@RyanCookAMR

Viral ecologist with @EvelienAdri at @TheQuadram | All things phage (but mostly viromes) | Formerly at @UniofNottingham with @milja001 | All opinions my own.

 Norwich, England
Joined May 2019
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New #MicrobiomeDigest is OUT microbiomedigest.com/2026/09…  • cattle virome / @RyanCookAMR • mothers-adult daughters vaginal microbiome / @SarahLebeer • microbiome biomarker recovery in CRC / André Salgado  See you next week at the Seerave & #MVIF!

September 11, 2026

See you at the Seerave & MVIF Symposium next week! General Integrating multi-omics technologies to decipher microbiome functions – Tim Van Den Bossche – Nature Communications Phylogenetic measu…

microbiomedigest.com
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Ryan Cook retweeted
Andrew millard@milja001Aug 19
with @RyanCookAMR and many others we have been working on INPHARED to incorporate more QC data and predictions, make it scale with increased data, and some basic visualisation of the data. Files will be linked from here phagebank.uk/inphared2/ in the future
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Delighted to see our work featured as a Research Highlight in @NatureEcoEvo 🧬 Ancient strep throat 🦠 nature.com/articles/s41559-0… 😷 Strep throat is nothing new – a 700-year-old mummy proves it 🙌@msabrysarhan @RyanCookAMR #Archaeology #aDNA #Genomics #StrepThroat #ScienceNews
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Salmonella Genomic Markers for Risk to Food Safety biorxiv.org/content/10.64898… #biorxiv_genomic
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🚨 We’re hiring! 🚨 The Integrative Viromics Lab @UCalgary is looking for a Lab Technician to join us starting November 2025. 🔬 Phage isolation & culture 🧫 Anaerobic chamber work 📦 Lab management & student mentoring Apply now & help us explore the virosphere!
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Stoked to finally have a preprint out for Phold, our tool that uses protein structural information to enhance phage genome annotation
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After hiatus, as @RyanCookAMR were a bit busy .... we have updated links to latest INPHARED dataset. With 37.5K genomes now millardlab.org/bacteriophage…

Phage Genomes Aug 2025 - Millardlab

See our publication in PHAGE to read about how this dataset is produced and some of our analyses of it. Please consider citing this paper if you are using this database of information on this...

millardlab.org
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Thrilled to see our Kiwa story out today! A membrane-associated supercomplex that senses infection and blocks replication and transcription. Huge congratulations to @ugobananas_uuu @Zhangzhiyi58692 and @TCTodeschini, and to all our collaborators. shorturl.at/l0ayB

Kiwa is a membrane-embedded defense supercomplex activated at phage attachment sites

Zhang, Todeschini, and Wu et al. show that the bacterial defense system Kiwa senses phage attachment at the membrane and assembles a transmembrane complex that halts infection by blocking phage DNA...

cell.com
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This is probably my last piece of work from my @MedResFdn funded PhD at @UniofNottingham (thanks for all the support over the years!). Contributions from @milja001 @APonsero (and many others not on here) 13/13
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The dairy cow gut virome is a dynamic ecosystem that could be an under-studied player in sustainable agriculture 🔑 Preprint: biorxiv.org/content/10.1101/… #Microbiome #Virome #ClimateScience #Agriculture #Dairy #Cows #Methanogens 12/13

Life-Stage Transitions Drive Distinct Gut Viral Communities in Dairy Cattle

Ruminant gut microbial communities profoundly influence host health and environmental impacts, yet their viral components remain poorly characterised across developmental transitions. Here, we...

biorxiv.org
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From a practical standpoint: The viral community shake-ups during weaning and drying-off suggest these could be critical windows for microbiome interventions Could targeted viral therapies help optimise cow health and productivity during these transitions? 🎯 11/13
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The transition from "human-like" calf viromes to specialised ruminant adult viromes mirrors what we see in human infant development, but continues changing throughout adult life stages - unlike humans where it typically stabilises 🐄👶 10/13
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Mapping to public databases corroborated the patterns described above: 🐄 Calves: more simple communities, similar to human gut viruses, and lots of prophages 🐂 Adults: High diversity, high novelty, and uniquely "ruminant" 9/13
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Not only phages though, we found 26 viruses that predicted to target methanogenic archaea 🌎 Absent in calves, but present in >50% of adults These viruses emerge as the cow's GI tract develops from monogastric (similar to humans) to a functional adult rumen 8/13
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Drying-off period emerged as a viral hotspot 🔥 -Highest viral diversity -Lowest bacterial diversity -High virus-to-host ratios -Most viral genes under evolutionary pressure -Peak viral loads This transition = a huge ecological reorganisation in the dairy cow microbiome 7/13
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Bacterial and viral communities were strongly associated across all groups but in adults, viral and bacterial diversity were NEGATIVELY correlated, especially during the "drying off" period (when cows stop producing milk) As bacterial diversity ⬇️, viral diversity ⬆️ 6/13
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We observed ecological shifts across life stages: 🐄 Calves: Low diversity, dominated by temperate phages, similar to human gut viruses 🐂 Adults: High diversity, mostly lytic phages, uniquely "ruminant" All 3 adult groups we profiled had distinct viral communities 5/13
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1,338 vOTUs predicted complete. @milja001 and I agreed to manually inspect annotations of every single one. I started at the top, he started at the bottom (I think he only did 50 though despite agreeing to do half 💁‍♂️). All of them looked viral in origin, and most were novel 4/13
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We profiled the faecal virome of dairy cows across key life stages with ultra-deep ONT and Illumina sequencing 🐮 We recovered over 30,000 vOTUs (approximate species), and included shallow bulk metagenomes to place the viruses within the context of their microbial hosts 3/13
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Why does this matter? Dairy cows = 265 million worldwide, huge importance in food production and greenhouse gas emissions. Yet we know very little about their gut viral communities across key life stages 🐄 2/13
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