Long read Metagenomics, #phage and #prophage in the gut by Ami Bhatt's group. Beautiful data showing changes in phages over two years #phagesky www.nature.com/articles/s41...

🧬🛡️How are new immune mechanisms created? We show how Lamassu antiphage system, originated from a DNA-repair complex and evolved into a compact and modular immune machine, wt Dinshaw Patel lab in @pnas.org. 👏 @matthieu-haudiquet.bsky.social, Arpita Chakravarti & all authors! doi.org/10.1073/pnas...

The host range of generalist and specialist phages in capsule-diverse Klebsiella hosts is driven by the evolvability of receptor-binding proteins @plosbiology.org from @pilardomingoc.bsky.social journals.plos.org/plosbiology/...

Two fully-funded PhD openings in my research group at the University of York. If you’re excited about viromes, phage biology, Nanopore sequencing, soils and the odd bit of alpine or agricultural field sampling, we’d love to hear from you! 🌱🦠🏔️ tiny.cc/c4pv001 tiny.cc/e4pv001

🚨Preprint alert - this is a big one! We transfer the revolutionary power of TnSeq to bacteriophages. Our HIDEN-SEQ links the "dark matter" genes of your favorite phage to any selectable phenotype, guiding the path from fun observations to molecular mechanisms. A thread 1/8

Two conferences two weeks apart, thank you to everyone who came and chatted to me at my poster (or in general) at the Phages.fr conference in Nancy and the @microbiologysociety.org #MicroEvo25 conference in Liverpool. It was great to show the first data from my postdoc and get advice and feedback

📢 New preprint is out on bioRxiv 📢: How much does virome prep influence our view of the human gut virome? Short answer: a lot. Long answer: doi.org/10.1101/2025... Different methods lead to distinct community structures, richness, and major virus-host abundance patterns. 🧵 1/5

Time to publish responsibly: DAFNEE, a database of academia-friendly journals in ecology and evolutionary biology url: academic.oup.com/jeb/article/...

Proud of this work led by Rocio Espinosa and Henriette Lyng Roder. Fun collaboration & innovation! *Used custom 3D-printed flow systems to study evolution in biofilms of two competing Pseudomonas species in communities of varying complexity, using microscopy + WGS www.nature.com/articles/s41...

Join our online course Orchestrating Microbiome Analysis with @bioconductor.bsky.social (2–6 Feb 2026)! Learn hands-on microbiome data analysis, diversity metrics, and multi-omics integration with @antagomir.bsky.social & Tuomas Borman . www.physalia-courses.org/courses-work...

Very excited to share a big part of my dissertation work with the Deutschbauer lab at LBNL and @ucberkeleyofficial.bsky.social! BarTn7: A method for bacterial lineage tracking at sub-species resolution in population, ecological, and evolutionary experiments. www.biorxiv.org/content/10.1...

Please apply to join the Diversity Committee of the American Society of Naturalists! www.amnat.org/announcement...

#microsky #phagesky Transposon mutagenesis of jumbo #phage using an anti-CRISPR factor as selectable marker www.biorxiv.org/content/10.1...

We are organising an AMR meeting next spring in Helsinki. Meeting includes evolution of AMR and environmental AMR sessions. Please submit your abstract now! Deadline Dec 1st.

👀 Eco/evo tweeps teaching undergraduate courses ... Can interactive web apps help biology students become better modellers? Stephan Peischl's group is running an ethics-approved study. Learn more at: peischllab.github.io/MEEW.html Contact [email protected] to receive the survey link.

Open faculty position (Assistant or Associate) in UW Medical Genetics. As you might expect, faculty often end up also interacting with Genome Sciences, so we're hoping for some great prospects! Note the clinical requirements for the position. apply.interfolio.com/176466

This has been an intense, crazy week. My plasmid competition paper is finally out and we have a new preprint on Bioarxiv! Plus I'm leaving the US after 10 years here. See you soon America! Hello Zurich!!!

🧫🦠🌍🧬 Alexander Harms group just made TnSeq possible for phages, enabling the possibility to infer functions over different hosts and conditions. This will revolutionise our toolbox to understand not only phage physiology, but also ecological plasticity! Congrats @aharms485.bsky.social!

Another great post from Sasha demonstrating what will ring true to many of us-- our environments include our siblings, making it unlikely that siblings have identical environments.

I wrote a little bit about the "missing heritability" question and several recent studies that have brought it to a close. A short 🧵

I have a PhD position available on freshwater phage pollution, in terms of AMR impact and persistance of phage used in food and agriculture. #PhageSky #MicroSky www.findaphd.com/phds/project...

Congratulations @daanspeth.bsky.social and the whole team. GlobDB has already been very helpful for several projects at @cemess.bsky.social, and it will no doubt be a useful resource for many microbiologists around the world. Really glad to see it out there.

UBC and SFU PIH chapters are partnering with us to host a Global Health Case Competition — built by students, for students. Happening next Sat, Nov 29th. If of interest @ubcpress.bsky.social @ccj-ubc.bsky.social @ires.ubc.ca @jwmartens.bsky.social @profterrig.bsky.social @lauraknelson.bsky.social

Kepler serving up some really sweet science (not sponsored by Crumbl)

Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/ www.science.org/doi/10.1126/...

#microsky #phagesky #phage

I wrote about the recent autism-microbiome paper, why I think it's the most important microbiome paper this year, and what it says about the field open.substack.com/pub/blekhman...

Did you publish part of your PhD work in @journal-evo.bsky.social or @evolletters.bsky.social this year? Submit your paper for the SSE Presidents’ Award! Up to two recipients will each present an award talk during the virtual portion of #Evol2026 in May. Deadline: January 30. shorturl.at/CnVo6

Another PhD!! Are you, or someone you know, looking for a PhD, starting in Oct 2026? Do you like phages, genomes & public health impact?🦠🧬🧩 Wanna work in a cutting edge of science, with some awesome people @quadraminstitute.bsky.social? Please apply or share by 6 Jan🗓️ #PhDposition #academicsky

I recently discovered Conventional Comments (conventionalcomments.org) for providing a pseudo-standard set of labels for feedback and just tried it for an article review and it was really helpful to specify issues vs. thoughts vs. suggestions, etc. Hopefully it's helpful for the authors too!

If you’ll teach about Adaptation this coming spring, would you be interested in testing whether having an explicitly inclusive activity improves student understanding of the concept? We’re recruiting instructors, please consider joining us!

Very happy to see this piece out in @plosbiology.org, on the bacterial immune systems and microbial communities. It was a great team effort with Rafael Custodio, @brockhurstlab.bsky.social , @brownlab.bsky.social, and Edze Westra! 🦠🧫 #phagesky #mevosky journals.plos.org/plosbiology/...

I’ve released a tool to sketch and edit phylogenetic trees! yawak.jp/PhyloWeaver/ Load a Newick file and intuitively add/remove/resize branches. Useful for quick conceptual trees, extracting subtrees, or turning ideas into Newick.

The default prior for the intercept in both {rstanarm} and {brms} are very wide. Counterintuitively - being on the logit scale, this is actually translates to a **strong** prior that p(y=1) is near 1 or near 0. Always check your priors! #rstats

I am recruiting graduate students to my genomics-focused lab in EEB at Illinois Urbana-Champaign. Please spread the word if you know any students with an interest in a computational focus to genomics research! evol.mcmaster.ca/brian/evoldi...

My radical edu take: LLMs devalue knowledge retrieval, so the 3 most important skills to learn in school now are 1. identifying high-qualilty information from the rest, 2. making good decisions in an oversaturated information environment 3. understanding the difference between data and knowledge

I’m excited to share my recent postdoc work. Here, we interrogate how different phage infection outcomes (productive vs. restrictive) affect the expression of phage defense systems. We find that a restricted infection not only inhibits the phage but also induces increased immune protein abundance.

If you'd like to celebrate the biology of viruses - or the fight against viral diseases - this winter, try out our free and updated #VirusSnowflake designs. Please share, and if you have any photos of Virus Snowflakes in your area it would be lovely to see them! cvr-engagement.co.uk/virus-snowfl...

Hello bluesky community! I'm hiring a postdoc to do machine learning in population genetics. Starting to build up a lab at Indiana University Bloomington where I just started a faculty position. Apply with the below link: indiana.peopleadmin.com/postings/30325

OK, #bioinformatics folk. We have some (many many) reads from a metagenome. They have been binned into a bacterial genome. They have no matches to any known genome in any database. They code for "bacterial" genes. What are good triple-checks to do to argue that they are not, in fact, euk sequence?

Science People: We at NSF are still recovering/catching up/getting our lives together. But the agency posted these FAQs about post-shutdown resumption of operations which might answer a lot of Qs for you: www.nsf.gov/resumption-o...

We wrote the Strain on scientific publishing to highlight the problems of time & trust. With a fantastic group of co-authors, we present The Drain of Scientific Publishing: a 🧵 1/n Drain: arxiv.org/abs/2511.04820 Strain: direct.mit.edu/qss/article/... Oligopoly: direct.mit.edu/qss/article/...

gggenomes: A Grammar of Graphics for Comparative Genomics thackl.github.io/gggenomes/ #Rstats

We are excited to share @probstlab.bsky.social's latest publication on the diversity of CRISPR-Cas spacers, led by @katharinasures.bsky.social !! 🧬 Have a read!! ➡️ doi.org/10.1093/gbe/... @emilruff.bsky.social @alexjaffe.bsky.social @geomicrosoares.bsky.social & others not in Bluesky!

Does anyone have a -80 that they like? Ideally one that doesn't require a thaw every year and constant software updates. I really want one from 1990.

Another new preprint from former PhD student Daniel Wong (now @ ENS) has been a long time in the making, and builds on our recent efforts to model eco-evolutionary feedbacks in rapidly evolving microbial populations that compete for different resources (1/n)

We show that despite this large mutational influx, rapidly evolving pop'ns naturally cluster into a smaller # of distinct “ecotypes”, even when their genetic diversity is much larger. This non-eq analogue of competitive exclusion is driven by a dynamical priority effect that favors resident strains.

Theres still time to apply for our PhD project on UPEC/immune cell interactions. Deadline December 4th

We discovered a universal scaling law linking copy number and plasmid size, which can be used to predict the PCN of your favorite plasmid! 6/7

The first is from former PhD student Zhiru Liu @zzzhiru.bsky.social (now in @bengrbm.bsky.social's group @ MSK) examining the long-term patterns of selective constraint – measured by the classical ratio of nonsynonymous to synonymous mutations (dN/dS) – within recombining populations of bacteria.