Density-dependent feedback and higher-order interactions enable coexistence in phage-bacteria community dynamics Abstract. Diverse phage-bacteria communities coexist at high densities in environmental, agricultural, and human-associated microbiomes. Phage-bacteria coe

🚨NEW PAPER @isme-microbes.bsky.social on phage-bacteria dynamics. Collab between us and @joshuasweitz.bsky.social labs. "Density-dependent feedback and higher-order interactions enable coexistence in phage-bacteria community dynamics". 👉 doi.org/10.1093/isme...

Bacteriophage data on capsular Klebsiella bacteria barcoded library

New paper 🔔

Collaboration
@sullivan-lab.bsky.social
Marissa Gittrich led the work

Klebsiella phage biology has focused almost entirely on capsulated strains, but capsule loss is the #1 resistance mechanism under phage predation. We used a naturally acapsular host to reveal the receptor landscape

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

Congratulations Gary!

#viruses #soilviruses #ecology

"Seasonal enhancement of the viral shunt catalyzes a subsurface oxygen maximum in the Sargasso Sea" https://www.nature.com/articles/s41467-025-67002-1

Viruses transform microbes, populations, & ecosystems.

In new work jointly led w/@tn-marine-micro.bsky.social + more, we find a link between enhanced viral infection and productivity 50 meters below the surface in the otherwise nutrient limited Sargasso Sea.

a 🧵

www.nature.com/articles/s41...

#virology #oceanBiogeochemistry #EarthSystemModels #viralEcology #climateChange #systemsBiology

Frontiers | Viruses in multi-scale ocean models: challenges and opportunities While viruses affect the flow of elements and energy at a planet-wide scale through lysis, gene transfer, and metabolic reprogramming, they are yet to be inc...

Critical review for integrating viruses into ocean modelling now in Frontiers: www.frontiersin.org/journals/mar...

Bringing viruses into Earth system models will sharpen predictions of carbon sequestration, nutrient retention, and climate sensitivity in the ocean.

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

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

🚨vConTACT3 now in Nature Biotechnology:
- >95% agreement with ICTV for known viruses
- Classifies both prokaryotic and eukaryotic viruses
- Extends beyond genus → subfamily, family & order
- Systematically assigns taxonomy to tens of thousands of previously unclassified viruses

• In soils: broad host links recovered, but genus/species resolution remains challenging
• Practical thresholds + guidance offered for applying Hi-C in complex microbiomes

#Virology #HiC #VirusHost #Microbiome #Metagenomics #virusecology

• Synthetic community (4 hosts, 9 phages) provides a ground-truth benchmark
• Raw Hi-C links: ~100% sensitivity but only ~26% specificity
• Z-score ≥0.5: specificity → ~99%, sensitivity → ~62%

Benchmarking with synthetic communities provides a baseline for virus-host inferences from Hi-C proximity linking Virus discovery has accelerated but linking viruses to hosts remains challenging. This study uses synthetic microbiomes to optimize and benchmark Hi-C for virus-host linkage inference, and applies thi...

🚨NEW paper: Benchmarking Hi-C for virus–host inference
journals.plos.org/plosbiology/...

A clear baseline for anyone mapping virus–host interactions that establishes robust, benchmarked thresholds for Hi-C linkages.

Key results: 👇

Scalable and systematic hierarchical virus taxonomy with vConTACT3 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 wi...

📊 Machine-learning–optimized thresholds benchmarked across 6 realms

🧩 Identifies taxonomic inconsistencies and areas for ICTV revision

#ViralTaxonomy #Metagenomics #ViralEcology #Bioinformatics #ICTV #PhageResearch #MachineLearning #VirusDiscovery #BioRxiv #vConTACT3

With vConTACT3, we rebuilt the system from the ground up:

🎯 Multi-rank hierarchical classification (genus → order)

⚙️ Scales to tens of thousands of genomes

🧬 Expands beyond dsDNA phages to include eukaryotic and RNA viruses

👇

Scalable and systematic hierarchical virus taxonomy with vConTACT3 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 wi...

🚨vConTACT3 preprint live!🚨(Peer Review soon...!)

vConTACT3 delivers a unified, scalable, and transparent framework for genome-based virus taxonomy — helping translate big viral data into systematic classification.

🔗 Read the preprint: doi.org/10.1101/2025...

Improvements details below 👇

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

Sub-daily Bermuda Atlantic Time Series virus sampling reveals taxonomy, host, and functional differences at the population, but not community level Ocean microbes contribute to biogeochemical cycles and ecosystem function, but they do so under top-down pressure imposed by viruses. While viruses are increasingly understood spatially and beginning ...

We found that overall virus-community diversity remains stable, but individual populations show clear diel and depth-linked shifts, with distinct viral archetypes peaking at day or night.

Read the full story on BioRxiv: doi.org/10.1101/2025...

Lead author: Alfonso Carrillo

Using high-frequency metagenomics, we tracked 48,000+ viral populations and their hosts, from Prochlorococcus to SAR11.

The ocean’s got rhythm — and so do its viruses.
With the Bermuda Atlantic Time-Series (BATS), we dove deep — every 4 to 12 hours — to see how viral populations swing through day and night.

From tracking SARS-CoV-2 in wastewater to discovering hidden marine RNA viruses, CLAE unlocks read-level viral variant detection and fixes short-read misassemblies.

⚡ Portable, field-ready
🧬 A game-changer for epidemiology & environmental surveillance.

#RNAvirus #metagenomics

🚨 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

Virocell resource manipulation under nutrient limitation | mSystems This study addresses a knowledge gap in understanding how nutrient limitation shapes virus-infected bacterial cell (virocell) metabolism and its ecosystem footprints. Using multi-omics approaches, we ...

🚨NEW VIROCELL PAPER🚨 from Cristina Howard-Varona et al: "Virocell resource manipulation under nutrient limitation".

@howard-varona.bsky.social

How do virocells use resources during nutrient limitation to build phages and alter the ecosystem? Check out the link!

journals.asm.org/doi/10.1128/...

Microbiome researchers! Join Dr. Shareef Dabdoub (U of Iowa) for a free webinar on multi-omics microbiome data analysis. Learn to integrate DNA, RNA, proteins, & metabolite data. April 1st, 10 am EST.
go.osu.edu/2025_microbi...

#microbiome #workshop

Time's ticking, microbiome researchers! ⏰ Submit your abstract for the Midwest Microbiome Symposium at Ohio State by March 31st.

Submit here: coms.osu.edu/midwest-micr... #microbiome #research #science #OhioState #CoMS

🚨 Microbiome researchers! The deadline to submit your abstract for the Midwest Microbiome Symposium at Ohio State is March 31st! 🚨 Don't miss this chance to share your work with leading experts.

Submit here: coms.osu.edu/midwest-micr... #microbiome #microbiology
#symposium #OhioState #microbiome

🚨Multiple positions open in Bas Duthil's group (Viral Ecology and Omics Group, Jena, Germany):
- Postdoc experimental: lnkd.in/dJZ2GRUX
- PhD experimental: lnkd.in/ddqQmvA9
- PhD bioinformatics: lnkd.in/d-nTJfAh

Group: www.bio.uni-jena.de/en/2245/team

New week, new microbiome webinar topic: learn the DRAM tool for annotation and curation of function for microbial and viral genomes, presented by Dr. Garrett Smith.

📅 Date: March 11, 2025
🕒 Time: 10am EST
📍 Link: go.osu.edu/2025_microbi...
More details on full course: coms.osu.edu/webinars/mic...

A framework for integrating genomics, microbial traits, and ecosystem biogeochemistry - Nature Communications Microbes drive the Earth’s biogeochemical cycles. Here, Li et al. present a framework for integrating genome-inferred microbial kinetic traits into ecosystem mechanistic models, and use it to benchmar...

🚨New paper from NSF EMERGE BII: A framework for integrating genomics, microbial traits, and ecosystem biogeochemistry. Read here: www.nature.com/articles/s41...

The Microbiome Informatics Webinar continues tomorrow with
Dr. Dylan Cronin, teaching how to go from metagenomic data MAGs.

March 4, 2025 at 10am EST
Virtual Event zoom link: go.osu.edu/2025_microbi...

🔗 More details on the SP25 Microbiome Informatics series schedule: coms.osu.edu/webinars/mic...