Bas E. Dutilh

Bas E. Dutilh

@bedutilh.bsky.social

482 followers126 following34 posts

Bas E. Dutilh reposted

David Giron Villalobos
@dagivi.bsky.social

Our review from the @uti-revisited.bsky.social consortium is out in @lancetmicrobe.bsky.social 🥳. We bring together the urinary tract microbiome and its (often overlooked) role in infections. Understanding this could improve UTI diagnosis and treatment. 🦠🔗👤 www.thelancet.com/journals/lan...

thelancet.comRole of the urobiome in urinary tract infections: current knowledge and research prospectsUrinary tract infections (UTIs), particularly cystitis, are among the most common bacterial infections worldwide, with a disproportionate burden on adult female individuals, who often have recurrence....
Bas E. Dutilh
@bedutilh.bsky.social

Join us and be part of the VirusREvolution! Study the link between the environment and phage host range in soil and groundwater systems 👇👇

Kuesel Lab@kuesellab.bsky.social

We're hiring! Join the Aquatic Geomicrobiology group as a PhD researcher to explore virus–host interactions and host range evolution in soil and groundwater using cultivation experiments, viral tagging & metagenomics. 🦠🧬 📍Jena | 🗓️ Apply by Oct 1, 2026 jobs.uni-jena.de/jobposting/2...

jobs.uni-jena.deDoctoral Researcher in Viral Ecology (m/f/d)
Bas E. Dutilh
@bedutilh.bsky.social

Join us and become part of PhageOrder: study the evolution of phage genetic modules!

Jessica Andreani@jessicaandreani.bsky.social

🚨📣 Hiring a postdoc in bioinformatics 🧬🧑‍💻 Join our team at @i2bcparissaclay.bsky.social to explore biomolecular interactions and improve protein function prediction in bacteriophages! 📍 Gif-sur-Yvette, France ⏳ 13 months (+ possible extension) 📅 Apply here: emploi.cnrs.fr/Offres/CDD/U...

emploi.cnrs.fr Portail Emploi CNRS - Job offer - Post-doctoral researcher in bioinformatics (M/F): exploring biomolecular interactions for bacteriophage protein function prediction
Bas E. Dutilh
@bedutilh.bsky.social

There are many types of urinary tract microbiomes, and UTIs can happen with most of them. Even more interesting is that healthy individuals have almost the same microbial communities! Check out David's new preprint to see the details 👇

David Giron Villalobos@dagivi.bsky.social

1/4. Excited to share the first preprint from my PhD at @binfutrecht.bsky.social and @uti-revisited.bsky.social 🐥. In this work, we explored the urinary tract microbiome composition (urobiome) by combining data from multiple metagenomic sequencing studies 💛🦠. www.biorxiv.org/content/10.6...

biorxiv.orgCross-study metagenomics analysis reveals distinct microbial signatures of urinary tract infectionsBackground Urinary tract infections (UTIs) represent a major public health concern, increasingly complicated by rising antibiotic resistance, diminishing treatment efficacy, and increasing prevalence ...

Bas E. Dutilh reposted

Piotr Rozwalak
@prozwalak.bsky.social

Mushuvirus is the most widespread phage genus in the human gut. 🌍 Together with other family members, these viruses occur in 89% of humans worldwide, including the Iceman Ötzi! How is it possible that they were hidden in previous metagenomic analyses? [1/7] Read: doi.org/10.64898/202...

Bas E. Dutilh reposted

Jeroen Meijer
@jeroenmeijer.bsky.social

Thrilled that our paper "Eco-evolutionary dynamics of massive, parallel bacteriophage outbreaks in compost communities" is out! 🎉🦠🧬 www.science.org/doi/10.1126/... w/ @paulbrainey.bsky.social, Petros Skiadas, Paulien Hogeweg, @bedutilh.bsky.social

science.orgEco-evolutionary dynamics of massive, parallel bacteriophage outbreaks in compost communitiesA single bacteriophage can dominate microbial communities yet only evolves when migration changes its ecological context.
Bas E. Dutilh
@bedutilh.bsky.social

When the student surpasses his advisor: Mushu bigger than crAss? Check out Piotr's new preprint 👇

Piotr Rozwalak@prozwalak.bsky.social

Mushuvirus is the most widespread phage genus in the human gut. 🌍 Together with other family members, these viruses occur in 89% of humans worldwide, including the Iceman Ötzi! How is it possible that they were hidden in previous metagenomic analyses? [1/7] Read: doi.org/10.64898/202...

Bas E. Dutilh
@bedutilh.bsky.social

Everyone knows that space and spatial structure is super important in shaping the Microverse 🌎🌍🌏 Check out this amazing review where @marcelbaecker.bsky.social and @bramvandijk.bsky.social et al bring together a huge body of knowledge @microverse.bsky.social @binfutrecht.bsky.social

Marcel Bäcker@marcelbaecker.bsky.social

Most microbes don't live in shaking flasks; spatial structure shapes how microbes interact and evolve at every scale, as we discuss in our recent review @jeroenmeijer.bsky.social @simonvanvliet.bsky.social @bedutilh.bsky.social @bramvandijk.bsky.social and others academic.oup.com/femsre/artic... 🧵👇

academic.oup.comSpatial structure: shaping the ecology and evolution of microbial communitiesSpatial structure naturally emerges in microbial communities, shaping growth, interactions, and evolution, and revealing how microscale processes scale up
Bas E. Dutilh
@bedutilh.bsky.social

VirJenDB.org: the database for all virus sequence- and curated metadata with API access, and version control 👇

virjendb.orgVirJen DB
jenarna.bsky.social@jenarna.bsky.social

📣Excited to share our (first) VirJenDB publication! 🎁Check it out to see how your #virus database supports #metadata #biocuration and #bioinformatics integration. 🎶Stay tuned for collaboration opportunities in 2026, including a hackathon at #ViBioM2026! 📃 doi.org/10.1093/nar/... 💻 www.virjendb.org

Bas E. Dutilh reposted

Böckerlab
@boeckerlab.bsky.social

🚨 A quick reminder: the PhD and postdoc positions within the ERC project #BindingShadows are still open! We’ve just moved into a brand-new building, and during the transition our servers and website were occasionally down, meaning we might not have received some applications.

Bas E. Dutilh
@bedutilh.bsky.social

Try our new Nanopore barcode trimming and data cleaning tool Barbell & get insights into the structure of your reads! 👇

Rick Beeloo@rickbitloo.bsky.social

Around 10% of your Nanopore reads (SQK-RBK114) are incorrectly trimmed. Here is why, and how our new tool Barbell solves it: www.biorxiv.org/content/10.1... Want to get started? github.com/rickbeeloo/b...

Bas E. Dutilh reposted

Xiu Jia
@xiujia.bsky.social

💧🌊 What happens when freshwater bacteria meet their salty counterparts? Our new preprint explores the ecological factors driving community coalescence 👉https://www.biorxiv.org/content/10.1101/2025.09.09.675091v1 @bedutilh.bsky.social @microverse.bsky.social

biorxiv.orgBacterial community adaptation after freshwater and seawater coalescenceMicrobial 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...

Bas E. Dutilh reposted

Susie Grigson
@susiegriggo.bsky.social

Thrilled to share our new review just published in Microbiology and Molecular Biology Reviews (@asm.org #MMBR): “Computational Function Prediction of Bacteria and Phage Proteins” with @gbouras13.bsky.social @linsalrob.bsky.social @bedutilh.bsky.social 🔗 journals.asm.org/doi/10.1128/...

journals.asm.orgComputational function prediction of bacteria and phage proteins | Microbiology and Molecular Biology ReviewsSUMMARYUnderstanding protein functions is crucial for interpreting microbial life; however, reliable function annotation remains a major challenge in computational biology. Despite significant advance...
Bas E. Dutilh
@bedutilh.bsky.social

This paper is now published with @jcheminf.bsky.social : jcheminf.biomedcentral.com/articles/10....

jcheminf.biomedcentral.comChemical characteristics vectors map the chemical space of natural biomes from untargeted mass spectrometry data - Journal of CheminformaticsUntargeted metabolomics can comprehensively map the chemical space of a biome, but is limited by low annotation rates (< 10%). We used chemical characteristics vectors, consisting of molecular fingerp...

Bas E. Dutilh reposted

Balance of the Microverse
@microverse.bsky.social

🧬 New tool alert: Vclust helps researchers rapidly sort through millions of viral genomes—even fragmented ones. @bedutilh.bsky.social co-developed Vclust, a tool for ultrafast clustering of viral genomes. It's open-source, web-accessible, and just published. 📄 doi.org/10.1038/s415...

doi.orgUltrafast and accurate sequence alignment and clustering of viral genomes - Nature MethodsVclust generates fast and accurate estimation of average nucleotide identity for viral genomes, scaling clustering to millions of genomes.
Bas E. Dutilh
@bedutilh.bsky.social

Faster && more accurate virus sequence clustering with Vclust! Thanks to Andrzej, Sebastian, et al. for the great collaboration. The author list also includes @prozwalak.bsky.social from the VEO Group.

Sebastian Deorowicz@sdeorowicz.bsky.social

Vclust (the ultra-fast, high-accuracy tool for viral genome comparison & clustering) is now published: www.nature.com/articles/s41... Great collaboration with A.Zielezinki, UAM guys and @bedutilh.bsky.social

nature.comUltrafast and accurate sequence alignment and clustering of viral genomes - Nature MethodsVclust generates fast and accurate estimation of average nucleotide identity for viral genomes, scaling clustering to millions of genomes.

Bas E. Dutilh reposted

Tatiana Demina
@deminatanja.bsky.social

Interested in #soil #viruses? We are! Excited to share our study on #Acidobacteriota #phages in #Arctic #tundra #soils being now published together with an easy-to-follow video abstract: microbiomejournal.biomedcentral.com/articles/10....

microbiomejournal.biomedcentral.comTunturi virus isolates and metagenome-assembled viral genomes provide insights into the virome of Acidobacteriota in Arctic tundra soils - MicrobiomeBackground Arctic soils are climate-critical areas, where microorganisms play crucial roles in nutrient cycling processes. Acidobacteriota are phylogenetically and physiologically diverse bacteria tha...

Bas E. Dutilh reposted

Theoretical Biology & Bioinformatics @ UU
@binfutrecht.bsky.social

📣 New, free webtool by the Snoek lab! Meet SpeSpeNet, an intuitive platform for automated network analysis of microbiomes to uncover complex interactions between microbes and their environments @ismepublications.bsky.social @isme-microbes.bsky.social doi.org/10.1093/isme... #microsky #mevosky

doi.orgSpeSpeNet: an interactive and user-friendly tool to create and explore microbial correlation networksAbstract. Correlation networks are commonly used to explore microbiome data. In these networks, nodes are taxa and edges represent correlations between the
Bas E. Dutilh
@bedutilh.bsky.social

One more week until the deadline!

Bas E. Dutilh@bedutilh.bsky.social

We have an opening for a 4-year postdoc position to study the #rhizosphere #microbiome in @utrechtuniversity.bsky.social @w-u-r.bsky.social, joint project with @marnixmedema.bsky.social in the context of MiCRop. Please tag/forward this to potential candidates and/or repost: www.uu.nl/en/organisat...

uu.nlBioinformatics Postdoc at UU/WUR: Map Metabolic Interactions in the RhizosphereContribute to plant health and our understanding of the metabolic interactions between microbes and plants in the rhizosphere by computational modelling!
Bas E. Dutilh
@bedutilh.bsky.social

We have an opening for a 4-year postdoc position to study the #rhizosphere #microbiome in @utrechtuniversity.bsky.social @w-u-r.bsky.social, joint project with @marnixmedema.bsky.social in the context of MiCRop. Please tag/forward this to potential candidates and/or repost: www.uu.nl/en/organisat...

uu.nlBioinformatics Postdoc at UU/WUR: Map Metabolic Interactions in the RhizosphereContribute to plant health and our understanding of the metabolic interactions between microbes and plants in the rhizosphere by computational modelling!
Bas E. Dutilh
@bedutilh.bsky.social

Do you (plan to) use genome-scale metabolic models in your research? DNNGIOR facilitates model reconstruction from incomplete genomes and MAGs. See Meine Boer's new publication 👇 and the code on Github: github.com/MGXlab/DNNGIOR

mdboer.bsky.social@mdboer.bsky.social

Exciting news! 🎉 My article is out in iScience presenting DNNGIOR, a deep learning tool advancing gap-filling in metabolic models. Huge thanks to co-authors @cmelkonian.bsky.social, @hariszaf.bsky.social, Daniel Garza, Andreas Haas and @bedutilh.bsky.social. Read at shorturl.at/REOm8

shorturl.atImproving genome-scale metabolic models of incomplete genomes with deep learningMicrobial genomics; Biocomputational method; Computational bioinformatics; Genomic analysis.