Ryan Cook

Happy to say this has now been published in @CellReports 🫁🦠 #Phages #Viromics cell.com/cell-reports/f…

Really enjoyed writing a piece for @ConversationUK - trying to write for a general audience, you suddenly realise how much jargon is deeply embedded in your brain #Phages #Microbiome #SciComm theconversation.com/a-virus-hiding…

🚨 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!

Stoked to finally have a preprint out for Phold, our tool that uses protein structural information to enhance phage genome annotation

After hiatus, as @RyanCookAMR were a bit busy .... we have updated links to latest INPHARED dataset. With 37.5K genomes now millardlab.org/bacteriophage-…

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

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

The dairy cow gut virome is a dynamic ecosystem that could be an under-studied player in sustainable agriculture 🔑 Preprint: biorxiv.org/content/10.110… #Microbiome #Virome #ClimateScience #Agriculture #Dairy #Cows #Methanogens 12/13

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

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

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

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

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

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

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

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

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

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

🧬🐄 NEW PREPRINT: Really happy to finally share the last big piece of work from my PhD! Spoiler: Cows are great and so are their viromes 🧵1/13 biorxiv.org/content/10.110…

This was a fun collaboration with scientists/clinicians from University of Leicester and Guangzhou, China. With contributions from @milja001 @APonsero (and many others not on here). #Phages #Virome #Microbiome #Respiratory #COPD biorxiv.org/content/10.110… 9/9