hyperthermophilic Aquificae viruses with unique genomic features and proposes a new genus based on their distinct replication strategy and gene-sharing networks.

Proteome specialization of anaerobic fungi during ruminal degradation of recalcitrant plant fiber

This study identifies fungal-specific carbohydrate-active enzymes involved in rumen fiber degradation, highlighting their role in complementing bacterial cellulolytic activity.

Glacier ice archives fifteen-thousand-year-old viruses

This paper develops clean sampling methods to study microbes and viruses in glacier ice, revealing 33 viral populations including potential novel genera and their associations with bacteria.

Impact of soil salinity on the cowpea nodule-microbiome and the isolation of halotolerant PGPR strains to promote plant growth under salinity stress

The paper examines how soil salinity affects cowpea nodule microbiomes and identifies halotolerant PGPR strains that enhance plant growth under salinity stress.

Metabolic Architecture of the Deep Ocean Microbiome

The paper analyzes deep ocean microbial metagenomes to reveal functional diversity and metabolic strategies in the dark ocean.