The object that he showed me

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.

That’s what we say, only 6 months earlier 😂

It’s the binchicken effect

The answer can now be found at gtdb.ecogenomic.org

Thermoaminiphila catenidiffluenda gen. nov., sp. nov.: A novel thermophilic, strictly anaerobic bacterium representing Thermoaminiphilia class nov., a newly described class thriving in hydrocarbon-rich habitats and biogas fermenters www.biorxiv.org/content/10.6... #jcampubs

Immensely rewarding part of this work was working with Indigenous language experts and elders in the naming of our species of Asgard….’marumarumayae’ derived from the Malgana language from the people of Gathaagudu (#Shark Bay)

Ecology of metagenomes: incorporating genotype-to-phenotype maps into ecological models www.biorxiv.org/content/10.6... #jcampubs

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.

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!

MBE Call for Papers on the Major Transitions of Life

MBE is excited to launch our newest Call for Papers on the Major Transitions of Life, covering all aspects of phylogenomic research.

🔗 academic.oup.com/mbe/pages/call-for-papers-on-the-major-transitions-of-life

Guest Editors:
Davide Pisani
Anja Spang

#evobio #molbio #phylogenetics

Micro-scale spatial metagenomics opens a new era in microbiome ecology Understanding microbial communities requires moving beyond 2D representations toward a holistic view that couples 3D spatial organization with ecological function, integrating microbial inventories, g...

Micro-scale spatial metagenomics opens a new era in microbiome ecology

@cp-trendsmicrobiol.bsky.social Opinion from @mizrahilab.bsky.social

www.cell.com/trends/micro...

Metagenomic mining reveals extensive novelty, enhanced biodegradation potential, and untapped biosynthetic capacity in Chinese oilfield microbiomes journals.asm.org/doi/full/10.... #jcampubs

Redox chemistry of early Earth and the origin of life - Communications Chemistry Redox reactions played an important role in shaping the conditions that enabled the emergence of life on the early Earth, but how these relate to specific environmental conditions and whether they led...

Redox chemistry of early Earth and the origin of life www.nature.com/articles/s42... #jcampubs

Figure 1 shows the conceptual workflow of the algorithm. It first loads the configuration file and the input data of one or multiple binned metagenomes, yet evaluates each bin individually. It then iteratively processes each candidate bin in the input, going through the refinement tasks, potentially multiple times. The refinement either stops when the last step or a preset stop task have been reached or an unrecoverable error has been encountered. The algorithm tasks can be configured individually.

🤯 Manual MAG refinement? Still doing it by hand??

We’ve been there... You could just leave those messy, ill-assigned contigs/scaffolds in your data for NCBI to pick up during your submission…

…OR you could add itBins, our new automated MAG refiner by @jmk-ude.bsky.social, to your pipeline!! 🔥

The SeqCode Committee has opened the call for applications to the SeqCode Prize 2026, sponsored by ISME.

@isme-microbes.bsky.social

Myloasm, our long-read metagenome assembler, is now published! w/ @mgmarin.bsky.social and @lh3lh3.bsky.social

Very rewarding after > a year of development and countless hours thinking about assembly. Thanks to beta testers, Li lab, and reviewers who gave very helpful feedback.

rdcu.be/famFj

How much protein diversity can Life on Earth actually generate?

With DIAMOND DeepClust, we show how billions of proteins across the tree of life can be clustered at low-identity for downstream analytics tasks.

📚Paper: www.nature.com/articles/s41...
💻Code: github.com/bbuchfink/di...

Aerobic sister lineage of breviates has gene-rich mitochondrial genomes Cho et al. describe a novel, aerobic sister lineage of Breviatea using flow cytometric single-cell sorting and genome amplification. The new lineage harbors gene-rich mitochondrial genomes, unlike Bre...

Aerobic sister lineage of breviates has gene-rich mitochondrial genomes
#microbiology #eukaryotes #mitochondria #protists #MicroSky #ProtistsOnSky
@cellpress.bsky.social
www.cell.com/current-biol...

New paper in mSystems! 🧵 - how much of your metagenome is actually bacterial/archaeal DNA? For many samples, nobody knows.

We built SingleM prokaryotic_fraction (SPF) to answer this, then ran it on >100,000 public metagenomes. 🧬🖥️🦠

Here's what we found 👇
doi.org/10.1128/msystems.01062-25

A novel planctomycetotal isolate from subsurface percolates belongs to the novel species Anatilimnocola aquadivae sp. nov. in the family Pirellulaceae
#microbiology #bacteria #NewSpecies #taxonomy #MicroSky
doi.org/10.1038/s415...

Image of the cover of the 1st volume of ISME Host Microbe a new official journal of the International Society for Microbial Ecology. Cover images shows a plant stomata with bacteria around and entering.

Excited to announce our new journal from @isme-microbes.bsky.social ISME Host Microbe is live and now accepting submissions. Look forward to receiving your papers! #Microsky 🧫 🦠

Automated genome mining predicts structural diversity and taxonomic distribution of peptide metallophores across bacteria Automated detection of metallophore biosynthesis reveals that metal-chelating non-ribosomal peptides are widespread, chemically diverse, and deeply rooted in bacterial evolution.

Are you interested in how to predict functions of natural product biosynthetic gene clusters (BGCs) and their products? And/or do you love metallophores and would love to identify their producers in microbiomes? Check out @zachreitz.bsky.social 's new paper!
elifesciences.org/articles/109... 1/n

The recovery of 12,789 genomes revealed the diversity, function, and microbial interactions of the geothermal spring microbiome www.biorxiv.org/content/10.64898/2026.03...

A very good likeness!

Genomic insights into adaptation and microevolution of two novel non-AOA #Nitrososphaeria, Acidarchaeum fankouense and Thermosulfuris yongpingense, in acid mine drainage ecosystems www.sciencedirect.com/science/arti...

Oops, typo in the family name in the abstract

Apolloniradiicaulis salifontis gen. nov., sp. nov., a New Prosthecate Aerobic Anoxygenic Phototroph Isolated from Lake Winnipegosis Region Salt Springs
#microbiology #NewSpecies #taxonomy #MicroSky
doi.org/10.3390/micr...

Thermophilic bacteria employ a contractile injection system in hot spring microbial mats Abstract. Bacterial contractile injection systems (CISs) are multiprotein complexes that facilitate the bacterial response to environmental factors or inte

Thermophilic bacteria employ a contractile injection system in hot spring microbial mats
#microbiology #thermophiles #bacteria #MicroSky
@isme-microbes.bsky.social
doi.org/10.1093/isme...

Diversity, ecology, cell biology and evolution of the Asgard archaea Nature Reviews Microbiology, Published online: 05 March 2026; doi:10.1038/s41579-026-01288-wThe Asgard archaea have become a cornerstone of archaeal research, particularly for studies aiming to unravel the origin and early evolution of eukaryotes. This Review outlines the current state of the research field focusing on these intriguing microorganisms and discusses future research directions aiming to resolve their diversity, ecology, cell biology and evolution.

New online! Diversity, ecology, cell biology and evolution of the Asgard archaea