Establishment of microbial strains from the river, groundwater, and soil in the hyporheic zone is limited despite connectivity https://www.biorxiv.org/content/10.64898/2026.06.04.730025v1

🔬 We have an open PhD position at SLU Uppsala! We're looking for a curious & driven PhD student to join the #ECOPHARM project funded by @kawresearch.bsky.social and investigate plasmid-dependent phages in aquatic ecosystems. Pls share with anyone who might be interested! www.slu.se/en/about-slu...

Looks promising but I need to read the paper first of course. I am unclear which primers were used. How well did they cover archaeal and bacterial diversity?

Eco-evolutionary dynamics of massive, parallel bacteriophage outbreaks in compost communities | Science Advances https://www.science.org/doi/full/10.1126/sciadv.aeb8246?af=R

Our method, savont, for generating amplicon sequence variants (ASVs) for long-read amplicons is now on bioRxiv. Work with @lh3lh3.bsky.social and help from @mkddueholm.bsky.social and team (Marie Riisgaard-Jensen, @kirk3gaard.bsky.social, Kasper Skytte Andersen) github.com/bluenote-157... 1/6

Single-phage profiling illuminates viral individuality during bacterial cell fate determination | Nature Communications https://www.nature.com/articles/s41467-026-73867-7

A survey of 2600 early-career researchers provides insights into good and bad practices of supervision - www.biorxiv.org/content/10.6... So valuable! I think supervision is, unfortunately, largely an after thought in scientific research...🧵

Now live! Submit a 100 word proposal to win free #PacBio HiFi sequencing for #metagenomics. Long-read metagenomics is rapidly gaining traction and this is a great time to apply it to your research. programs.pacb.com/l/1652/2026-...

Distribution of a novel DsrEFH sulfur transferase suggests widespread sulfur oxidation capacity in sulfate reducers #microbiology #sulfur #MicroSky @isme-microbes.bsky.social doi.org/10.1093/isme...

ZipStrain Enables Rapid and Precise Strain-Resolved Metagenomics doi.org/10.64898/202... ZipStrain follows the general workflow of inStrain, but is built from the ground up using high-performance libraries such as Polars, DuckDB, and PyTorch and exposes richer intermediate data for custom analyses.

You may recognize names like "Hantavirus" and "Ebola virus." But "Andes virus" & "Bundibugyo virus" may not ring a bell. I wrote about how recent outbreaks highlight virus diversity, and our difficulty putting names on it. Yet our survival depends getting names right. Gift link: nyti.ms/4dzRPqn

Sandpiper 2 is up. 913,000 metagenomic community profiles w @ace-gtdb.bsky.social R232, 200k more than 1.0. sandpiper.qut.edu.au GlobDB coming. Thanks to @aroneys.bsky.social @thepatientwait.bsky.social @iambrettb.bsky.social and especially the new kid @nhstefan.bsky.social

1 year preprint ban for those who don't state the species in the title or abstract

We need a microbial "culture announcement" journal, like we have genome announcements. ASMs MRA *could* work. But, they require deposition into a culture collection, which has many barriers from both sides (depositor and collection).

Extracellular electron transfer in cable bacteria enables growth rates comparable to aerobic respiration www.nature.com/articles/s41... #jcampubs

Dependency–Competition Tradeoffs Structure Microbial Niches and Nitrogen Cycling academic.oup.com/ismecommun/a... #jcampubs

Bacterial Physiology in the Context of Algal Partners www.annualreviews.org/content/jour... #jcampubs 🌊

Practical guide for marine exo-metabolomic sample preparation academic.oup.com/ismej/advanc... #jcampubs 🌊

Systematic discovery of enzyme promiscuity in Escherichia coli using in vitro metabolomics www.nature.com/articles/s42... #jcampubs

SAASI: Sampling Aware Ancestral State Inference | Nature Communications https://www.nature.com/articles/s41467-026-72851-5

Is there a good colony counting tool for images as this one out there? I tried OpenCFU here and it didn't work at all. 🧪

Interesting results from continuous cultivation of co-cultures of a host bacterium and episymbiotic Patescibacteria Resolving Host-Episymbiont Interaction Dynamics through Continuous Cultivation www.biorxiv.org/content/10.6...

Does anyone know if there's written documentation on how ONT put together their dorado bacterial polishing model? I know it fares well on benchmarks, but what is it based on and how did they put it together? Is anyone testing alternate polishing models these days? 💻🧬🧪

Lots of people have reached out asking how they can support us after the devastating fire in the MSL building, the heart of @cmarinescience.bsky.social Here’s one way, a GoFundMe organized by our graduate students - gofund.me/4373c6ff3. Please share widely, and thanks for helping our community!

IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models academic.oup.com/mbe/article/...

Very excited to share our new paper out in Nature. Congrats to Xiaoqian (Annie) Yu and all the coauthors. www.nature.com/articles/s41...

Interested in working on the evolution of photosynthetic endosymbioses? Come join us! I have 2 open positions in my new group @cemess.bsky.social in Vienna 3yr postdoc info: tinyurl.com/4emkjpn4 4yr PhD info: tinyurl.com/mtxmsjpy Apply by 1st June! Please share/repost #Protists #Symbiosis #PhD

Isoprenoid quinone profiling in complex biological samples using a novel semi-quantitative HPLC-MS/MS method www.biorxiv.org/content/10.6...

Two positions at Aalborg University (Denmark) in microbial single cell genomics: Laboratory Engineer → aau.varbi.com/what:job/job... Bioinformatics Engineer → aau.varbi.com/what:job/job... Deadline: May 8, 2025 #Hiring #Microbiology #Bioinformatics #SingleCell #Microbiome #Denmark

Out Now! Cayman enables large-scale analysis of gut microbiome carbohydrate-active enzyme repertoires #MicroSky

Our first collaboration with the Levine lab! Defining metabolic niches for marine microbial heterotrophs www.science.org/doi/full/10.... #jcampubs 🌊

Defining metabolic niches for marine microbial heterotrophs doi.org/10.1126/scia...

Out Now! Hunting for new lineages and mechanisms of life #MicroSky

Isolation of two species of Caldatribacterium (Atribacterota) and the importance of folate for their culturability www.researchsquare.com/article/rs-6... "~folate provided in vitamin solutions was inadvertently removed by filter sterilization according to standard media preparation protocols."

Most bacteria remain uncultured with vast microbial ‘dark matter’ awaiting discovery.. to address this am excited to share EDEN - an enhanced domestication method to grow uncultured bacteria & new diversity. Using EDEN we isolate a new species active against MDR pathogens.. doi.org/10.1093/isme...

It is crazy that in 2026, major research findings published in high impact journals are still being built on a dichotomous view of p-values without any consideration of effect sizes or biological context! Just because you get p < 0.05 that doesn’t mean it is biologically significant....

Feels like this paper on protein-templated DNA synthesis by a natural enzyme warrants some comment. So here's a 🧵. /1 www.science.org/doi/10.1126/...

1/8 🔥 New preprint dropped: Dynamic co-existence of bacteriophages and their hosts 🦠 in the Arabidopsis thaliana 🌱 phyllosphere Work led by the indomitable @sheilaroitman.bsky.social‬ #plantscience #microbiome #holobiont www.biorxiv.org/content/10.6...

High-density microdroplet cultivation reveals the essential role of microbial interactions in the growth of environmental microbes.🦠🧫 journals.asm.org/doi/10.1128/...

How every layer of science's "self-correcting machinery" failed when Iva Veseli and I simply wanted to reproduce the findings of a high-profile study on gut microbiome and autism: merenlab.org/2026/04/15/u...

New publication out @natcomms.nature.com! We identify novel viruses that actively infect highly productive chemoautotrophs, and reveal key trophic interactions and virus-host dynamics that impact microbial carbon cycling in aphotic environments. www.nature.com/articles/s41...

High-throughput characterization of Mycobacterium tuberculosis gene function across diverse conditions | PLOS Biology https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3003529

📣We have 5 PhD positions in hadal biogeochemistry and microbial ecology at the Danish Center for Hadal Research: lnkd.in/eJ6rp_Rk. 📣 Deadline: 4 May 2026 Please share widely! fa-eosd-saasfaprod1.fa.ocs.oraclecloud.com/hcmUI/Candid...

GTDB release 11 based on RefSeq 232 (R11-RS232) is live at gtdb.ecogenomic.org. This release covers 901,341 genomes (23% increase) and has 199,923 species clusters (39% increase). Release notes at: forum.gtdb.ecogenomic.org/t/announcing.... Release statistics at: gtdb.ecogenomic.org/stats/r232.

An ocean-wide partnership: How #diatoms use a sulfated #polysaccharide to keep #bacteria close & friendly. mpi-bremen.de/en/How-diato... Out now #Microbiome by J. Krull @chandnisidhu.bsky.social J.-H. Hehemann C. J. Crawford et al. @marumunibremen.bsky.social @unibremen.bsky.social (C) M. Reich

Quite a few flowcells going beyond 200 gbp

Notice for users submitting MAGs to INSDC Issue: MAGs submitted to INSDC without taxonomic annotations, typically listed as ‘metagenome’, are not included in GTDB. Examples: www.ncbi.nlm.nih.gov/datasets/gen... What to do: Provide at least a domain-level taxonomic affiliation in the Taxon field.

Multiple fully funded PhD/postdoc positions available: experimental evolution of tumour suppression, egalitarian & fraternal ETIs, jumbo phage ecology & genetics. Related EoIs welcome. Email CV/statement of motivation written in own words. Open until filled. Grateful for reposting 🙏

Metabuli & Metabuli App v1.2 improve novel species classification with higher precision and recall. New light mode is 1.8× faster and requires 50% less storage while keeping precision. New RefSeq, GTDB, HRGM, and HROM databases added. 💾 github.com/steineggerla... 📄 doi.org/10.64898/2026.03.13.711249

Given a discussion on another thread, thought it might be useful to start a separate thread on how users are achieving higher ONT yields—extraction kits, size selection, sample type, basic stats, etc. Anyone welcome to chime in. @acritschristoph.bsky.social @kirk3gaard.bsky.social