Bas E. Dutilh
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View article: Scalable and systematic hierarchical virus taxonomy with vConTACT3
Scalable and systematic hierarchical virus taxonomy with vConTACT3 Open
Viruses are key players in diverse ecosystems, but studying their impacts is technically and taxonomically challenging. Taxonomic complexities derive from undersampling, diverse DNA and RNA genomes with multiple evolutionary origins, and l…
View article: Unraveling Plasmid Contributions to Phosphorus Acquisition in Soil Microbiomes
Unraveling Plasmid Contributions to Phosphorus Acquisition in Soil Microbiomes Open
Background Phosphorus (P) is a fundamental macronutrient for plant and microbial growth, but its availability in soils is often constrained by strong interactions with minerals and organic matter. While the role of bacteriophages in P cycl…
View article: Barbell Resolves Demultiplexing and Trimming Issues in Nanopore Data
Barbell Resolves Demultiplexing and Trimming Issues in Nanopore Data Open
Background Oxford Nanopore sequencing enables long-read sequencing across diverse applications, yet the experimental artifacts introduced by Nanopore barcoding are not well characterized. These artifacts can affect demultiplexing accuracy …
View article: Bacterial community adaptation after freshwater and seawater coalescence
Bacterial community adaptation after freshwater and seawater coalescence Open
Microbial community coalescence, the merging of entire microbial communities, is common across ecosystems, particularly in estuaries where freshwater and seawater mix. The complexity of these habitats makes the in situ study of community d…
View article: Computational function prediction of bacteria and phage proteins
Computational function prediction of bacteria and phage proteins Open
SUMMARY Understanding protein functions is crucial for interpreting microbial life; however, reliable function annotation remains a major challenge in computational biology. Despite significant advances in bioinformatics methods, ~30% of a…
View article: Summary of taxonomy changes ratified by the International Committee on Taxonomy of Viruses (ICTV) from the Bacterial Viruses Subcommittee, 2025
Summary of taxonomy changes ratified by the International Committee on Taxonomy of Viruses (ICTV) from the Bacterial Viruses Subcommittee, 2025 Open
This article summarises the activities of the International Committee on Taxonomy of Viruses Bacterial Viruses Subcommittee, detailing developments in the classification of bacterial viruses. We provide here an overview of all new, abolish…
View article: Deletion of the moeA gene in Flavobacterium IR1 drives structural color shift from green to blue and alters polysaccharide metabolism
Deletion of the moeA gene in Flavobacterium IR1 drives structural color shift from green to blue and alters polysaccharide metabolism Open
Structural color (SC), generated by light interacting with nanostructured materials, are responsible for the brightest and most vivid coloration in nature. Despite being widespread within the tree of life, there is little knowledge of the …
View article: Author response: Deletion of the moeA gene in Flavobacterium IR1 drives structural color shift from green to blue and alters polysaccharide metabolism
Author response: Deletion of the moeA gene in Flavobacterium IR1 drives structural color shift from green to blue and alters polysaccharide metabolism Open
View article: Chemical characteristics vectors map the chemical space of natural biomes from untargeted mass spectrometry data
Chemical characteristics vectors map the chemical space of natural biomes from untargeted mass spectrometry data Open
View article: Ultrafast and accurate sequence alignment and clustering of viral genomes
Ultrafast and accurate sequence alignment and clustering of viral genomes Open
View article: Tunturi virus isolates and metagenome-assembled viral genomes provide insights into the virome of Acidobacteriota in Arctic tundra soils
Tunturi virus isolates and metagenome-assembled viral genomes provide insights into the virome of Acidobacteriota in Arctic tundra soils Open
View article: Deletion of the moeA gene in Flavobacterium IR1 drives structural color shift from green to blue and alters polysaccharide metabolism
Deletion of the moeA gene in Flavobacterium IR1 drives structural color shift from green to blue and alters polysaccharide metabolism Open
Structural color (SC), generated by light interacting with nanostructured materials, are responsible for the brightest and most vivid coloration in nature. Despite being widespread within the tree of life, there is little knowledge of the …
View article: Deletion of the moeA gene in Flavobacterium IR1 drives structural color shift from green to blue and alters polysaccharide metabolism
Deletion of the moeA gene in Flavobacterium IR1 drives structural color shift from green to blue and alters polysaccharide metabolism Open
Structural colors (SC), generated by light interacting with nanostructured materials, is responsible for the brightest and most vivid coloration in nature. Despite being widespread within the tree of life, there is little knowledge of the …
View article: Author response: Deletion of the moeA gene in Flavobacterium IR1 drives structural color shift from green to blue and alters polysaccharide metabolism
Author response: Deletion of the moeA gene in Flavobacterium IR1 drives structural color shift from green to blue and alters polysaccharide metabolism Open
View article: Chemistry-based vectors map the chemical space of natural biomes from untargeted mass spectrometry data
Chemistry-based vectors map the chemical space of natural biomes from untargeted mass spectrometry data Open
Untargeted metabolomics can comprehensively map the chemical space of a biome, but is limited by low annotation rates (<10%). We used chemistry-based vectors, consisting of molecular fingerprints or chemical compound classes, predicted fro…
View article: Deletion of the <i>moe</i> A gene in <i>Flavobacterium</i> IR1 drives structural color shift from green to blue and alters polysaccharide metabolism
Deletion of the <i>moe</i> A gene in <i>Flavobacterium</i> IR1 drives structural color shift from green to blue and alters polysaccharide metabolism Open
Structural colors (SC), generated by light interacting with nanostructured materials, is responsible for the brightest and most vivid coloration in nature. Despite being widespread within the tree of life, there is little knowledge of the …
View article: Prophage induction drives soybean rhizobacterial community differentiation and nutrient cycling benefiting root development
Prophage induction drives soybean rhizobacterial community differentiation and nutrient cycling benefiting root development Open
Bacteriophages, lytic or lysogenic, play critical roles in structuring different soil bacteriomes and driving their functionality. Lysogeny is favored in the plant rhizosphere and may play a major role in plant–rhizobacteria assembly and f…
View article: SpeSpeNet: an interactive and user-friendly tool to create and explore microbial correlation networks
SpeSpeNet: an interactive and user-friendly tool to create and explore microbial correlation networks Open
Correlation networks are commonly used to explore microbiome data. In these networks, nodes are microbial taxa and edges represent correlations between their abundances. As clusters of correlating taxa (co-abundance clusters) often indicat…
View article: Author Correction: Examining the healthy human microbiome concept
Author Correction: Examining the healthy human microbiome concept Open
View article: Author Correction: Phylogeny and disease associations of a widespread and ancient intestinal bacteriophage lineage
Author Correction: Phylogeny and disease associations of a widespread and ancient intestinal bacteriophage lineage Open
View article: Improving genome-scale metabolic models of incomplete genomes with deep learning
Improving genome-scale metabolic models of incomplete genomes with deep learning Open
View article: Changes to virus taxonomy and the ICTV Statutes ratified by the International Committee on Taxonomy of Viruses (2024)
Changes to virus taxonomy and the ICTV Statutes ratified by the International Committee on Taxonomy of Viruses (2024) Open
View article: Seasonal dynamics and diversity of Antarctic marine viruses reveal a novel viral seascape
Seasonal dynamics and diversity of Antarctic marine viruses reveal a novel viral seascape Open
View article: Examining the healthy human microbiome concept
Examining the healthy human microbiome concept Open
View article: Graphite: painting genomes using a colored de Bruijn graph
Graphite: painting genomes using a colored de Bruijn graph Open
The recent growth of microbial sequence data allows comparisons at unprecedented scales, enabling the tracking of strains, mobile genetic elements, or genes. Querying a genome against a large reference database can easily yield thousands o…
View article: Jaeger: an accurate and fast deep-learning tool to detect bacteriophage sequences
Jaeger: an accurate and fast deep-learning tool to detect bacteriophage sequences Open
Viruses are integral to every biome on Earth, yet we still need a more comprehensive picture of their identity and global distribution. Global metagenomics sequencing efforts revealed the genomic content of tens of thousands of environment…
View article: Tunturi virus isolates and metagenome-assembled viral genomes provide insights into the virome of Acidobacteriota in Arctic tundra soils
Tunturi virus isolates and metagenome-assembled viral genomes provide insights into the virome of Acidobacteriota in Arctic tundra soils Open
Background: Arctic soils are climate-critical areas, where microorganisms play crucial roles in nutrient cycling processes. Acidobacteriota are phylogenetically and physiologically diverse bacteria that are abundant and active in Arctic tu…
View article: Phylogeny and disease associations of a widespread and ancient intestinal bacteriophage lineage
Phylogeny and disease associations of a widespread and ancient intestinal bacteriophage lineage Open
Viruses are core components of the human microbiome, impacting health through interactions with gut bacteria and the immune system. Most human microbiome viruses are bacteriophages, which exclusively infect bacteria. Until recently, most g…
View article: Structural color in the bacterial domain: The ecogenomics of a 2-dimensional optical phenotype
Structural color in the bacterial domain: The ecogenomics of a 2-dimensional optical phenotype Open
Structural color is an optical phenomenon resulting from light interacting with nanostructured materials. Although structural color (SC) is widespread in the tree of life, the underlying genetics and genomics are not well understood. Here,…
View article: High-resolution quantification of the rhizosphere effect along a soil-to-root gradient shows selection-driven convergence of rhizosphere microbiomes
High-resolution quantification of the rhizosphere effect along a soil-to-root gradient shows selection-driven convergence of rhizosphere microbiomes Open
Plants secrete a complex array of organic compounds, constituting about a third of their photosynthetic products, into the surrounding soil. As a result, concentration gradients are established from the roots into the bulk soil, known as t…