Ryan Cook @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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George Bouras @GB13Faithless

4 weeks ago

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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Andrew millard @milja001

4 weeks ago

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

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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

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Ryan Cook @RyanCookAMR

4 months ago

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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Ryan Cook @RyanCookAMR

4 months ago

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

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Ryan Cook @RyanCookAMR

4 months ago

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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Ryan Cook @RyanCookAMR

4 months ago

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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Ryan Cook @RyanCookAMR

4 months ago

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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Ryan Cook @RyanCookAMR

4 months ago

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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Ryan Cook @RyanCookAMR

4 months ago

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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Ryan Cook @RyanCookAMR

4 months ago

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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Ryan Cook @RyanCookAMR

4 months ago

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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Ryan Cook @RyanCookAMR

4 months ago

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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Ryan Cook @RyanCookAMR

4 months ago

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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Ryan Cook @RyanCookAMR

4 months ago

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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Ryan Cook @RyanCookAMR

4 months ago

🧬🐄 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…

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Ryan Cook @RyanCookAMR

3 months ago

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

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Ryan Cook @RyanCookAMR

3 months ago

These findings establish altered bacteriophage ecology as an unrecognised feature of COPD pathobiology, with differential phage-bacteria relationships that reshape lung microbial ecosystems, offering new perspectives for microbiome-targeted interventions 8/9

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Ryan Cook @RyanCookAMR

3 months ago

Found (pro)phages carrying virulence genes. Patients with neuA-encoding Haemophilus phages had 82-fold higher bacterial loads (p=5.5×10⁻⁴). First evidence of virulence factor-encoding phages enhancing pathogen colonisation in human respiratory tract (that I know of?) 7/9

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Ryan Cook @RyanCookAMR

3 months ago

Four patients had extreme viral loads (>10% metagenomic reads). Two had eukaryotic viruses, two had bacteriophage "blooms" - single phages dominating the community. These acute events may reveal boom-bust dynamics in COPD viral ecology 6/9