Bas E Dutilh
Germany
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Articles by Bas E Dutilh
Structural signatures of salinity adaptation in Microviricetes capsids
Abstract Phages, like their bacterial hosts, have evolved to proliferate across the full range of environments on Earth, but the specific amino acid residues that underlie their environmental adaptations remain elusive. Here, we developed a computational framework that uses structure-based multiple sequence alignments, a random forest classifier, and a phylogeny-aware regression model to find amino acid residues linked to specific environments.
Three distinct uterine microbiome community types in healthy women and their interconnection with the vaginal microbiome
Abstract There is no consensus on the composition of the uterine microbiome in healthy women. Bacteria in the uterine cavity engage in reciprocal interactions with endometrial cells and the immune system, thereby maintaining a microecological balance. Given the continuity of the genital tract, the vagina may serve as a potential source of uterine microbiota, which should be included in the investigation.
Eco-evolutionary dynamics of massive, parallel bacteriophage outbreaks in compost communities
Abstract INTRODUCTION RESULTS DISCUSSION MATERIALS AND METHODS Acknowledgments Supplementary Materials REFERENCES Information & Authors Metrics & Citations View Options References Figures Tables Media Share Abstract Bacteriophages play critical roles in microbial ecosystems, yet their dynamics in complex natural communities remain poorly understood compared to simplified laboratory systems. Here, we tracked viral dynamics in 20 compost-derived microbial communities over 1 year.
Machine learning enables scalable and systematic hierarchical virus taxonomy
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Machine learning enables scalable and systematic hierarchical virus taxonomy - Nature Biotechnology
Abstract Although virus ecogenomics has expanded access to and understanding of the virosphere, existing classification tools lack taxonomic resolution and are unable to scale to modern discovery-based datasets or classify previously unknown sequence space. Here we develop vConTACT3—a machine learning-based tool that improves scalability and accuracy of virus taxonomy.
Ultrafast and accurate sequence alignment and clustering of viral genomes - Nature Methods
Abstract Viromics produces millions of viral genomes and fragments annually, overwhelming traditional sequence comparison methods. Here we introduce Vclust, an approach that determines average nucleotide identity by Lempel–Ziv parsing and clusters viral genomes with thresholds endorsed by authoritative viral genomics and taxonomy consortia. Vclust demonstrates superior accuracy and efficiency compared to existing tools, clustering millions of genomes in a few hours on a mid-range workstation.
Author Correction: Phylogeny and disease associations of a widespread and ancient intestinal bacteriophage lineage - Nature Communications
Correction to: Nature Communications https://doi.org/10.1038/s41467-024-50777-0, published online 27 July 2024 The original version of the Supplementary Datasets associated with this Article included an incorrect Supplementary Data file 4, which was a duplicate of the Supplementary Data file 5.
Seasonal dynamics and diversity of Antarctic marine viruses reveal a novel viral seascape - Nature Communications
Abstract The Southern Ocean microbial ecosystem, with its pronounced seasonal shifts, is vulnerable to the impacts of climate change. Since viruses are key modulators of microbial abundance, diversity, and evolution, we need a better understanding of the effects of seasonality on the viruses in this region.
Phylogeny and disease associations of a widespread and ancient intestinal bacteriophage lineage - Nature Communications
Abstract 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 gut virome studies focused on low taxonomic resolution (e.g., viral operational taxonomic units), hampering population-level analyses. We previously identified an expansive and widespread bacteriophage lineage in inhabitants of Amsterdam, the Netherlands.
High-resolution quantification of the rhizosphere effect along a soil-to-root gradient shows selection-driven convergence of rhizosphere microbiomes
Abstract 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 the rhizosphere.
Integrating taxonomic signals from MAGs and contigs improves read annotation and taxonomic profiling of metagenomes - Nature Communications
Abstract Metagenomic analysis typically includes read-based taxonomic profiling, assembly, and binning of metagenome-assembled genomes (MAGs). Here we integrate these steps in Read Annotation Tool (RAT), which uses robust taxonomic signals from MAGs and contigs to enhance read annotation. RAT reconstructs taxonomic profiles with high precision and sensitivity, outperforming other state-of-the-art tools.
A global survey of host, aquatic, and soil microbiomes reveals shared abundance and genomic features between bacterial and fungal generalists
Highlights • Bacterial and fungal generalists are widely distributed in aquatic, host, and soil biomes • Generalists have larger genomes with more secondary metabolites and AMR genes • Samples containing generalists show higher alpha diversity • Generalists underpin cross-kingdom community structure Summary Environmental change, coupled with alteration in human lifestyles, is profoundly impacting the microbial communities critical to the health of the Earth and its inhabitants.
Ultraconserved bacteriophage genome sequence identified in 1300-year-old human palaeofaeces - Nature Communications
Abstract Bacteriophages are widely recognised as rapidly evolving biological entities. However, knowledge about ancient bacteriophages is limited. Here, we analyse DNA sequence datasets previously generated from ancient palaeofaeces and human gut-content samples, and identify an ancient phage genome nearly identical to present-day Mushuvirus mushu, a virus that infects gut commensal bacteria.
Graphite: painting genomes using a colored De Bruijn graph
Abstract The recent growth of microbial sequence data allows comparisons at unprecedented scales, enabling tracking of strains, mobile genetic elements, or genes. Querying a genome against a large reference database can easily yield thousands of matches that are tedious to interpret and pose computational challenges. We developed Graphite that uses a colored De Bruijn graph (cDBG) to paint query genomes, selecting the local best matches along the full query length.
Phylogeny and disease links of a widespread and ancient gut phage lineage
Abstract Viruses are a core component of the human microbiome, impacting health and disease through interactions with gut bacteria and the immune system. Most viruses in the human microbiome are bacteriophages, which exclusively infect bacteria. Individual gut bacteriophages can affect bacterial bile acid deconjugation, and can alter their infection strategy based on dietary content.
Identifying and tracking mobile elements in evolving compost communities yields insights into the nanobiome - ISME Communications
Abstract Microbial evolution is driven by rapid changes in gene content mediated by horizontal gene transfer (HGT). While mobile genetic elements (MGEs) are important drivers of gene flux, the nanobiome—the zoo of Darwinian replicators that depend on microbial hosts—remains poorly characterised. New approaches are necessary to increase our understanding beyond MGEs shaping individual populations, towards their impacts on complex microbial communities.
Ultra-conserved bacteriophage genome sequence identified in 1300-year-old human paleofaeces
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A global survey of host, aquatic, and soil microbiomes reveals shared abundance and genomic features between bacterial and fungal generalists
Abstract Environmental change coupled with alteration in human lifestyles are profoundly impacting the microbial communities that play critical roles in the health of the earth and its inhabitants. To identify bacteria and fungi that are resistant and susceptible to habitat changes respectively, we retrieved paired 16S and ITS rRNA amplicon sequence data from 1,580 host, soil, and aquatic samples and explored the ecological patterns of the thousands of detected bacterial and fungal genera.
Metagenomic ventures into outer sequence space
Skip to main content Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation Journal List Bacteriophage v.4(4); 2014 PMC4588555 As a library, NLM provides access to scientific literature. Inclusion in an NLM database does not imply endorsement of, or agreement with, the contents by NLM or the National Institutes of Health. Learn more about our disclaimer.
A social niche breadth score reveals niche range strategies of generalists and specialists - Nature Ecology & Evolution
Abstract Generalists can survive in many environments, whereas specialists are restricted to a single environment. Although a classical concept in ecology, niche breadth has remained challenging to quantify for microorganisms because it depends on an objective definition of the environment.
On specialists and generalists: niche range strategies across the tree of life
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Gut virome profiling identifies a widespread bacteriophage family associated with metabolic syndrome - Nature Communications
Abstract There is significant interest in altering the course of cardiometabolic disease development via gut microbiomes. Nevertheless, the highly abundant phage members of the complex gut ecosystem -which impact gut bacteria- remain understudied. Here, we show gut virome changes associated with metabolic syndrome (MetS), a highly prevalent clinical condition preceding cardiometabolic disease, in 196 participants by combined sequencing of bulk whole genome and virus like particle communities.
Identical sequences found in distant genomes reveal frequent horizontal transfer across the bacterial domain
Abstract Horizontal gene transfer (HGT) is an essential force in microbial evolution. Despite detailed studies on a variety of systems, a global picture of HGT in the microbial world is still missing. Here, we exploit that HGT creates long identical DNA sequences in the genomes of distant species, which can be found efficiently using alignment-free methods. Our pairwise analysis of 93,481 bacterial genomes identified 138,273 HGT events.
Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT
Abstract Current-day metagenomics analyses increasingly involve de novo taxonomic classification of long DNA sequences and metagenome-assembled genomes. Here, we show that the conventional best-hit approach often leads to classifications that are too specific, especially when the sequences represent novel deep lineages. We present a classification method that integrates multiple signals to classify sequences (Contig Annotation Tool, CAT) and metagenome-assembled genomes (Bin Annotation Tool, BAT).
Minimum Information about an Uncultivated Virus Genome (MIUViG)
1. Breitbart, M., Bonnain, C., Malki, K. & Sawaya, N.A. Phage puppet masters of the marine microbial realm. Nat. Microbiol. 3, 754–766 (2018). 2. Youle, M., Haynes, M. & Rohwer, F. in Viruses: Essential Agents of Life (ed. Witzany, G.) 61–81 (Springer Netherlands, 2012). 3. Brum, J.R. & Sullivan, M.B. Rising to the challenge: accelerated pace of discovery transforms marine virology. Nat. Rev. Microbiol. 13, 147–159 (2015). 4. Páez-Espino, D. et al. Uncovering Earth's virome. Nature 536, 425–430 (2016). 5. Shi, M.
Bridging the divide: bacteria synthesizing archaeal membrane lipids
Bridging the divide: bacteria synthesizing archaeal membrane lipids Laura Villanueva, F. A. Bastiaan von Meijenfeldt, Alexander B. Westbye, Ellen C. Hopmans, Bas E. Dutilh, Jaap S. Sinninghe Damste bioRxiv 448035; doi: https://doi.org/10.1101/448035
Molecular and Evolutionary Determinants of Bacteriophage Host Range
Broad-host-range phages are more common in nature than previously thought, and most environments have a variety of narrow-range and broad-host-range phages. In phenotypic broad-host-range phages, individual phage particles can infect multiple hosts. In genotypic broad-host-range phages, individual particles infect only one host, but specific mutations enable rapid host switching between generations, leading to a broad-host-range quasispecies.
A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes
Metagenomes, and especially viral metagenomes, are often characterized by a majority of unknown sequences that have no homologues in the database21. Assembly of the short, second generation sequencing reads into longer contigs may facilitate their annotation and interpretation.
Preservation of bacterial DNA in 10-year-old guaiac FOBT cards and FIT tubes
With great interest we read the article of Taylor et al in the Journal of Clinical Pathology regarding the use of guaiac faecal occult blood test (gFOBT) cards for microbiome studies.1 gFOBT cards were found to be an easy to use option for stool collection and gained results comparable to fresh stool, even when cards were stored for up to 3 years at ambient temperature before DNA extraction.
Preservation of bacterial DNA in 10-year-old guaiac FOBT cards and FIT tubes
With great interest we read the article of Taylor et al in the Journal of Clinical Pathology regarding the use of guaiac faecal occult blood test (gFOBT) cards for microbiome studies.1 gFOBT cards were found to be an easy to use option for stool collection and gained results comparable to fresh stool, even when cards were stored for up to 3 years at ambient temperature before DNA extraction.
Preservation of bacterial DNA in 10-year-old guaiac FOBT cards and FIT tubes
With great interest we read the article of Taylor et al in the Journal of Clinical Pathology regarding the use of guaiac faecal occult blood test (gFOBT) cards for microbiome studies.1 gFOBT cards were found to be an easy to use option for stool collection and gained results comparable to fresh stool, even when cards were stored for up to 3 years at ambient temperature before DNA extraction.
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