Sullivan Lab at OSU

6 July

🚨VIROMICS WORKSHOP 2026🚨 Application is now OPEN for the 8th International Viromics Workshop, Oct. 14-16, 2026, in-person at Ohio State University. Application closes Aug. 7. Apply: forms.gle/pJFLDCNEBvAe... Full details: u.osu.edu/viruslab/vir... #viromics #viruses #ecology #workshop

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Sullivan Lab at OSU reposted

Replying to @sullivan-lab.bsky.social

🧵 More details & relevant topics: Perfect for postdocs, PhDs, and researchers working with viral metagenomics, phage biology, and environmental samples. Full details: u.osu.edu/viruslab/vir... Topics: #MicroSky #Virology #CompBio #PostdocSky #Phage #MetaGenomics #Rstats #Python #PhDSky #ECR

Sullivan Lab at OSU reposted

📢 Applications open! Join us for our upcoming Viromics Workshop! 🧬 Learn cutting-edge metagenomic assembly, viral identification, and annotation pipelines. 🗓️ Dates: Oct 14-16 ⏰ (Extended) Deadline: Aug 20, 2026 🔗 Apply here: forms.gle/pJFLDCNEBvAe... #Viromics #Bioinformatics #AcademicSky

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go.nature.comMobile genetic elements shape microbial diversity and functions in thawing permafrost soilsNature Microbiology, Published online: 29 June 2026; doi:10.1038/s41564-026-02391-7An 8-year soil meta-omic time series shows how mobile genetic elements shape permafrost microbial diversity and impact a range of functions, including carbon and nutrient cycling.

Sustainable Microbiology journal Calls for Papers! #Microbiology #CallForPapers #MicroSky #Sustainability #EnvironmentalMicrobiology

Sullivan Lab at OSU reposted

Sarah Bagby

@scbagby.bsky.social

29 June

Out today in Nature Microbiology: a paper that started in 2021 with an email from @sullivan-lab.bsky.social. Subject line: "Crazy ideas". www.nature.com/articles/s41... 1/23

Sullivan Lab at OSU reposted

Nature Microbiology

@natmicrobiol.nature.com

29 June

Out Now! Mobile genetic elements shape microbial diversity and functions in thawing permafrost soils #MicroSky

tinyurl.comPlease wait whilst we redirect youAll content on this site: Copyright © 2026 Elsevier B.V., its licensors, and contributors. All rights are reserved, including those for text and data mining, AI training, and similar technologies. For all open access content, the relevant licensing terms apply.

23 June

New review in @cp-trendsmicrobiol.bsky.social led by postdoc Marion Urvoy: "Beyond AMGs: Phage-encoded transcription and sigma factors as understudied virocell reprogramming tools" Read here: tinyurl.com/5f3z3wzr TLDR:👇

23 June

• AMGs have transformed how we think about viral reprogramming, but metabolism is only part of the story. • We argue that phage-encoded transcription and sigma factors are tractable to uncover how viruses rewire host regulatory networks and potentially influence ecosystem processes.

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

18 Mar

🚨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...

Sullivan Lab at OSU reposted

Vivek Mutalik

@vivekmutalik.bsky.social

15 Mar

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

nature.comDiversity and ecological roles of hidden viral players in groundwater microbiomes - Nature CommunicationsGroundwater 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...

4 Mar

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

doi.orgPopulation ecology and biogeochemical implications of ssDNA and dsDNA viruses along a permafrost thaw gradient - Nature CommunicationsThe potential roles of viruses in microbial-induced permafrost thaw, which is accelerated by climate change, are unclear. Here, Trubl et al. sample a permafrost thaw gradient and identify thousands of...

16 Jan

Congratulations Gary! #viruses #soilviruses #ecology

Gareth (Gary) Trubl@gtrubl.bsky.social

New paper published in @natcomms.nature.com! Population ecology and biogeochemical implications of ssDNA and dsDNA viruses along a permafrost thaw gradient doi.org/10.1038/s414... www.nature.com/collections/... @sullivan-lab.bsky.social

Sullivan Lab at OSU reposted

Joshua Weitz

@joshuasweitz.bsky.social

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...

frontiersin.orgFrontiers | Viruses in multi-scale ocean models: challenges and opportunitiesWhile 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 #oceanBiogeochemistry #EarthSystemModels #viralEcology #climateChange #systemsBiology

🚨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

nature.comClient Challenge

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

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

journals.plos.orgBenchmarking with synthetic communities provides a baseline for virus-host inferences from Hi-C proximity linkingVirus 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...

21 Nov 2025

🚨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: 👇

21 Nov 2025

• 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%

21 Nov 2025

• 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

doi.orgScalable and systematic hierarchical virus taxonomy with vConTACT3Viruses 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...

7 Nov 2025

🚨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 👇

7 Nov 2025

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 👇

7 Nov 2025

📊 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

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.

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doi.orgSub-daily Bermuda Atlantic Time Series virus sampling reveals taxonomy, host, and functional differences at the population, but not community levelOcean 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

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

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.

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

12 Sept 2025

🚨 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

12 Sept 2025

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

journals.asm.orgVirocell resource manipulation under nutrient limitation | mSystemsThis 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 ...

27 June 2025

🚨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/...

27 Mar 2025

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

coms.osu.eduMidwest Microbiome Symposium Abstract Guidelines | Center of Microbiome ScienceWe are excited to invite you to submit your abstract to the Midwest Microbiome Symposium, Tiny architects: The microbiomes shaping our world. This year's symposium will be held May 12-14 at the Nation...

26 Mar 2025

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

20 Mar 2025

🚨 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

18 Mar 2025

🚨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

10 Mar 2025

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...

nature.comA framework for integrating genomics, microbial traits, and ecosystem biogeochemistry - Nature CommunicationsMicrobes 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...

5 Mar 2025

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

3 Mar 2025

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...

27 Feb 2025

Summer School on Quantitative Phage-Bacteria Dynamics Across Scales -> Application date: March 21, 2025. Open to MS + PhD students + postdocs Application site: bit.ly/phageschool2...

24 Feb 2025

🚨Spring 2025 Updated Microbiome Informatics Webinar Series starts tomorrow Feb. 25!🚨 Free to attend, join us to learn with leaders in the field. More info and registration: coms.osu.edu/webinars/mic...

journals.plos.orgIsolation and characterization of 24 phages infecting the plant growth-promoting rhizobacterium Klebsiella sp. M5alBacteriophages largely impact bacterial communities via lysis, gene transfer, and metabolic reprogramming and thus are increasingly thought to alter nutrient and energy cycling across many of Earth’s ...

24 Feb 2025

New paper from our PhD student Marissa Gittrich! In-depth characterization of 24 phages of rhizobacterium Klebsiella sp. M5al at PLOS One. Congrats Marissa and team! journals.plos.org/plosone/arti...

19 Feb 2025

Watch our latest research as a Video Byte about global ocean AMG function and distribution: www.researchsquare.com/article/rs-6...! From our lab's work in Microbiome (Tian & Wainana et al., 2024:https://doi.org/10.1186/s40168-024-01876-z)

10 Feb 2025

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

news.osu.eduIdentifying the genes that viruses ‘steal’ from ocean microbesThe microbes that cycle nutrients in the ocean don’t do the work on their own – the viruses that infect them also influence the process. It’s a vital job for the rest of the planet, enabling oceans to...

17 Oct 2024

Our 'global ocean AMGs in marine viruses' paper featured in @OhioStateNews! Congrats to Funing Tian and James Wainaina et al: "Identifying the genes that viruses ‘steal’ from ocean microbes" news.osu.edu/identifying-... #virus #phage #ecology #biogeochemistry #viromics #oceans