I’m excited to share our effort to obtain one of the first estimates of the net rate, in physical time, of lateral gene transfer (LGT) – nature’s own genetic engineering - across a complex, global microbiome: doi.org/10.1093/isme...

Phage defence-system abundances vary across environments and increase with viral density Phil. Trans. R. Soc. B by @seanmeaden.bsky.social, Edze Westra and @peterfineran.bsky.social royalsocietypublishing.org/doi/10.1098/...

very nice, it's a natural spike-in! I wonder what are the GDPR implications, though, of sharing human reads. I guess participants now will be asked to consent to their genomic data being shared.

Happy to team up with @microbe-enjoyer.bsky.social to highlight fantastic work by @gibbological.bsky.social, Alex Carr, and colleagues using community scale metabolic models to predict risk for C. difficile colonization! See the initial study here: www.cell.com/cell-systems...

Stoked to finally have a preprint out for Phold, our tool that uses protein structural information to enhance phage genome annotation #phagesky 1/n www.biorxiv.org/content/10.1...

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 🦠🌊

𝗕𝗿𝗶𝗻𝗴𝗶𝗻𝗴 𝗣𝗵𝗮𝗴𝗲 𝗟𝘆𝘁𝗶𝗰 𝗖𝘆𝗰𝗹𝗲 𝘁𝗼 𝗟𝗶𝗳𝗲 🦠🧬 Dive into the lytic cycle! A bacteriophage injects DNA, hijacks the host, and rapidly replicates until the bacterium lyses, releasing a new swarm of virulent phages! #blender #3D #cgi #science #research #biology #phage #lyticcycle #bacteria #scicomm #sciart

New online! Viromics approaches for the study of viral diversity and ecology in microbiomes

Excited to try this one!

"How Little We've Seen" Imagine measuring an area the size of Houston, then making generalizations about the entire globe. From analysis of Bell et al., that's just what we're doing with the deep seafloor. www.science.org/doi/full/10....

We have a new 3-year postdoc position in our group at the @hifmb.de to study plasmids and plasmids systems of the marine environment to survey their utility in microbial responses to environmental change. Please see the official job ad here, and spread the word: jobs.awi.de/Vacancies/20...

Simons Graduate Fellowships in Ecology and Evolution www.simonsfoundation.org/grant/simons... Application Deadline July 31, 2025

NIH funding supporting the HMMER and Infernal software projects has been terminated. NIH states that our work, as well as all other federally funded research at Harvard, is of no benefit to the US.

#phagesky Some partnerships are always fun!! Excited to share one such 🎉 product w Simon Roux, perspectives on our favorite “atypical” phages, for special issue to celebrate my former mentor Carol Gross @ UCSF Tapping the treasure trove of atypical phages www.sciencedirect.com/science/arti...

Time to catch up on the past week’s news about science and medicine in the US. Whew. 1/10

Not really my announcement to make--I am but a lesser co-author--but IQ-TREE 3 has just been released! (Most credit to Minh Bui and @roblanfear.bsky.social and their labs) ecoevorxiv.org/repository/v...

CoverM is published! CoverM: Read alignment statistics for metagenomics academic.oup.com/bioinformati... #jcampubs

Check out this list of awesome #virome tools and be sure to add yours! github.com/shandley/awe... #phagesky #microsky

We're looking for suggestions on how to update and adapt the Minimum Information about an Uncultured Viral Genome (MIUVIG) reporting standard. What works? What needs updating? Check out the survey forms.gle/DPHvMFe8Gsdj... 🧵

Out now, a comprehensive guide to metagenomics -- from sample collection to data analysis. This primer covers best practices, challenges, and applications in health, agriculture & environment. A roadmap for studying microbial communities 👇 www.nature.com/articles/s43...

Characteristics of Phages and Their Interactions With Hosts in Anaerobic Reactors enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/... #jcampubs

Genomes assembled from #metagenomes (a.k.a. MAGs) are awesome and have revolutionized our ability to study uncultivated microbes ...BUT: they still don't capture a lot of the 🦠 species that are out there New @jgi.doe.gov paper led by Dongying Wu and Natalia Ivanova: www.science.org/doi/10.1126/...

Phage-induced disturbance of a marine sponge microbiome. DOI: 10.1186/s40793-024-00637-7 https://pubmed.ncbi.nlm.nih.gov/39593141/

If you had a really nice looking alignment of about thirty 100kb virus genomes and you wanted to find recombination breakpoints, what software/methods would you use? All suggestions, snark, links to papers etc. welcome. Trying to navigate a new field... Please repost! 🧪

Excited to share “Bin Chicken”, substantially improving genome recovery through rational metagenomic assembly. Applied to public 🌍 metagenomes, it recovered 24,000 novel species 🦠, including 6 novel phyla. doi.org/10.1101/2024... @wwood @rhysnewell @CMR_QUT 🧵1/6

A community consensus paper about a contentious subject like the Last Eukaryotic Common Ancestor does feel very bluesky in late 2024 doesn't it? It was pretty fun to write. Hopefully you'll have fun reading it:) Kudos to @Tom Richards for his writing and cat herding abilities! plos.io/4g0alq4

Protein sequencing with nanopores? The latest review on the subject dropped yesterday 🤓 www.nature.com/articles/s44...

📢 Postdoc opening! 📢 @soreklab.bsky.social and we are looking for outstanding candidates for a position at the intersection of computational biology & innate immunity. Dive into impactful research in two dynamic fields. Interested? Let’s connect! 👇 www.genzentrum.uni-muenchen.de/career/postd...

Download our database of 492 (!) funding opportunities for EARLY-CAREER FACULTY AND RESEARCHERS. For each entry, we provide link to funder, description, amount, deadline, and eligibility criteria (e.g. citizenship). Download freely here: research.jhu.edu/rdt/funding-...

I made a quick Starter Pack for scientists working on virus discovery - please reply if you’d like me to add you to the pack (or remove you) or to recommend anyone! #scisky go.bsky.app/HK1wxRb

I wrote about the backstory of our recently published metagenomic profiler called sylph (www.nature.com/articles/s41...), partially to celebrate the new migration to bluesky Check out the blog here: jim-shaw-bluenote.github.io/blog/2024/de... -- and I apologize in advance for the lack of brevity :)

One week left to apply for this faculty position in marine ecology at UMass Boston! Take a look, and please let me know if you have any questions. Great department, great marine systems, great students! employmentopportunities.umb.edu/boston/en-us... 🧪🌍🌊

Twitter account's deactivated, it's all blue sky now! I look forward to continuing the conversation.

Seasonal dynamics and diversity of Antarctic marine viruses reveal a novel viral seascape www.nature.com/articles/s41... #jcampubs 🌊

A new program from NSF is targeting graduate fellowship money to people who received Honorable Mention on a GRFP within the past three years, who are currently enrolled in grad school in EPSCoR states. here is the solicitation: new.nsf.gov/funding/oppo... and a map of EPSCoR eligible states:

I love maps. This is a hand-drawn map of Allen Island Maine by Rick Donaghue. “Possession of this map by sheep strictly prohibited”

Latest from my lab: we show that extracellular vesicles and viral-like particles are distinct vehicles for horizontal gene transfer, differing in DNA capacity and functional content. EVs harbor an incredible diversity of mobile elements! #MicroSky #ViroSky www.researchsquare.com/article/rs-4...

I hope this in-depth comparison of single amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) will help inform data interpretation and experimental design in a broad range of research projects: link.springer.com/article/10.1...

Two weeks left on our cruise to the Oxygen Minimum Zone off the coast of Chile... content is coming out! Cameos from Laura Bristow, Osvaldo Ulloa and Chief Scientist Maria Pachiadaki (@microbiaki.bsky.social) www.youtube.com/watch?v=fGi6...

Just looked up whether the plural of phage is phage or phages, and found this gem of an article: www.tandfonline.com/doi/full/10....

Phages reconstitute NAD+ to counter bacterial immunity https://www.biorxiv.org/content/10.1101/2024.02.11.579819v1

Phage folks who do culturing… how do you preserve your environmental samples for later plaque assays? I was taught just 0.2 micron filter & store in fridge but anecdotally hearing more about glycerol and freezing? Thoughts? Advice? Papers to read? Working with fresh samples isn’t an option #phagesky

excited to have played a role in this cool discovery www.biorxiv.org/content/10.1...

SingleM finally has a preprint associated with it!! I've juxtaposed two of their figures - that is a heck of a benchmark. Assemble, but for an unassembled read-based perspective in environmental microbiomes, SingleM is a strong option.

Decoding Huge Phage Diversity: A Taxonomic Classification of Lak Megaphages https://www.biorxiv.org/content/10.1101/2024.02.01.578382v1

Hello BlueSky World. :) Delighted to share our work "Large language models improve annotation of prokaryotic viral proteins" by my awesome MSTP student Zach Flamholz with Steve Biller at Wellesley rdcu.be/dxcnE www.nature.com/articles/s41... (1/9)

There are four more days to apply for the Bioinformatics of Microbial Single Cells Workshop at Bigelow Laboratory in Maine! For more information, and a link to the application: bigelowlab.github.io/scgc-bioinfo...

The best part: Funds are available to fully reimburse student and postdoc registration fees!

psst... it's Friday afternoon and I know y'all are packing up, but... Application is open for the the Bioinformatics of Microbial Single Cells workshop at Bigelow Laboratory for Ocean Sciences happening in Maine next April! Check it out and apply: bigelowlab.github.io/scgc-bioinfo...

How do people feel about short reads alignment accuracy for minimap2? I'm primarily working long reads with minimap2 anyway, so maybe I should consolidate instead of switching between bwa and minimap2. Just talking within microbial/phage genome contexts. 🧬🖥️🧫🦠🧪