CRESSENT: a bioinformatics toolkit to explore and improve ssDNA virus annotation ssDNA viruses are important components of diverse ecosystems; however, it remains challenging to systematically identify and classify them. This is partly due to their broad host range and resulting genomic diversity, structure and rapid evolutionary rates. In addition, distinguishing genuine ssDNA genomes from contaminating sequences in metagenomic datasets (e.g. from commercial kits) has been an unresolved issue for years. Here, we present CRESSENT (CRESS-DNA Extended aNnotation Toolkit), a comprehensive and modular bioinformatic pipeline focused on ssDNA virus ‘genome-to-analysis’ and annotation. The pipeline integrates multiple functionalities organized into several modules: sequence dereplication, decontamination, phylogenetic analysis, motif discovery, stem-loop structure prediction and recombination detection. Each module can be used independently or in combination with others, allowing researchers to customize their analysis workflow. With this tool, researchers can comprehensively and systematically include ssDNA viruses in their viromics workflows and facilitate comparative genomic studies, which are often limited to dsDNA viruses, therefore leaving behind a crucial component of the microbiome community under study. Benchmarking analyses demonstrated that CRESSENT efficiently processes ssDNA virus datasets of varying scales, completing small family-level analyses within minutes and moderate comparative genomics studies within hours using standard computing resources. Its modular, parallelized design ensures scalability and low memory usage, making it accessible to research groups with diverse computational capacities.

🔬 New #ssDNA virus annotation toolkit CRESSENT accelerates #viromics & ecosystem virus discovery with modular, scalable analyses for decontamination, structuring & phylogeny. 🧬💻#Virology #Bioinformatics #Metagenomics
📄 https://doi.org/10.1099/mgen.0.001632
👤 EVBC member: Matthew Sullivan

Diversity and ecological roles of hidden viral players in groundwater microbiomes - Nature Communications Groundwater viruses are less well studied. Here, using large-scale sequencing, the authors uncover extensive, largely uncharacterized viral diversity in groundwater, showing that viruses infect domina...

New paper from @adjiep.bsky.social on viral impacts in groundwater at Nature Comms. Congratulations Adjie and team!

Read: www.nature.com/articles/s41...

#viruses #viromics #groundwater

📢Join us for the next ECR #Viromics Webinar
"Scalable annotation and curation of auxiliary viral genes with CheckAMG"
‍🎙️James Kosmopoulos, Anantharaman Lab, University of Wisconsin-Madison, USA
🗓️11 March 2026, 4 PM CET
📍Online/Zoom (register for login details)
👉 evbc.uni-jena.de/events/ecr-v...

James Kosmopoulos Karthik Anantharaman Lab Decoding viral gene function across ecosystems

Join us for next week's MDTP student seminar, featuring James Kosmopoulos from Karthik Anantharaman's Lab!

@kosmopoulos.bsky.social @karthik-a.bsky.social
#UWMadison #viromics #MDTP

Unveiling the global urban virome through wastewater metagenomics - Nature Communications Wastewater-based surveillance tends to focus on specific pathogens. Here, the authors mapped the wastewater virome from 62 cities worldwide to identify over 2,500 viruses, revealing city-specific virome fingerprints and showing that wastewater metagenomics enables early detection of emerging viruses.

#Viruses & #Epidemiology

Unveiling the global urban virome through wastewater metagenomics

@marionkoopmans.bsky.social @nathalieworp.bsky.social @bom1986.bsky.social

#metagenomics #viromics

📢Join us for the next ECR #Viromics Webinar
"How viral evolution is shaped during long-term infections of immune-compromised hosts"
‍🎙️Jonas Fuchs, University Hospital Freiburg, Germany
🗓️11 Feb 2026, 4 PM CET
📍Online/Zoom (register for login details)
👉 evbc.uni-jena.de/events/ecr-v...

Unveiling the global urban virome through wastewater metagenomics - Nature Communications Wastewater-based surveillance tends to focus on specific pathogens. Here, the authors mapped the wastewater virome from 62 cities worldwide to identify over 2,500 viruses, revealing city-specific virome fingerprints and showing that wastewater metagenomics enables early detection of emerging viruses.

#Viruses & #Epidemiology

Unveiling the global urban virome through wastewater metagenomics

@marionkoopmans.bsky.social @nathalieworp.bsky.social @bom1986.bsky.social

#metagenomics #viromics

#virology #virusTaxonomy #bioinformatics #machineLearning #viromics #ICTV

📢Join us for the next ECR #Viromics Webinar
"Ocean physics, phytoplankton-virus interactions and the carbon cycle: implications for aggregation and export"
‍🎙️Dr. Kay Bidle, Rutgers University, USA
🗓️14 Jan 2026, 4 PM CET
📍Online/Zoom (register for login details)
👉 evbc.uni-jena.de/events/ecr-v...

Viromics approaches for the study of viral diversity and ecology in microbiomes - Nature Reviews Genetics In this Review, Roux and Coclet outline current viromics approaches and discuss how they have contributed to our growing understanding of viral genomic diversity, focusing on uncultivated viruses of microorganisms.

Viromics approaches now integrate experimental and computational pipelines to map virus diversity, activity, and host links across microbiomes, enabling large-scale virus ecogenomics. 🧬🔬 #Viromics #Metagenomics 
📄 https://doi.org/10.1038/s41576-025-00871-w
👤 EVBC members: Simon Roux

📢Join us for the next ECR #Viromics Webinar
"Drawing from phage diversity to uncover genomic factors shaping host interaction"
‍🎙️Antônio P. Camargo, Uni São Paulo, Brazil 
🗓️10 Dec. 2025, 4 PM CET
📍Online/Zoom (register for login details)
👉 evbc.uni-jena.de/events/ecr-viromics-webi...

🦠 VIRE: Mapping Earth's viral universe with 1.7M genomes! Unraveling viral mysteries across 100k+ metagenomes. Ecosystem genomics just got wild! 🌍🧬 #Viromics #GenomicFrontiers #ScienceBreakthrough https://emmecola.github.io/genomics-daily

Viruses and virus satellites of haloarchaea and their nanosized DPANN symbionts reveal intricate nested interactions - Nature Microbiology An exploration of the viromes of haloarchaea and their ultra-small DPANN symbionts reveals plasmid-derived satellites of viruses from both archaeal groups, highlighting the complexity of nested symbiotic interactions.

Deep genomic exploration of haloarchaea uncovers complex networks of viruses and virus satellites nested within DPANN symbionts, revealing unexpected layers of microbial interaction. #Viromics #Microbiology #Evolution 🧬🦠
📄 https://doi.org/10.1038/s41564-025-02149-7
👤 EVBC member: Mart Krupovic

Redirecting

Increased COPD severity correlates with lower bacteriophage diversity and viral-bacterial ecological coupling breaks down in frequent exacerbators. #Viromics #RespiratoryMicrobiome 📉🦠
📄 https://doi.org/10.1016/j.celrep.2025.116413
👤 EVBC members: Evelien Adriaenssens, Andrew Millard

📢Join us for the next ECR #Viromics Webinar:
"Untangle the complexity of the virosphere using single-cell RNA-sequencing"
‍🎙️ Amir Fromm | Weizmann Institute of Science, Israel
🗓️ 12 November 2025, 4 PM CET
📍 Online | Zoom (register for login details)
👉 coms.osu.edu/webinars/ecr...

#MarineVirology #ViralEcology #BATS #SargassoSea #OceanTimeSeries #MicrobialEcology #Metagenomics #Prochlorococcus #SAR11 #HostPrediction #DielCycles #BioRxiv #OceanScience #MicrobiomeScience #Viromics

Congratulations, Ryan! Excellent job in bringing this all together and the really cool findings. #viromics

Happy to say this has now been published in @cp-cellreports.bsky.social 🫁🦠 #Phages #Viromics

www.cell.com/cell-reports...

Thanks for an inspiring and fruitful @nfdi4microbiota.bsky.social Annual Conference last week 💛
Our team of the #VirJenDB (Noriko, Sharam, Kilian) contributed with a poster💬 and a workshop with demo🤝 about this comprehensive virus sequence database 🦠 🧬 💻 #FAIRdata #metadata #viromics
➡️ virjendb.org

📢Join us for the next ECR #Viromics Webinar:
"Characterising novel viral proteins using protein language models (PLMs)"
‍🎙️ Kieran Lamb (@kieranlamb.bsky.social) | University of Glasgow/UK
🗓️ 8 October 2025, 4 PM CEST
📍 Online | Zoom (register for login details)
👉 coms.osu.edu/webinars/ecr...

🚨 New tool for viral genomics!

Meet CLAE: a high-fidelity Nanopore sequencing strategy that pushes accuracy to Q30, boosts throughput >800 Mb/100 pores, and recovers full-length viral genomes from complex samples 🌊🦠

👉 [https://doi.org/10.1002/advs.202505978]

#viromics #nanopore #genomics

A call for caution in the biological interpretation of viral auxiliary metabolic genes - Nature Microbiology This Perspective discusses virus-encoded auxiliary metabolic genes and provides a framework for the biological interpretation of these genes.

A timely perspective urges restraint in calling viral #AMGs from #metagenomes and introduces “auxiliary viral genes (#AVGs)” with a framework for making robust biological inferences. #Viromics #Bioinformatics #ViralEcology 🦠🔬🧬
📄 https://doi.org/10.1038/s41564-025-02095-4
👤 EVBC members: Simon Roux

📢Join us for the next ECR #Viromics Webinar:
"Chronotyping the #Ocean Virome: Fine-Scale Temporal Clustering Reveals Viral Ecological and Evolutionary Patterns"
‍🎙️Luis Bolaños Avellaneda, Exeter, UK
🗓️10 Sep 2025, 4 PM CEST
📍Online, Zoom (register for login details)
🔗 evbc.uni-jena.de/events/ecr-v...

Meet our new lab workhorse: a Thermo Scientific KingFisher for automated nucleic-acid extractions. Faster, cleaner DNA/RNA from wastewater, wetlands & phage isolates = more discovery time. DOE-supported Phage Pathways!
#PhagePathways #Viromics #Microbiology #AMR @sfstatebio.bsky.social

Used any new tools or databases (released in the past ~year) for #metagenomics or #viromics? Found something especially useful- or seen recent insights using old methods? Reply with your favorites! I'm trying to compile a list of new resources and approaches.

What a week in Lisbon! 🇵🇹 ViBioM 2025 brought 150+ virus bioinformaticians from 34 countries to explore viral evolution, ML tools, & taxonomy challenges. 🌱 All plant-based thanks to @desafiovegetariano! Huge thanks to organizers, speakers, and community! #ViBioM2025 #Viromics

Metagenomics for pathogen surveillance In this webinar, we learn how Oxford Nanopore sequencing can provide a rapid and comprehensive metagenomic approach for characterising bacteria, fungi, and viruses directly from respiratory samples.

Missed our knowledge exchange on Oxford #Nanopore comprehensive metagenomic sequencing for pathogen surveillance? Watch the recording here! buff.ly/IDhJt0S
This approach allows for discovery of #bacteria, #fungi, and viruses directly from respiratory samples
#metagenomics #viromics

🧬 ECR Viromics Webinar Series
Join us on April 9, 2025, for an exciting talk by @Marcel Ribeiro-Dantas
"Nextflow Pipelines: Connecting Data to Discoveries"
📅 Time: 10 AM EST | 4 PM CET
🔗 Register evbc.uni-jena.de/events/ecr-v...
#Viromics #Nextflow #VirusBioinformatics #Seqera

Upcoming wastewater virome webinar from Dr. Mike Tisza, Feb. 12! Free for everyone.
More: coms.osu.edu/events/early...

#virus #virome #viromics #pathogen #sequencing #microbiome #microbe #bacteria #science #microbiology #webinar

Reminder👇Only 2 weeks remaining (deadline 29/01, 12pm UK time) to apply to the #ILESLA #PhD training program. DM me for more info if interested in projects with me at the Open University and collaborators on #vectorbornediseases #mosquitoes #ticks #viromics