Genuine question for folx who look at bacterial phylogenies: How do you interpret the bootstrap support and posterior probabilities that you get on your tree estimates? Do you take them seriously? Do you think: "Wow, all 99%, that must be a reliable tree!"? 1/

Enrichment of polyphenol metabolism within the ubiquitous SAR116 Puniceispirillales bacterioplankton https://www.biorxiv.org/content/10.64898/2026.07.17.739263v1

Benchmarking DNA extraction protocols across use cases for culture-independent Nanopore metagenomics www.microbiologyresearch.org/content/jour... #jcampubs

We have a bunch of MAGs sitting in GenBank queues for many months. I run all MAGs through PGAP so they’re BLAST-able & assigned accessions, which I refer to when discussing genes in MAGs in papers. This has ground to a halt w/ NCBI processing delays in recent years. Is there anyway to expedite this?

Bacteriophage continue to have so much to teach us. It's in our interest to understand how they work and impact human & environmental health. New joint work led by @mariandm.bsky.social & @rantahan.bsky.social inferring single-cell latent period & burst size heterogeneity from population dynamics.

Long read and short read whole genome sequencing are equivalent for genomic characterisation of bacteriophage~ www.biorxiv.org/content/10.6... "native Nanopore sequencing failed to assemble several Pbunavirus genomes, likely due to modified DNA bases, but an amplification-based library preparation~"

In some recent blog posts, I had a Klebsiella genome with a mysteriously higher ONT error rate. But Michael Biggel (University of Zurich) emailed me with the likely explanation: 7-deazaguanine mods. Thanks, Michael! Here's his preprint about this: www.biorxiv.org/content/10.6...

Synteny-aware microbial pangenome graphs reveal blueprints of genomic variation https://www.biorxiv.org/content/10.64898/2026.07.03.736256v1

Glad to see it finally out in #mSystems @asm.org! 🥳 See the thread below to read what it is about! journals.asm.org/doi/10.1128/...

Hi ocean -omics folks, someone (a while back) mentioned to me that they thought the Tara Oceans metagenome sequencing effort did some "blanks" sequencing - negative controls intended to get at contam & artifacts. I can't find any mention of them in papers tho. Can anyone help me find 'em? thx!

A simple mathematical model for the discontinuity in average nucleotide identity distributions in prokaryotes doi.org/10.21203/rs....

A representative of a ubiquitous bacterial lineage parasitically feeds on host RNA https://www.biorxiv.org/content/10.64898/2026.06.21.733656v1

Follow-up to my last blog post: I now look at assembly polishing with Dorado v2 and the new [email protected] model from @nanoporetech.com. rrwick.github.io/2026/06/19/d...

Isolation of genome-predicted Caldatribacterium (Atribacterota) reveals pervasive microbial cultivation problem due to folate precipitation #microbiology #bacteria #MicroSky @natcomms.nature.com doi.org/10.1038/s414...

Excited to share the latest version of FlashPPI published with @pnas.org ! And stay tuned for updates soon…👀

A multilayered cell envelope of a member of the Chloroflexota offers an anchoring platform for the archaellum doi.org/10.3389/fmic...

New Experimental Google Colab Notebook now integrates AlphaFold3 with OpenFold3 and py2Dmol: colab.research.google.com/github/sokry... (1/3)

The Elusive Fraction of Marine Plankton Diversity: Size, Abundance and Taxonomic Composition of 0.2 μm-Filterable Prokaryotes Across Three Contrasting Coastal Environments onlinelibrary.wiley.com/doi/10.1111/... #jcampubs 🌊

Long-read single-cell genomics: resolving chimeras in multiple displacement amplification www.biorxiv.org/content/10.6... #jcampubs

MBARI captured these views of glass squids in family Cranchiidae. I want to talk about some of the unique adaptations these Ghosts of the Midwater have & how they're adaptive to life in the twilight waters of the mesopelagic zone (200 m to 1000 m). (📷: Monterey Bay Aquarium Research Institute)

Amino acid auxotrophy is a feature of a distinct bacterial lifestyle across environments www.biorxiv.org/content/10.6... #jcampubs

Genomic Traits Associated with Copiotrophy Decouple from Maximum Growth Rate Predictions Along Temperature Gradients academic.oup.com/ismej/advanc... #jcampubs

Isolation of genome-predicted Caldatribacterium (Atribacterota) reveals pervasive microbial cultivation problem due to folate precipitation www.nature.com/articles/s41... #jcampubs

New blog post! I analyse the new [email protected] basecalling model from @nanoporetech.com and discuss the conspicuous lack of a new sup model: rrwick.github.io/2026/06/11/d...

Rational engineering of facultative anaerobiosis enables commensal survival in the oxygenated gut https://www.biorxiv.org/content/10.64898/2026.06.05.730451v1

The new OrthoFinder paper is out now! In this new work, we introduce major advances in accuracy and scalability, allowing analysis on much larger datasets www.nature.com/articles/s41... github.com/OrthoFinder/...

Scaffold-level validation is needed for phage–host inference from metagenome-assembled genomes dx.doi.org/10.21203/rs....

Multimodular flavobacterial enzymes specialized in coordinated decomposition of cellulose and alginate in brown algal cell walls | The ISME Journal | Oxford Academic https://academic.oup.com/ismej/article/20/1/wrag112/8673214?login=false

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...