Announcing a new tool for "denoising" long-read amplicon sequences: savont. Savont enables amplicon sequence variants (ASVs) directly from nanopore (or HiFi) long reads. Tested on 16S nanopore amplicons -- seems to work okay. 1/4 github.com/bluenote-157...

We just released #anvio v9, "eunice" 🎉 This version represents over 2,000 changes in the codebase since v8, increasing the total number of programs in the anvi'o ecosystem to 176. Read the release notes: github.com/merenlab/anv... Visit our up-to-date web page: anvio.org

Troubleshooting common errors in assemblies of long-read metagenomes - @merenbey.bsky.social @banfieldlab.bsky.social go.nature.com/44P7nSm

Looking back at a highlight from 2025: Great energy at the 2025 SALTO Symposium we organized at the MPI for Marine Microbiology! Researchers from Germany, France, Spain, Portugal, and Australia joined us in Bremen to explore the evolutionary links between specialized bacteria and their algal hosts.

🎉 The #SeqCode has reached a significant milestone: with the validation of the genus Skiveiella, a total of 1,000 #names have now been validly published under the SeqCode. This achievement marks a major step forward in the adoption and impact of the SeqCode within the scientific community.

Our data descriptor that includes surface ocean metagenomes (with Illumina & PacBio), metatranscriptomes, and tRNAs transcripts from Hawaiʻi is now out: www.nature.com/articles/s41... Just so you don't have to wait for our own investigations to finish. More data are here: merenlab.org/data/hads/

🔊 APPLY NOW for our #MarMic #MSc/#PhD program! Come to #Bremen and take an interdisciplinary approach to #marine #microbiology, #molecularbiology, #biochemistry, #evolution and more. ⏳ Open until Feb 28 2026 ➡ marmic.mpg.de #graduatestudents #marinescience #sciencecareer #IMPRS @maxplanck.de

Don’t miss this amazing opportunity to join Miguel's group in Denmark!

Akkermansia muciniphila has potential as a next-generation #probiotic, but can it claim a niche and persist in a pre-existing, complex microbial community (in vitro)? 🦠🔍 #microsky #microbiomesky #glycotime link.springer.com/article/10.1...

I knew early on I wanted to work with computers, but because of dyslexia I ended up in a lower-tier German school. The career office said a tech job wasn’t realistic. I ignored that, took a convoluted path into university, discovered bioinformatics, got hooked on algorithms&proteins, and became a PI

SingleM v0.20.2 - ONT/PacBio input reads now supported (if somewhat inefficiently), plus improved Lyrebird database for phage profiling. Microbial fraction is now prokaryotic fraction, easier to specify input genomes.

Starting this week, I set aside one hour each week to meet ECRs outside my group who want to discuss career development, mentorship, or any non-technical professional questions. Here is a blog that explains my motivation for this and how to schedule a meeting: merenlab.org/2025/11/16/E...

Excellent work from @aroneys.bsky.social here. Free to read version at rdcu.be/ePJp4

ICYMI: New online! Average nucleotide identity — the backbone of modern ecological genomics

New online! Average nucleotide identity — the backbone of modern ecological genomics

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 🧬

We are live from Bremen! #microsky

Two new positions are available at the MPI for Evolutionary Biology to support development of our genomics facility. Both stand to become permanent. Both offer a ton of opportunity to engage in a wide range of creative science. Pls repost 🙏 www.evolbio.mpg.de/3838377/job_...

Struc­tures of meth­ane-ac­tiv­at­ing en­zyme in elu­sive ar­chaea @mariecmueller.bsky.social @cuwelte.bsky.social @mpimarinemicrobio.bsky.social #methane #ANME #archaea #MCR #microbiology #biochemistry #StructuralBiology mpi-bremen.de/en/Structure...

The #MaxPlanckPostdocProgram offers a guaranteed contract of at least 3 years, targeted mentoring, and career workshops. The call for applications is open now! 🚀 Take advantage of this opportunity and browse the job vacancies. www.mpg.de/en/max-planc...

I'm very happy to share that our paper describing the evolution of sex chromosomes in brown algae is out!🎉 This project was a long journey, but it came together into a nice story 🧬 🌊 Grateful to everyone who helped along the way!

You know sulfoquinovose (SQ)? No?! You should if you are interested in diet-gut microbiome 🦠🧫interactions 😉 SQ is a sulfosugar that this part of a ubiquitous sulfonolipid in photosynthetic organisms and thus part of your diet - if you like leafy greens and algae 🥬 www.nature.com/articles/s41...

Happy to share our Practical Guide on Environmental Genomics for Prokaryotic Nomenclature, led by @nathanernster.bsky.social and part of SAM's special issue on @seqcode.bsky.social www.sciencedirect.com/science/arti...

Very excited to share our new paper! #microsky #mevosky #microbiomesky 🧬🖥️

Out in @natbiotech.nature.com: Metagenome taxonomy profilers usually ignore unknown species. SingleM is an accurate profiler which doesn't, even detecting phyla with no MAGs. Profiles of 700,000 metagenomes at sandpiper.qut.edu.au. A 🧵

🎉 Excited to share our latest work led by Tomeu! We deeply sequenced water column and sediment metagenomes using PacBio. Among the key findings: Woeseiaceae bacteria adapt to benthic vs. planktonic niches with distinct metabolic strategies. @tomeuviver.bsky.social @mpimarinemicrobio.bsky.social

I’ve officially started my research group at the MPI for Marine Microbiology! I’m incredibly grateful for the opportunity to begin this new chapter in Bremen, with the support of the @erc.europa.eu (Starting Grant ERODERS) and the @maxplanck.de. Excited to share what we discover—stay tuned!

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...

@rossenzhao.bsky.social's shiny new phage profiling tool for finding (novel) phage in metagenome reads a la SingleM. New SingleM release also brings @ace-gtdb.bsky.social R226. Manuscript is draft, but working code is here pre-pre-publication. Feedback most welcome.

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.

Bacterial symbionts enjoy their seasonal produce! Our new work shows how chemosynthetic symbionts adjust their energy sources during seasonal upwelling in the Tropical Eastern Pacific, highlighting the resilience of animal-microbe partnerships to environmental change journals.asm.org/doi/10.1128/...

Dear fellow olds - recognize that the term 'next generation sequencing' is confusing to those that never had experience with the first generation. Also - what 'generation' are we on anyways?

🚀 Apply now 🚀 The new Max Planck #Postdoc Program offers a guaranteed contract of at least 3 years, targeted mentoring, and career workshops. postdocprogram.mpg.de #ScienceCareer #PostdocProgram

Great thread on graduate positions in Austria and Germany. For more info on our graduate program see marmic.mpg.de/marmic2/. The deadline for this year's MSc program has passed, but PhD program doesn't have a deadline.

Roughly 6,000 readers answered our poll, with many declaring that Bluesky was nicer, kinder and less antagonistic to science than X https://go.nature.com/42tH8Ai

Calling all structural enthusiasts! An accurate depiction of the structure of DNA in #Lego is under 2000 supporters away from being considered to become a real set! It even has Franklin, Watson, and Crick minifigures and a Lego photgraph 51 and Bragg's law! ideas.lego.com/projects/c92...

I'm very happy to report that Matt Schechter's PhD work is now online as a pre-print: "Ribosomal protein phylogeography offers quantitative insights into the efficacy of genome-resolved surveys of microbial communities", www.biorxiv.org/content/10.1... Here's a little 🧵 about it.

Excited to share our new study in @ismepublications.bsky.social showing that microbial niche breadth specialisation (being a generalist or a specialist) impacts ecological and evolutionary adaptation following environmental change doi.org/10.1093/isme...

We are very happy to announce a free-to-attend #anvio workshop and ECR symposium in Oldenburg to discuss integrated microbial 'omics and learn applications of anvi'o. More information and application link (application deadline is Jan 10): anvio.org/workshops/20... Please apply and/or circulate 😇

1. I feel like this is such obvious advice that it gets taken for granted & consequently no one says this to young scientists but READ PAPERS, read all the papers. As you move up in your career you will have less & less time to do this. Read everything that appeals to you not just in your field

Looking for a new target microbes for cultivation? Check out our new review on "Earth's most needed uncultivated aquatic prokaryotes"! www.sciencedirect.com/science/arti...

📚 I am happy to share that our latest paper is out in Glycobiology! 🦠 We developed a synthetic community of human gut microbes that completely degrades mucin glycans. 🔬 We studied its enzymes and ecological interactions in vitro. #glycotime #mucin #microbiome academic.oup.com/glycob/artic...

Finally! 🙏

Verrucomicrobiota are found everywhere, yet we know very little about this group. Here, @iwilkie.bsky.social described and named an unrecognized marine group (previously known as MB11C04). Here, we introduce Seribacter and Chordibacter bacteria.

The remaining step to complete the transition!

We strongly suggest that academic publishers and other platforms that host research rapidly implement a Share to Bluesky button for their articles. Here's how: docs.bsky.app/docs/advance... #AcademicSky #HigherEd #Altmetrics

Genomics, evolution, and more starter pack! Help build community with this starter pack. This list is currently incomplete. Want to be included? Reply and I will remedy that! go.bsky.app/JjvzkWU

In June 2025 we are hosting #ICoN9 – the 9th #International #Conference on #Nitrification and Related #Processes! These are our invited speakers. Stay tuned for more news!

Love this idea for helping the community make the transition to Bluesky, so I’ve compiled a woefully incomplete list of microbial ecologists and -omics peeps I know are here. Please make suggestions and share. Let me know if you’d like to be added. go.bsky.app/TQpaTqF

I’m incredibly happy to announce that ERODERS is funded! I’m forever grateful for the help, encouragement, and advice from friends and colleagues. Thank you also to the reviewing panel and reviewers. I can’t wait to tell you what we find! @mpimarinemicrobio.bsky.social #ERCStG