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.

Our work on 'hidden diversity' in unbinned contigs is now published in @natmicrobiol.nature.com :

www.nature.com/articles/s41...

See the linked threads for more details!

MetaPointFinder:
A new approach for detecting mutation-driven antimicrobial resistance directly from metagenomic reads.
Fills a major gap in current resistome profiling by capturing chromosomal AMR mutations that metagenome tools miss.

github.com/aldertzomer/...

You could use approaches from multi-omics integration, e.g. MEFISTO to calculate joint factors and then look at the loadings, or something like RDA. Could also train random forest regression models to predict relative abundance of species of interest from fluoro and eval the channel importance

I am searching for a lab manager/researcher to come and work with a friendly, collaborative, and interdisciplinary group of students, postdocs, and staff on the microbial ecology of cyanobacterial blooms. careers.umich.edu/job_detail/2...

Logo of Bin Chicken (Australian white ibis) on a rubbish bin, pulling out a strand of DNA

“Bin Chicken” is now published in Nature Methods! It substantially improves genome recovery through rational coassembly 🧬🖥️. Applied to public 🌍 metagenomes, we recovered 24,000 novel species 🦠, including 6 new phyla.
doi.org/10.1038/s415...
@benjwoodcroft.bsky.social @rhysnewell.bsky.social
🧵1/6

The only thing more scientifically dispiriting than reading a potentially exciting paper that turns out to be a ton of hype and little else is seeing your colleagues uncritically holding it up as a breakthrough

🦖 Something HUGE just hatched.

Plasmidsaurus now offers RNA sequencing for gene expression analysis:
• As fast as 3 day turnaround
• $50/sample for academia, $80 for industry
• Up to ~10M unique transcript 3’ end reads per sample
• Interactive results

Explore Plasmidsaurus RNA-Seq today.

Efficient and accurate search in petabase-scale sequence repositories - Nature MetaGraph enables scalable indexing of large sets of DNA, RNA or protein sequences using annotated de Bruijn graphs.

After years of research and continuous refinement, we’re thrilled to share that our paper on the MetaGraph framework — enabling Petabase-scale search across sequencing data — has been published today in Nature (www.nature.com/articles/s41...)

Another amazing opportunity at UMD in Mihai Pop's lab! Mihai is looking for a bioinformatics software engineer. Consider applying here if you're interested: umd.wd1.myworkdayjobs.com/en-US/UMCP/j...

A roadmap for equitable reuse of public microbiome data - Nature Microbiology In this Consensus Statement, a consortium of microbiome scientists discuss current sequencing data sharing policies and propose the use of a Data Reuse Information (DRI) tag to promote equitable and collaborative data sharing.

Our own @alexjprobst.bsky.social @geomicrosoares.bsky.social and Cristina Moraru have recently authored a @natmicrobiol.nature.com Consensus Statement where they discuss new mechanisms for sequencing data reuse! 🧬💻

Check out their manuscript here:
www.nature.com/articles/s41...

Associate or Senior Editor, Nature Communications (Geosciences) Job Title: Associate or Senior Editor, Nature Communications (Geosciences) Location(s): Shanghai, Beijing, Nanjing, New York, Washington, Jersey City, Madrid, Milan (hybrid) Closing date: 8th October,...

My team is hiring again! 📣

springernature.wd3.myworkdayjobs.com/SpringerNatu...

De novo discovery of conserved gene clusters in microbial genomes with Spacedust - Nature Methods This work presents Spacedust, a tool for de novo identification of conserved gene clusters from metagenomic data.

Spacedust: a tool for de novo identification of conserved gene clusters from metagenomic data.
@ruoshiz.bsky.social @milot.bsky.social

www.nature.com/articles/s41...

GitHub - bluenote-1577/skani: Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs. Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs. - bluenote-1577/skani

skani v0.3.0 is released. github.com/bluenote-157...

- 30-40% potential reduction in memory with approximately the same runtime.
- Breaking changes to indexing and searching databases

Calculate ANI for contigs, genomes -- even search > 140k genomes. Pre-indexed GTDB-R226 available for download.

Not sure how many scientists here have tried Claude Code or similar command line coding assistants. I had a complicated family property tax problem that was best solved by a brute force Monte Carlo simulation approach, so I spent a few days coding up and analyzing a model with Claude Code.

The Transcriptional Architecture of Bacterial Biosynthetic Gene Clusters Bacterial biosynthetic gene clusters (BGCs) drive the production of diverse bioactive specialized metabolites regulated by transcription factors (TFs) in response to environmental signals. In this met...

Useful paper: "The Transcriptional Architecture of Bacterial Biosynthetic Gene Clusters" #microsky #streptomyces

pubs.acs.org/doi/abs/10.1...

Announcing myloasm, a new long-read (ONT R10/PacBio) metagenome assembler that I've been working on during my postdoc in the Heng Li lab (@lh3lh3.bsky.social).

myloasm-docs.github.io

Millions of People Depend on the Great Lakes’ Water Supply. Trump Decimated the Lab Protecting It. The Trump administration’s slashing of budgets and staff have Great Lakes scientists concerned that they have lost the ability to protect the public from toxic algal blooms, which can kill animals…

NEW: The Trump administration’s slashing of budgets and staff have Great Lakes scientists concerned that they have lost the ability to protect the public from toxic algal blooms, which can kill animals and sicken people.

By @annaleighclark.bsky.social

Agree, and looks like a nice new tool! I'll also make a plug for the fantastic Kingfisher from @benjwoodcroft.bsky.social that can flexibly pull from either ENA or SRA, and also cloud providers: github.com/wwood/kingfi...

Assemblies of long-read metagenomes suffer from diverse errors Genomes from metagenomes have revolutionised our understanding of microbial diversity, ecology, and evolution, propelling advances in basic science, biomedicine, and biotechnology. Assembly algorithms...

I am very happy (and anxious) to share with you our most recent work in which we evaluated four of the most popular long-read assemblers,

www.biorxiv.org/content/10.1...

and tell you just a little bit about it in the following 🧵

High-quality metagenome assembly from nanopore reads with nanoMDBG www.biorxiv.org/content/10.1101/2025.04....

From #CIGLR on the other place: 🚨 Cuts would cripple NOAA’s wide-ranging science partnerships, because of the ongoing funding delays, “we’re looking at having to lay off a substantial number of our workers in the next few months,” said #CIGLR Dir. Greg Dick: #GreatLakes

Release 10-RS226 (16th April 2025)
GTDB - Genome Taxonomy Database https://gtdb.ecogenomic.org/

1. LLM-generated code tries to run code from online software packages. Which is normal but
2. The packages don’t exist. Which would normally cause an error but
3. Nefarious people have made malware under the package names that LLMs make up most often. So
4. Now the LLM code points to malware.

Trump seeks to end climate research at premier U.S. climate agency White House aims to end NOAA’s research office; NASA also targeted

BREAKING from @science.org: The Trump admin is seeking to kill nearly all climate research at NOAA, its climate science agency.

Its near-final budget proposal would end all NOAA research labs, academic institutes, and regional climate centers. And it wants to fully end the NOAA Research division.

Genomic Identification and Characterization of Saxitoxin Producing Cyanobacteria in Western Lake Erie Harmful Algal Blooms Saxitoxins (STXs), a group of closely related neurotoxins, are among the most potent natural toxins known. While genes encoding STX biosynthesis have been observed in Lake Erie, the organism(s) responsible for producing STXs in the Laurentian Great Lakes have not been identified. We identified a full suite of STX biosynthesis genes in a Dolichospermum metagenome-assembled genome (MAG). The content of sxt genes suggest that this organism can produce STX, decarbamoyl and deoxy-decarbamoyl saxitoxins, and other congeners. The absence of sxtX indicates this organism is unable to produce neosaxitoxin, a potent congener. However, a distinct, lower abundance sxt operon from an unidentified organism did contain sxtX, indicating neosaxitoxin biosynthesis potential. Metatranscriptomic data confirmed STX biosynthesis gene expression. We also recovered highly similar Dolichospermum MAGs lacking sxt genes, implying gene loss or horizontal gene transfer. sxtA was detected by quantitative polymerase chain reaction during 47 of 76 sampling dates between 2015 and 2019, demonstrating higher sensitivity than metagenomic approaches. sxtA gene abundance was positively correlated with temperature and particulate nitrogen:phosphorus ratio and negatively correlated with ammonium concentration. All Dolichospermum MAGs had genes required for nitrogen fixation. Collectively, this study provides a foundation for understanding potential new threats to Lake Erie water quality.

Great to see this paper from Paul Den Uyl's MS work out in
ES&T

"Genomic Identification and Characterization of Saxitoxin Producing Cyanobacteria in Western Lake Erie Harmful Algal Blooms" doi.org/10.1021/acs....
@GreatLakesGreg @pubs.acs.org #greatlakes #ciglr #noaaglerl

NOAA just fired us, again 🤡

Retroactive to February 🤡

Most bacterial gene families are biased toward specific chromosomal positions The arrangement of genes along bacterial chromosomes influences their expression through growth rate–dependent gene copy number changes during DNA replication. Although translation- and transcription-...

Wow

ⓁⓄⒸⒶⓉⒾⓄⓃ
ⓁⓄⒸⒶⓉⒾⓄⓃ
ⓁⓄⒸⒶⓉⒾⓄⓃ

Thought bacterial gene regulation is all about promoters and repressors?

𝙏𝙃𝙄𝙉𝙆 𝘼𝙂𝘼𝙄𝙉

WHERE a gene sits on the chromosome can dictate its expression—especially in fast growing bacteria

Evolution won’t leave genome layout to chance

Hu et al SCIENCE

CoverM: Read alignment statistics for metagenomics AbstractSummary. Genome-centric analysis of metagenomic samples is a powerful method for understanding the function of microbial communities. Calculating r

CoverM is published!

CoverM: Read alignment statistics for metagenomics academic.oup.com/bioinformati... #jcampubs

Strain-resolved de-novo metagenomic assembly of viral genomes and microbial 16S rRNAs - Microbiome Background Metagenomics is a powerful approach to study environmental and human-associated microbial communities and, in particular, the role of viruses in shaping them. Viral genomes are challenging ...

A bit late to this thread, but another option is Penguin / PLASS microbiomejournal.biomedcentral.com/articles/10....