Have you ever looked at some differentially occurring gene clusters in a microbial #pangenome and thought to yourself "I wonder if they contribute to any metabolic modules"? With the most recent changes, the answer is a few clicks away in #anvio 😇

Excited to share our latest preprint on agtools, an open-source Python framework for analysing and manipulating assembly graphs. (1/n) www.biorxiv.org/content/10.1... #Bioinformatics #genomics #assembly #assemblygraphs #software

Three new kids on the block. ARMADA, BRIGADE, and TALON. Impressive how multiple labs all come together to contribute to discovery. Great collaboration with Simon, Chase, and Eugene. From the very talented Ryan Bell, together with Thomas Gaudin and our own Yi Wu. www.biorxiv.org/content/10.1...

Interested in healthy aging and the microbiome? Join my lab to explore how ex vivo microbiome assays can guide personalized interventions that modulate specific microbiome-derived metabolites critical for health.

Interested in compound- microbiome interactions, and how they affect health? Join my lab at the Quadram Institute.

🚨 We’re hiring! 🚨 The Integrative Viromics Lab @UCalgary 🇨🇦 is looking for a Lab Technician! 🔬 Phage isolation & culture 🧫 Anaerobic chamber work 📦 Lab management & student mentoring Apply now & help us explore the virosphere! You must have work authorization to work in Canada already.

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

🆕 Vacancy! We’re looking for a Chief Scientific Officer to support the development of the institute’s scientific strategy and scientific leadership of the institute. 💷 Competitive 🗓️ Apply by 12 October 2025 ➡️ buff.ly/mKUhD3K

Only 5 days left to apply for our Soil metagenomics position: estimating the impact microbiomes in restored agricultural sites can have on climate change (closing 19th Sep): jobs.earlham.ac.uk/Details.asp?...

🆕 Blog! Our Research Scientist Dr Revathy Krishnamurthi reflects on her recent visit to the village where she grew up in India to inspire the next generation to discover the world of science 🔍 @norwichmicro.bsky.social

I thought I'd try this technical molecular microbiology question here. #MicroSky Does anyone have experience with cloning 7-10 kbp fragments into a vector for Gram-positives? We are trying, but the vectors we generally use become quite unstable when we try to clone in a fragment of that size.

🚨New Review Out🚨 We explore how phage-antibiotic synergy can dismantle efflux-driven resistance in multidrug-resistant ESKAPEE pathogens. By reprogramming bacterial defences, phages offer a precision strategy to restore antibiotic efficacy. journals.asm.org/doi/10.1128/...

🆕 Vacancy! We’re looking for a #Metagenomics Research Scientist to join the Laboratory of Dr Falk Hildebrand @bioinf.bsky.social to study diet impact on the gastrointestinal microbiome. 💷 £37,500 - £42,000 🗓️ Apply by 30 September 2025 ➡️ buff.ly/uwqGQQm

Today, I'm excited to announce the publication of the Duplodnaviria realm Profile and Chapter. The realm includes viruses of archaea, bacteria and eukaryotes and is best known for its inclusion of herpesviruses and tailed phages. www.microbiologyresearch.org/content/jour...

The ICTV Report chapters, which are linked to the profiles and get updated when the taxonomy changes, can be found on the ICTV website: ictv.global/report

We have expanded our ICTV Virus Taxonomy profiles and chapters to include higher ranks, which have been recently introduced and may not be familiar to all virologists. You can find our 2-page Profiles (citable record) in JGV @microbiologysociety.org www.microbiologyresearch.org/content/ictv...

New paper alert! We suggest caution in the analyses of viral auxiliary metabolic genes and propose a new overarching term - 'auxiliary viral genes' (AVGs) to describe different types of such genes. @simrouxvirus.bsky.social #phagesky #Microsky www.nature.com/articles/s41...

New in @asm.org #MMBR Computational function prediction of bacteria and phage proteins. How to annotate your #phage and #bacteria genomes by @susiegriggo.bsky.social @bedutilh.bsky.social @gbouras13.bsky.social and Bob #phagesky #microsky journals.asm.org/doi/epub/10....

Have to take a deep breath and remember that I am a grown-up and not an angry toddler. But still, reviewing a paper in your field that directly ignores (aka doesn’t cite) all of your papers despite them being pretty much the only other papers like it can hit hard sometimes : /

After a busy period , @ryancook94.bsky.social and I have have updated links to latest INPHARED dataset. With 37.5K genomes now. If some "iffy" genomes have got thought the automated and then out manual filters. Let us know the accession numbers so we can exclude millardlab.org/bacteriophage-…

Protein Structure Informed Bacteriophage Genome Annotation with Phold https://www.biorxiv.org/content/10.1101/2025.08.05.668817v1

(1/5) 🧵 Three reasons why you should you follow our starter packs: 🥼Connect with our staff and students: buff.ly/yTBFgk0 🔎Connect with our research, science support and community groups: buff.ly/B8my1Nj

Do you love phage? I have an opening for a postdoc in my lab at the University of South Florida College of Marine Science (@cmarinescience.bsky.social) looking at interactions between marine phage and iron, which is an important limiting trace metal in the oceans (1/5) 🧵#phagesky 🦠🌊

Synteny-aware functional annotation of bacteriophage genomes with Phynteny https://www.biorxiv.org/content/10.1101/2025.07.28.667340v1

Great to see this out. The impact of antibiotics on the gut phages and what it tells us of the disruption associated with antibiotics . www.cell.com/cell-reports... Check @eugenpfeifer.bsky.social thread

We (with Clement Coclet, not on Bsky) had the chance to work on a broad "state of viromics" review. We tried to use this to give an overview of how the field changed over the last ~ 15 years, and also what we think are some of the major remaining challenges. Full-text access at -> rdcu.be/excHt

A really great review written by @simrouxvirus.bsky.social and Clement Coclet on the state of the field of viromics and viral ecology. Well worth a look, and provides a solid reading list for those entering the field wanting more background on how it has developed and what tools are available.

📣 New preprint alert! Happy to share the first results from our effort to reannotate Pseudomonas #phage proteins of unknown function, using structural bioinformatics. 📄 doi.org/10.1101/2025...

New manuscript from the group 'IS1216 drives the evolution of pRUM-like multidrug resistance plasmids in Enterococcus faecium' www.biorxiv.org/content/10.1... /1

Looking forward to presenting the latest results from the PhageLand project during the ‘Phages in Health and Remediation’ session at 4.30pm in Brown 1&2 at @femsmicro.org #FEMS2025 #phagesky #microsky

We’re excited to bring the @phagecollection.bsky.social to #SummerScience at @royalsociety.org next week. Big thanks to James Gallagher for covering the project in the BBC Read more here: www.bbc.com/news/article... Hope to see some of you there! #PhageTherapy #AMR #OpenScience

Happy to announce that we have a new 2.5 year post on food-associated changes in gut microbiomes. We are looking for a strong bioinformatician with experience in metagenomics, metabolic modelling, functional genomics, system biology. (application deadline 20.7.25) quadram.ac.uk/vacancies/me...

Do you have an interest in soil microbiology and biogeochemical cycling, and statistics/programming skills (either R, python, Perl, C++, or equivalent)? Check our current vacancy ⤵️ 💷 £36,720 to £42,000 per annum 🗓️ Apply by 08 July 2025 ➡️https://buff.ly/BSB0Qfh

This is probably my last piece of work from my @medresfdn.bsky.social funded PhD at @uniofnottingham.bsky.social (thanks for all the support over the years!). Contributions from @milja001.bsky.social @evelienadri.bsky.social (and many others not yet on Bluesky) 13/13

The dairy cow gut virome is a dynamic ecosystem that could be an under-studied player in sustainable agriculture 🔑 Preprint: www.biorxiv.org/content/10.1... #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

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

The 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" 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

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 www.biorxiv.org/content/10.1...

This was a fun collaboration with scientists/clinicians from Uni of Leicester and Guangzhou, China. With contributions from @milja001.bsky.social @evelienadri.bsky.social (and many others not yet on Bluesky) #Phages #Virome #PhageSky #Microbiome #Respiratory #COPD www.biorxiv.org/content/10.1... 9/9

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

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