Dangers of no confirmation screen + me being an idiot. I'm gonna make some coffee ☕️

Found (pro)phages carrying bacterial virulence genes (neuA, lytA). 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

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

Phages infecting oral anaerobes were disproportionately lower. Porphyromonas phages: 40-fold lower despite only 4-fold bacterial reduction. Meanwhile, pathogen-associated phages unchanged. Kill-the-Winner dynamics persist but weaken with severity (maybe the winner's been killed?) 5/9

Despite diversity loss, viral communities showed minimal structuring by clinical phenotype. Only 4.5% variance explained by ABE groups. With bacterial communities showing stronger clinical associations 4/9

Viral diversity progressively declined with COPD severity. Most striking: frequent exacerbators (Group E) showed complete decoupling of viral-bacterial diversity (ρ=0.052, p=0.833) while other groups maintained strong correlations (ρ>0.5) 3/9

We analysed the lung virome in 135 COPD sputum metagenomes spanning the full clinical spectrum of COPD. Found 1,308 vOTUs, including those predicted to infect Streptococcus, Haemophilus and Moraxella (key bacterial pathogens in COPD) 2/9

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

The drying-off period emerged as a viral hotspot 🔥

- Highest viral diversity
- Lowest bacterial diversity
- Highest virus-to-host ratios
- Most viral genes under evolutionary pressure
- Peak viral loads

This transition period = a huge ecological reorganisation in the dairy cow microbiome 7/13

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"

And all three adult groups we profiled had distinct viral communities 5/13

1,338 vOTUs were predicted complete. @milja001.bsky.social and I agreed to manually inspect the 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 Nanopore and Illumina sequencing 🐮

We recovered over 30,000 vOTUs (approximate to species), and included shallow bulk metagenomes for each sample to place the viruses within the context of their microbial hosts 3/13

Continued....

An update...

An intermediate assembly graph for a metagenome I'm working on. Can anybody spot the virus with 30,000x coverage?