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

HIFMB newsletter out now! 🦑 In our top story, Bettina Meyer outlines the Krill Stock Hypothesis, a scientific framework for setting krill catch quotas to protect the ecological balance in the Southern Ocean. That and more here: 241806.seu2.cleverreach.com/m/16677411

New blog post for my microbiologist colleagues: merenlab.org/2025/12/15/r... In which Meren talks about a paper by Valentina Marcheselli on how microbiologists navigate the tension between reductionism and complexity in their everyday practices.

More than a year ago researchers from @hifmb.de and @icbm-uol.bsky.social started to write about different perspectives on marine biodiversity change from natural and social science perspectives. This morphed into a review paper that was published online today link.springer.com/article/10.1... 🧪

📝 We need YOUR input! We're writing a perspective piece to share a vision for a future global observatory for marine microbial 'omics. One aspect of the perspective piece is to synthesize ongoing marine microbiome time-series. Please review our list and add any we've missed: tinyurl.com/4bmeenp9

What would a marine microbiome observing system meant to last decades look like? 🌊🦠 We explored this at the recent MMOFF Workshop, which brought together diverse partners to envision the future of marine microbiome observations. merenlab.org/workshops/MM...

I am happy to share that our data descriptor on the Hawaiʻi Diel Sampling is now published! 🌊🦠https://www.nature.com/articles/s41597-025-06166-3 Every 1.5 hours for 48 hours, we collected ocean microbes from within and adjacent to Kāneʻohe Bay, Oʻahu, Hawaiʻi and produced a multi-omics dataset.

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/

Check out our latest paper on mirusviruses, one of the most remarkable new groups of protist viruses - extremely diverse, carry lots of spliceosomal introns (including new homing introns) and are at the evolutionary crossroads between tailed phages and herpesviruses! www.nature.com/articles/s41...

Need to predict whether a given contig in your assembly was circular in the environment? Here is a new program in #anvio ecosystem that will look into your BAM file and use paired-end read mapping data to conservatively assess circularity: anvio.org/help/main/pr...

Our paper describing the GlobDB is now published in @bioinfoadv.bsky.social doi.org/10.1093/bioa... The GlobDB is the largest species dereplicated genome database currently available, containing 306,260 species representatives. More information on globdb.org 1/5 🖥️🧬🦠

Out today in Science Magazine — First author Veronika Kivenson and PIs Jill Banfield (The Banfield Lab) and Alanna Schepartz team up to reveal a new genetic code in #archaea, with implications for #methane and #climate, and #bioengineering! Learn more: https://ow.ly/Kuem50Xurh0

Are you are working with seqeunces? Does diversity matter to you? Well, then you will love #anvio 🥲

We have a date for the free-to-attend #anvio workshop and ECR Symposium for 2026, and we look forward to meeting you at the @hifmb.de in Oldenburg, Germany! Please find more information on the venue, program, and the application form here, and spread the word 😇 anvio.org/workshops/20...

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...

This paper has been a must! Great collaboration with @mkrupovic.bsky.social and @yifanzhou.bsky.social, a N&V by a legend of halophilic archaea tinyurl.com/yc3dcv72, and one picture of one of our expeditions to Dallol making the cover of the November issue of @natmicrobiol.nature.com rdcu.be/eLtCH

Great to see this finally published! Metalog: curated and harmonised contextual data for global metagenomics samples now out in @narjournal.bsky.social academic.oup.com/nar/advance-...

I wrote a new tutorial on competitive metagenomic read recruitment (and profiling of the results with #anvio), for those of us nerds who would like to get their hands dirty with data: anvio.org/tutorials/co...

Evidence from 14 research funding programmes confirms that early winners tend to keep winning (Matthew effect). But the idea that an early setback makes you stronger later doesn’t replicate widely. buff.ly/UEtcRd4

Read the annual report from @elife.bsky.social: elifesciences.org/inside-elife... I welcome that eLife is no longer indexed by SCIE. And I admire that they have not backed away from their innovative model, which makes me even more motivated to send our best work to eLife.

Please share this with anyone who may be interested in a post-doc in Germany: jobs.awi.de/Vacancies/20... This is quite an exciting opportunity to push the boundaries of what is known regarding the molecular basis of the formation and demise of photosymbiotic relationships in marine habitats.

I'm delighted our paper is out: doi.org/10.1093/isme... With new SAR11 isolate genomes and time-series metagenomes, we reveal coastal and offshore SAR11 ecotypes, identify associated metabolic traits, and pinpoint selective gene sweeps as a likely evolutionary driver to niche partitioning. 🌊🦠

A new review study shows the invisible transport pathways for #iron through #hydrothermal plumes. More on Iron’s Irony here ➡️ www.marum.de/en/Iron-sIro... @icbm-uol.bsky.social #ConstructorUniversity @geomarkiel.bsky.social @awi.de @marumunibremen.bsky.social

One of the things I find hardest to get used to in science is seeing how scientists can completely mischaracterize approaches developed by others just to justify their own. Here is a fresh example in which the highlighted statements are 100% objectively wrong about what PlasX or MobMess does

TL;DR: "I use AI myself to do things that would have required expertise and training I didn't have, such as making sense of my blood work or writing faster & better, but do not like to see that it is being used for things for which I have expertise and training". theoatmeal.com/comics/ai_ar...

🪸🧪 We’re hiring! Join our ERC-funded group at the @hifmb.de in Oldenburg, Germany to explore the cellular origins of photosymbiosis:⁣ ⁣ 𝟏 𝐏𝐨𝐬𝐭𝐝𝐨𝐜 + 𝟐 𝐏𝐡𝐃𝐬 𝐩𝐨𝐬𝐢𝐭𝐢𝐨𝐧𝐬.⁣ Deadlines: Oct 29 & Nov 5. Links below. ⁣ Questions: [email protected]⁣ #Photosymbiosis #HIFMB #ERC #AcademicJobs

💫 #MVIF Season 5 💫 Feel free to join the keynotes by presenting your work–abstract submission is open: www.microbiome-vif.org/en-US/how-to... #MVIF is proudly supported by #illumina @corundumsb.bsky.social and our non-commercial co-organizing partners Seerave Foundation @cunysph.bsky.social

You like phages ? In this publication, we use metaHiC and our new version of the MetaTOR pipeline to challenge the traditional view of phages with a narrow host range. @rkoszul.bsky.social @natmicrobiol.nature.com @cnrs.fr @institutpasteur.bsky.social www.nature.com/articles/s41...

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 😇

How do you long-read sequence metagenomes? I would argue it starts with the right sample storage & DNA extraction, to enable efficient @nanoporetech.com /@pacbio.bsky.social sequencing, which we investigated in our new paper: www.biorxiv.org/content/10.1... Massive thanks to Klara for driving this

Congratulations to HIFMB colleague Kim de Luca, who was selected by MIT Technology Review as one of the 35 Innovators Under 35. www.technologyreview.com/innovator/ki...

A blog post that covers my visit to Barhal, the village where my family comes from: merenlab.org/2025/09/01/b... No science this time, just life and personal reflections.

PSA: This is what the real male loneliness syndrome looks like.

I was a PhD student when this paper came out. I printed it out with excitement and brought it to the lab next morning. My advisor Michael Ferris skimmed through the supplementary material and said "this is cryptic growth with As resistance". I was shocked and learned something essential that day.

Here's our new broad review on the extended mobility of plasmids, about all mechanisms driving and limiting their transfer. From conjugation to conduction, phage-plasmids to hitchers, molecular to evolutionary dynamics, ecology to biotech. The state of affairs. 1/9 academic.oup.com/nar/article/...

A comment I wrote for you is now online at @natcomms.nature.com: www.nature.com/articles/s41... Oh, oh, it says "time travel will likely remain forever off the table in our universe" with a citation, so read it maybe? (am I doing the click-bait thing right? 🥲).

The mantra “location, location, location” isn’t just about real estate. For life scientists, more than 50% of their productivity can be attributed to the institution where they work, according to a new study. scim.ag/4kKs1YO

POV: When you're a middle author of a study, and everything is a matter of life and death 💀 I AM BECOME REVIEWER #2, DESTROYER OF RELATIONSHIPS BEFORE THE STUDY WENT OUT TO REVIEW.

New blog post I wrote on 'how we do not choose our families but we can choose people who push us', and ONLY for my scientist colleagues who are looking for things to procrastinate with style (by requiring them to be longer than a post on BlueSky) :p merenlab.org/2025/07/16/s...

Our paper demonstrating that within-species warfare interactions are ecologically important on human skin is now published in Nature Micro! www.nature.com/articles/s41...

Join our team! MARUM and partner institutes within the #ExcellenceCluster Ocean Floor are offering ➡️ 15 doctoral researcher positions. Please find out more about it here: www.marum.de/en/career/op... @icbm-uol.bsky.social @hifmb.de @awi.de

A short preprint describing the GlobDB is now on arXiv: arxiv.org/abs/2506.11896 If you find the resource useful, please also check globdb.org for info on how to cite the underlying resources and tools.

I'm so extremely thankful for the National Radio and Television Administration of China for supporting the production of Three-Body (三体). Seeing a product that is so faithful to its inspiration, and taking its time with delivery in the era of shallow entertainment was such a great experience.

I'm happy to announce the latest release of the GlobDB, available at globdb.org. The GlobDB is a database of "species dereplicated" microbial genomes, and as of release 226 contains twice the number of species-representative genomes (306,260) than the latest GTDB release.

🌊🦠#FieldworkFriday! Last March, C-CoMP set out on the RV Atlantic Explorer to compare diel surface ocean microbial dynamics between oligotrophic and productive regions. Time to batten down the hatches! Photo by McKenzie Powers.

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...

Not that you care, but I still wanted to let you know that if I see a paper full of bogus citations with your name on it, I'm not talking to you anymore. I was so triggered by a paper I was reading this morning, I am drinking my second coffee.

Ribbon diagrams are the ubiquitous face of proteins across science, known for their particular combination of clarity and beauty. “It’s hard to imagine a scientific representation of data that is more meaningful.” — Philip Bourne, University of Virginia

Out in Science! Zakem et al. mechanistically modeled global marine prokaryotic functional diversity, grounded with field data. Shifts in community composition drive respiration and thus biological C storage. This facilitates C cycle projections in a warming ocean www.science.org/doi/10.1126/...

Very excited to present the Great Barrier Reef Microbial Genomes Database (GBR-MGD), a comprehensive DB of 1000s of high-quality prokaryote, virus, plasmid, and chromosome-level eukaryote MAGs using Nanopore long reads. Subthreads incoming. Please share widely. 🙂 www.biorxiv.org/content/10.1...