If you're a senior PhD student or recent graduate interested in doing work at the intersection of AI and microbial genomics and/or microbiomes, please feel free to reach out to discuss the possibility of applying together for an MIT Novo Nordisk Fellowship engineering.mit.edu/novo-nordisk

I am seeking a postdoc to join my group at UCLA -- ideally the candidate would have some experience in either population genetics or microbes/microbiome (computational background needed). We have a range of projects and are happy to tailer to your interests. Please dm/email me if interested.

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...

#microsky #phagesky #phage in the gut www.nature.com/articles/s41...

🚨New preprint out! We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8) www.biorxiv.org/content/10.1...

🐝🦠 New paper: rdcu.be/eOf7A Phages may drive microbial diversity, yet we often don’t even know how phages & bacteria correlate in nature. Our new study tackles this in the honeybee gut, thanks to the great work of PhD student @malickndiaye.bsky.social at @dmf-unil.bsky.social @fbm-unil.bsky.social

The average nucleotide identity (ANI) underpins how we map microbial diversity, compare species, and connect genomes to ecology. I wrote a short piece reflecting on the discovery and significance of this metric (and really enjoyed digging into the context and story behind it!) #microsky 🧬

Fantastic piece of research that discovered the atypical lifestyle of the prototypic crAssphage. This project showcased so much determination, brilliance, and open-mindedness, proving that great discoveries are made by following the evidence wherever it leads.

Phage people - does anyone have a lambda phage with a deletion/mutation in the integrase gene (unable to lysogenize)? If so, can you please share it with us to help us test a cool hypothesis? Thanks! Please RT. 🦠🙏

Replicative selfish genetic elements are driving rapid pathogenic adaptation of Enterococcus faecium https://www.biorxiv.org/content/10.1101/2025.03.16.643550v1

Talking about read-based methods to profile phages in metagenomes, check out Marker-MAGu by @miketisza.bsky.social —a marker gene-based method for identifying phages. bsky.app/profile/natu...

Check out my "tools of the trade" piece on Phanta! I cover the need it addresses (phage inclusion in microbiome studies), the features we prioritized (sensitivity & ease of use), our vision (phage profiling as the norm), and the future we envision. Check it out and try Phanta! tinyurl.com/ToTPhanta

This paper has been a long time coming: We looked at the genomes of historical bacterial samples over a century to look for trends of antibiotic resistance genes, finding multiple instances of them in infections before the age of antibiotics, but an increase in both frequency and mobility after

Starter pack for metagenomics and microbial genomics lovers. go.bsky.app/MFipoLH

I'm putting together a Microbial Bioinformatics starter pack to help get everyone connected in our community. Let me know if there are any bluesky users to be added and share so that twitter refugees can tune back in to the fantastic world microbes go.bsky.app/3ezLo7e

In the spirit of summaries, simple rules that, if everyone followed, would make academic publishing less painful in 2025. As a reviewer: *Separate major and minor comments *Write your explicit recommendation in the "for authors" section *If co-reviewing with trainees, read the paper yourself 1/2

Empathi: Embedding-based Phage Protein Annotation Tool by Hierarchical Assignment [new] Empathi: Classifies phage proteins using embeddings, IDs multi-func.

What a great way to end the year! ✨ Today in @cellpress.bsky.social we report the structure and function of the Shedu anti-phage defense system. tinyurl.com/4crj6dnx A long 🧵...

Finally out! Phage therapy for diabetic foot ulcers www.sciencedirect.com/science/arti...

We wrote a new review paper in @cp-trendsmicrobiol.bsky.social on recently developed bioinformatic tools that facilitate elucidating protein functions in the era of big genomics data. www.sciencedirect.com/science/arti... This is the 1st paper of 2 talented students Shani Cheskis and Avital Akerman.

Nice study from @annechevallereau.bsky.social's lab! www.biorxiv.org/content/10.1...

New paper from the Faber lab in @plosbiology.org characterizing the C. difficle ncRNA ModT, with effects on sporulation and the transition into stationary phase, evidence for RBP association -- and similar abundance to some ribosomal RNAs! 🧫🦠 journals.plos.org/plosbiology/...

nAtUrE iS bEaUtiFuL 🐞 #MedSky

Feel like this paper slipped under the radar on ‘the other platform’ so giving it another airing here. Phage can significantly remodel the bacteriome in faecal samples - yet another confounder 🙄 www.sciencedirect.com/science/arti...

Prophage induction contributes to alterations in the gut phageome during intestinal inflammation https://www.biorxiv.org/content/10.1101/2024.12.03.626644v1

Exploring the diverse RNA #virome in urban freshwater ecosystems, this study uncovers novel viruses with recombinant genomes, expanding our knowledge of virus diversity. #Metagenomics #FreshwaterEcology #ViralDiversity 📄 doi.org/10.3390/micr... EVBC👤: R. Zell

Scientists, academics, researchers: We’re excited to share that @altmetric.com is now tracking mentions of your research on Bluesky! 🧪

Excited to share our work on broadly effective phage-antibiotic cocktails. We report 4 cocktails that each work against 96% of 153 antibiotic resistant Pseudomonas isolates. Check it out here: www.nature.com/articles/s41... Congrats to Kevin Kim @KevinMinyo6651

Identification and Mitigation of microbial contaminant reads from long-read metagenomic samples https://www.biorxiv.org/content/10.1101/2024.11.26.625374v1

Very cool to see the SmartPill capsule in action here!🦠🧫 www.nature.com/articles/s41...

Amazing! Read how MGEs confered resistance to vibriophage, probably contributed to its spread during the 90s cholera epidemic in South America.

Non-native English speakers need 50% more time to write a paper When they do, they face a 2.5 times higher chance of being rejected because of language journals.plos.org/plosbiology/...

Here’s the updated Computational Biology Starter Pack! Let me know if you'd like to be included. go.bsky.app/QVPoZXp

Wow - bluesky! 📈 🦠 Please help me amplify a special faculty search. We're looking for someone in "Microbial Systems Biology" to join me and @kreynoldslab.bsky.social at UTSW Sys Bio / Bioinformatics. There is an empty lab space right next to us waiting for you! apply.interfolio.com/154339 1/4

The impact of transplant location on the gut microbiome and resistome in patients undergoing hematopoietic stem cell transplantation at home versus in the hospital https://www.biorxiv.org/content/10.1101/2024.11.19.624359v1

The first review article from my lab, helmed by @celiasouque.bsky.social, "From Petri Dishes to Patients to Populations: Scales and Evolutionary Mechanisms Driving Antibiotic Resistance" is now online and open access at Annual Reviews Microbiology: www.annualreviews.org/content/jour...

1/ A new preprint from the @gangfang.bsky.social group highlights challenges in detecting low-abundance modifications with ONT sequencing and proposes a framework to improve reliability.

(1st post @BlueSky) Preprint alert🚨a long thread. Cautions in the use of @nanopore sequencing to map DNA modifications: officially reported “accuracy” ≠ reliable mapping in real applications. We performed a critical assessment of nanopore sequencing (across different versions of models) for the 1/n

You think I’m kidding, but all our servers are actually named after mushrooms. 🍄‍🟫 🍄 🍄‍🟫 🍄 🍄‍🟫 🍄

I'm giving a guest lecture in computational genomics and have 90 minutes to inspire students to fall in love with the #microbiome and #metagenomics. I'll cover studies, approaches, algorithms, and their impact. Any findings/technologies/methods that blew your mind? Would love to brainstorm!

We found something interesting in the evolution of plant microbiota. It is under review and we published the preprint today. Avi Bograd from my lab analyzed the genomes of 38,912 bacteria and identified a clear depletion of all MGE types in plant-associated bacteria vs. non-plant associated bacteria

I didn't see one so I just created the Gut Microbiota starter pack! Please feel free to share, ask for joining or recommend must-added! go.bsky.app/UkXi7to

New preprint on our method aa-tRNA-seq: chemically capturing aminoacylated tRNA molecules & pulling them through nanopores. It’s been a blast working with my collaborator Aleks Radakovic to take this from idea to promising pilot data to some looking exciting biology to chase down in future work.

Hope I'm the first to post this all time classic on this platform

Trying to purify and sequence #phage for phage therapy? Try #sphae a new approach to identify if your phage could be useful for treatment #phagesky

Made my first starter pack! If I missed you, my apologies. I can add you. go.bsky.app/URt3Fbp

1/ Our review on sequencing-based #microbiome analysis is in the Dec 24 issue of Nature Reviews Genetics. We explore DNA/RNA-sequencing approaches for studying microbiome structure and function, highlighting the biological insights sequencing-based microbiome research offers. go.nature.com/3XFqonu

I created a long-read sequencing starter pack. I'm still finding people on here, so apologies if I missed you. Please suggest people who should be added and I'll add them! go.bsky.app/JGkefsJ

Hey BlueSkies! ONT question: Anyone using dorado to basecall PromethION flowcells with super-high accuracy? We're on V-series GPUs but exploring setups. We parallelize dorado per POD5, considering whether to buy more affordable GPUs (L40s) or fewer high-end ones (H100s). Thoughts/recommendations?