On real 16S ONT amplicon data, savont gets a lot more diversity and ASVs compared to existing methods. But these aren't just false positives. The dataset (from @mkddueholm.bsky.social and team) had paired PacBio HiFi data as a orthogonal reference: ~98% of the ONT ASVs mapped perfectly. 5/6

For long 16S nanopore amplicons (R10.4, sup-basecalled), savont requires 5-16x less depth for capturing ASVs. This improvement is more stark for longer amplicons (e.g. rRNA operon). For HiFi, savont + existing ASV methods are comparable, although savont misses a few intragenomic 16S copies. 4/6

Savont instead uses a high-resolution clustering approach: cluster similar reads --> create an error-free consensus. The problem is resolving clusters at the single nucleotide level to get true ASVs. To do this, we adopted the "SNPmer" technique: cluster reads by their polymorphic k-mers. 3/6

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

For many years you needed UMIs and similar dark molecular biology magic to get perfect amplicon sequences from @nanoporetech.com data. With recent accuracy improvements+really clever algorithms that is now changed. Savont unlocks ASVs from low coverage nanopore amplicon data 🤯🤯🤯

Between making ONT ASVs possible (Savont), meaningfully improving metagenomic assembly (Myloasm), and highly accurate metagenimic taxonomic profiling (Sylph), @jimshaw.bsky.social is kicking goals lately.

Come to ONT's industry event at ASM to hear about two exciting new tools from @jimshaw.bsky.social! SNPmers (polymorphic kmers) are leveraged for impressive performance in both myloasm (metagenomic assembly) and savont (16S ASVs). Registration link 👇

Think this is pretty cool. ONT now has an officially supported barcode kit for direct RNA sequencing. You can now run 24 samples at a time to recover full-length RNA transcripts with 8 different bp mods that aren't removed by amplification or cDNA synthesis. nanoporetech.com/resource-cen...

Integrated perspective on ocean carbon cycle:Untangling facts, fluxes, and fictions www.science.org/doi/10.1126/...

I have written a document that explains my preprint. It has generated a lot of interest, and a lot of emails to me. So, this is the explanation, minus most of the maths and formal science-speak: mol-evol.github.io/pangenome-be...

Hemp plastics have been an option for some time now too. Unless we FORCE manufacturing to change.. why wouid it? phys.org/news/2026-04...

WE DON'T NEED PETROLEUM-BASED PLASTICS ANYMORE! "The [bamboo plastic] outperforms most commercial plastics and bioplastics in mechanical and thermo-mechanical metrics while maintaining full biodegradability in soil within 50 days and closed-loop recyclability with 90% retained strength."

NEW ANALYSIS: What's going on in Spain? Spain's wholesale electricity price in early 2026: €44/MWh. Italy: €127. Germany: €96. UK: €103. Wind+solar now deliver 44% of generation. Gas sets the price in just 9% of hours, down from 55% in 2022. Full analysis: janrosenow.substack.com/p/spain-just...

StrainMake: reproducible hybrid metagenomics with MAG recovery and strain-level resolution academic.oup.com/bioinformati... #jcampubs

Sort your BAMs faster! I am looking for bug-resistant early alpha testers of mako to verify the speedup cl..ai..ms. I am seeing 1.1-1.9x speedups depending on data type and workload. github.com/fg-labs/mako

Really enjoyed this essay/review on the host microbiome through the lens of island biology. Great explanations, and a very good read throughout. www.sciencedirect.com/science/arti...

Ever wondered what microbes you could find in Denmark? Pupils from Danish schools collected soil samples across the country so you can now browse the microbes (cmc-aau.github.io/masseeksperi...).

Cool showcase dataset from compost produced by ONT. Not soil, but probs a decent proxy for soil? Please share around. * 1.5Tbp of sequencing * 5,598 MAGs (MQ+) * 1,353 circular, single-contig MAGs * 800+ circular phage genomes * 34,000+ phage defense systems * 497,000+ CAZymes * 25,000+ BGCs

A new method for inference and tracking the transmission of strains in metagenomes #MicroSky #MicroEco www.nature.com/articles/s41...

this would fix us

We're super excited to share MissAlignment: a new ML-based approach to reference-free tilt series alignment, spearheaded by @martenchaillet.bsky.social. We think it's going to make your cryo-ET life a lot better. Preprint: www.biorxiv.org/content/10.6... Code: github.com/warpem/miss-... 🧶 Thread:

For the past few weeks, I’ve been streaming episodes of Buffy as grading breaks. Given that the show debuted just under 30 years ago, I’m not particularly worried about posting some spoilers here. But there are some continuity issues that bother me. You may want to mute this thread if not interested

I’m increasingly convinced that the major lesson of the vibe coding era will be that ideas are anything but cheap

there's a lot to like in this paper! But it is just an evolutionary hypothesis, *not a conclusion*, that slightly increased abundances of soil Actinomyces could have any meaningful epidemiological impact on clinically relevant antimicrobial resistance. www.nature.com/articles/s41...

oh that's very very cool:

Improving metagenome binning by integrating intrinsic features and taxonomy www.nature.com/articles/s41... #jcampubs

Here's more info: www.cidrap.umn.edu/dengue/butan... Brazil recently began production of the vaccine, which could be a major step in limiting dengue -- also known as "bone-break fever" for reasons you can probably imagine

"Tell me who your friends are, and I’ll tell you who you are." It turns out, microbes follow the same rule! Very proud to share our lab's new paper in @natmicrobiol.nature.com showing that bacteria don't just respond to their environment, they respond to each other. www.nature.com/articles/s41...

I just caught this really interesting paper today. They obtained genomes for a new species of Treponema using genome-resolved metagenomics, associated with Noma diease:

Pseudoalteromonas is a symbiont of marine invertebrates that exhibits broad patterns of phylosymbiosis #ISMEJournal from @hollybik.bsky.social academic.oup.com/ismej/advanc...

New online! Phage host range: determinants, dynamics and applications

Our News and Views article discussing @mfels.bsky.social et al's work on how a giant virus manipulates its host's translation during infection is out today in Nature Microbiology. PhD student Danae Stephens is a co-author. www.nature.com/articles/s41...

Highlighting the long-read results from this paper, even though a small portion of the results. I'm less surprised that short-read MAGs have a few misbinned short contigs and more impressed that the long read MAG results show almost none?

I don’t know how much they paid Ryan Reynolds to head this up, but the science looks super interesting and I’m going to have fun reading it in Deadpool’s voice.

We saw this on biorxiv last year, nice to see it published! I like their table of efficiency by strain - tough luck in some species, but still very cool.

Bacterial rRNAs are highly modified, but their functions are often mysterious. Zac Park says that methylation of 16S rRNA by MraW(RsmH) enhances translation of structured mRNAs. Thus, mRNA structure and rRNA modifications likely co-evolved to fine-tune protein dosage. www.biorxiv.org/content/10.6...

From a quick read of this paper (correct me if i'm wrong), I think it's worth pointing out that most of these results are very specific to short-read MAGs. A few comments on the narrow section where long-read MAGs were included because the details seem critical for evaluation...

We've known the gut-brain axis is a key underpinning of Parkinson's disease. Today, for the 1st time, a gut microbiome signature denoting risk found in healthy individuals with genetic predisposition nature.com/articles/s41...

Crab evolution is so cool. Don’t mess with things that look like rocks in tide pools!!

Interesting…this has always been an issue in metatrascriptomics that I don’t think most realize lurks there. Try finding differently expressed genes in your study and then ask the question “are other genes in the same pathway also differentially expressed?” You very often find the answer is no.

4/ The method is simple and solid: → compute gene-level differential signal → aggregate into pathways → compare to a null via gene randomization

2/ Gene-level stats ≠ biological interpretation. You need pathway-level signals. That’s where gene set enrichment comes in. But most tools are: • slow • fragile with small n • stuck in R

Most RNA-seq pipelines are doing this wrong. They run differential expression… and stop there. You’re leaving biological signal on the table. I built pygage to fix that 👇 pip install pygage #Bioinformatics #rnaseq #computation #computationalbiology

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/...

"Pancreatic cancer mRNA vaccine shows lasting results in an early trial: Scientists caution that more research is needed, but nearly all of the patients who responded to the personalized vaccine are still alive six years later."

As a scientist, I am here to report that this headline is indeed accurate as I am in fact STUNNED!! Wow. This is incredible. 🧪 "Newly discovered bacterial defense system challenges genetic code’s central dogma.": www.science.org/content/arti...

So apparently viruses are doing protein-primed DNA synthesis now

World Ocean Database 2023: A Foundational Data Resource for and by the Global Ocean and Coastal Communities www.nature.com/articles/s41... #jcampubs 🌊

Polling the council of smart people again. What's the current state of the art tool(s) for calling/identifying AMR genes en masse--e.g. in metagenomic plasmids? Please share for reach. :-)

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...