Simon Roux
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View article: Population ecology and biogeochemical implications of ssDNA and dsDNA viruses along a permafrost thaw gradient
Population ecology and biogeochemical implications of ssDNA and dsDNA viruses along a permafrost thaw gradient Open
Anthropogenic-driven climate change is accelerating permafrost thaw, threatening to release vast carbon stores through increased microbial activity. While microbial roles are increasingly studied, the contributions of viruses remain largel…
View article: A genomic atlas of the human gut virome elucidates genetic factors shaping host interactions
A genomic atlas of the human gut virome elucidates genetic factors shaping host interactions Open
Viruses are key modulators of human gut microbiome composition and function. While metagenomic sequencing has enabled culture-independent discovery of gut bacteriophage diversity, existing genomic catalogues suffer from limited geographic …
View article: Meta-virus resource (MetaVR): expanding the frontiers of viral diversity with 24 million uncultivated virus genomes
Meta-virus resource (MetaVR): expanding the frontiers of viral diversity with 24 million uncultivated virus genomes Open
Viruses are ubiquitous in all environments and impact host metabolism, evolution, and ecology, although our knowledge of their biodiversity is still extremely limited. Viral diversity from genomic and metagenomic datasets has led to an exp…
View article: VirJenDB: a FAIR (meta)data and bioinformatics platform for all viruses
VirJenDB: a FAIR (meta)data and bioinformatics platform for all viruses Open
High-throughput sequencing has generated an unprecedented volume of data. However, researcher-submitted data in repositories requires extensive curation and quality control for reuse. These tasks are hindered by the multiplicity of reposit…
View article: Breaking the reproducibility barrier with standardized protocols for plant-microbiome research.
Breaking the reproducibility barrier with standardized protocols for plant-microbiome research. Open
Inter-laboratory replicability is crucial yet challenging in microbiome research. Leveraging microbiomes to promote soil health and plant growth requires understanding underlying molecular mechanisms using reproducible experimental systems…
View article: Comparison of short-read and long-read metagenome assemblies in a natural soil community highlights systematic bias in recovery of high-diversity populations
Comparison of short-read and long-read metagenome assemblies in a natural soil community highlights systematic bias in recovery of high-diversity populations Open
Comparisons of long-read and short-read (meta)genome assemblies typically show that short-read sequence assemblies are less error-prone, but struggle to assemble complicated genome regions (e.g. repeats) compared to long-read sequence asse…
View article: Phage-mediated lysis does not determine <i>Cutibacterium acnes</i> colonization on human skin
Phage-mediated lysis does not determine <i>Cutibacterium acnes</i> colonization on human skin Open
Despite Cutibacterium acnes being the most abundant and prevalent bacteria on human skin, only a single type of phage has been identified that infects this host. Here, we leverage this one-to-one system to systematically characterize how t…
View article: Breaking the reproducibility barrier with standardized protocols for plant–microbiome research
Breaking the reproducibility barrier with standardized protocols for plant–microbiome research Open
Inter-laboratory replicability is crucial yet challenging in microbiome research. Leveraging microbiomes to promote soil health and plant growth requires understanding underlying molecular mechanisms using reproducible experimental systems…
View article: A call for caution in the biological interpretation of viral auxiliary metabolic genes
A call for caution in the biological interpretation of viral auxiliary metabolic genes Open
Virus-encoded auxiliary metabolic genes (AMGs) are non-essential genes that increase viral fitness by maintaining or manipulating host metabolism during infection. AMGs are intriguing from an evolutionary perspective, as most viral genomes…
View article: Virus taxonomy proposal summaries: a searchable and citable resource to disseminate virus taxonomy advances
Virus taxonomy proposal summaries: a searchable and citable resource to disseminate virus taxonomy advances Open
Taxonomic classification of cellular organisms requires the publication of descriptions and proposed names of species and the deposition of specimens. Virus taxonomy is developed through a different system of annual submission of formal ta…
View article: Viromics approaches for the study of viral diversity and ecology in microbiomes
Viromics approaches for the study of viral diversity and ecology in microbiomes Open
Viruses are found across all ecosystems and infect every type of organism on Earth. Traditional culture-based methods have proven insufficient to explore this viral diversity at scale, driving the development of viromics, the sequence-base…
View article: Tetranucleotide frequencies differentiate genomic boundaries and metabolic strategies across environmental microbiomes
Tetranucleotide frequencies differentiate genomic boundaries and metabolic strategies across environmental microbiomes Open
Microbiomes are constrained by physicochemical conditions, nutrient regimes, and community interactions across diverse environments, yet genomic signatures of this adaptation remain unclear. Metagenome sequencing is a powerful technique to…
View article: Gaia: An AI-enabled genomic context–aware platform for protein sequence annotation
Gaia: An AI-enabled genomic context–aware platform for protein sequence annotation Open
Protein sequence similarity search is fundamental to biology research, but current methods are typically not able to consider crucial genomic context information indicative of protein function, especially in microbial systems. Here, we pre…
View article: Comparative Analysis of Phage Profiles in Environmental Samples: Metagenomic Sequencing Versus Culture-Based Isolation v2
Comparative Analysis of Phage Profiles in Environmental Samples: Metagenomic Sequencing Versus Culture-Based Isolation v2 Open
Culture-based isolation of bacteriophages from wastewater relies on a limited set of laboratory‐cultivable host strains, causing it to recover only a small fraction of the true viral diversity present in the influent (Chibani‐Chennoufi et …
View article: Small viruses reveal bidirectional evolution between HK97-fold viruses and encapsulins via procapsids
Small viruses reveal bidirectional evolution between HK97-fold viruses and encapsulins via procapsids Open
The HK97-fold is an ancient, conserved protein structure that forms protein shells. It is the building block of capsids that protect the genome of viruses in the Duplodnaviria realm, infecting organisms across all domains of life. It is al…
View article: Planetary-scale metagenomic search reveals new patterns of CRISPR targeting
Planetary-scale metagenomic search reveals new patterns of CRISPR targeting Open
Summary Interactions between microbes and their mobile genetic elements (MGEs), including viruses and plasmids, are critical drivers of microbiome structures and processes. CRISPR-Cas systems are important regulators of these host-MGE inte…
View article: Tool Choice drastically Impacts CRISPR Spacer-Protospacer Detection
Tool Choice drastically Impacts CRISPR Spacer-Protospacer Detection Open
1 Abstract CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) systems are a fundamental defense mechanism in prokaryotes, where short sequences called spacers are stored in the host genome to recognize and target exogenous …
View article: LISHURS 2024 Assignments
LISHURS 2024 Assignments Open
Library and Information Services Honours and Undergraduate Seminar (LISHURS) is an annual event organized and hosted by the Department of Library and Information Services, Teaching and Learning Division, at the University of the Free State…
View article: LISHURS 2024 Assignments
LISHURS 2024 Assignments Open
Library and Information Services Honours and Undergraduate Seminar (LISHURS) is an annual event organized and hosted by the Department of Library and Information Services, Teaching and Learning Division, at the University of the Free State…
View article: Virus species names have been standardized; virus names remain unchanged
Virus species names have been standardized; virus names remain unchanged Open
Virus taxonomy, comprising classification and nomenclature, is regulated by the International Committee on Taxonomy of Viruses (ICTV). Taxon names are standardized to facilitate recognition and communication, with defined suffixes for each…
View article: A cost and community perspective on the barriers to microbiome data reuse
A cost and community perspective on the barriers to microbiome data reuse Open
Microbiome research is becoming a mature field with a wealth of data amassed from diverse ecosystems, yet the ability to fully leverage multi-omics data for reuse remains challenging. To provide a view into researchers’ behavior and attitu…
View article: Virocell Necromass Provides Limited Plant Nitrogen and Elicits Rhizosphere Metabolites That Affect Phage Dynamics
Virocell Necromass Provides Limited Plant Nitrogen and Elicits Rhizosphere Metabolites That Affect Phage Dynamics Open
Bacteriophages impact soil bacteria through lysis, altering the availability of organic carbon and plant nutrients. However, the magnitude of nutrient uptake by plants from lysed bacteria remains unknown, partly because this process is cha…
View article: Mobile genetic elements that shape microbial diversity and functions in thawing permafrost soils
Mobile genetic elements that shape microbial diversity and functions in thawing permafrost soils Open
The world's ecosystems are shaped by microbiota. Their niches and their impacts depend on functional profiles influenced by gene gains and losses. While culture-based experiments demonstrate that mobile genetic elements (MGEs) can mediate …
View article: Tetranucleotide frequencies differentiate genomic boundaries and metabolic strategies across environmental microbiomes
Tetranucleotide frequencies differentiate genomic boundaries and metabolic strategies across environmental microbiomes Open
Microbiomes are constrained by physicochemical conditions, nutrient regimes, and community interactions across diverse environments, yet genomic signatures of this adaptation remain unclear. Metagenome sequencing is a powerful technique to…