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.

In our latest study, we show that HGT of the ccyA gene from cyanobacteria enables some methanotrophic Methylococcaceae gammaproteobacteria to synthesize intracellular amorphous calcium carbonate (iACC) inclusions.

enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...

With @animalculum.bsky.social, we have studied the phylogeny of cryptophyte nucleomorphs within an enriched dataset of red algae. Surprisingly, they seem to be related to Cyanidiophytina. The origin of red secondary plastids remains an open question!

nph.onlinelibrary.wiley.com/doi/10.1111/...

Fragile Research Systems, Brain Drain, and Predatory Publishing in Under-resourced Countries Abstract. Many countries with lower research & innovation capacity face persistent constraints in building stable research systems. Chronic underfundin

Latest output of the European Academy of Microbiology Task Force on Predatory Publishing Practices, initiated and steered by Stipan Jonjić and Ceren Karahan:

Fragile Research Systems, Brain Drain, and Predatory Publishing in Under-resourced Countries url: academic.oup.com/microlife/ar...

We have just published a short note on archaeal phylogeny: complex mixture models support a deep placement of Methanonatronarchaeia within Euryarchaea and indicate that three recently described groups (Halorutilales, Afararchaeaceae, and Ordosarchaeia) are actually the same.

shorturl.at/5GMpU

Redox distribution of Asgard archaea and co-occurring taxa in microbial mats from an early Proterozoic ecosystem analog Eukaryotes originated from the symbiosis of an Asgard archaeon, the alphaproteobacterial ancestor of mitochondria, and possibly additional bacterial contributions. This transition occurred in redox-transition environments such as microbial mats or shallow sediments ~2 billion years ago, when atmospheric oxygen was far lower than today. We investigated Asgard-enriched microbial mats from the low-oxygen, sulfidic Catherine volcano lake (Afar region, Ethiopia), mimicking early Proterozoic conditions. 16S rRNA gene metabarcoding, metagenomics, and metagenome-assembled genome analyses across redox-stratified layers of in situ and mesocosm-maintained mats revealed that Asgardarchaeota thrived in the sulfate-reduction zone, mainly co-occurring with Desulfurobacterota-Myxococcota, among others. Lokiarchaeia and Thorarchaeia preferred anoxic layers. Within Heimdallarchaeia, Heimdallarchaeales were enriched in upper layers, correlating with oxygen-tolerant hydrogenase and sulfate-reduction genes, and Hodarchaeales, in anoxic layers, correlating with methanogenesis. Although reactive-oxygen-species defense mechanisms were widespread, Asgardarchaeota lacked aerobic respiration. These results support the idea that Asgard archaea engaged primarily in syntrophic interactions with sulfate-reducers under early-Earth-like conditions. ### Competing Interest Statement The authors have declared no competing interest. European Research Council, https://ror.org/0472cxd90, 101141745, 787904 Agence Nationale de la Recherche, ANR-23-CE02-0016-01, ANR-22-CE02-0012 Gordon and Betty Moore Foundation, https://ror.org/006wxqw41, GBMF9739

Redox distribution of Asgard archaea and co-occurring taxa in microbial mats from an early Proterozoic ecosystem analog | bioRxiv www.biorxiv.org/content/10.64898/2026.03...

Amazing! (and very surprising)

So you are using IQ-TREE to estimate a tree for "deep time" phylogenetics using amino acid alignments. There is a lot of confusion about how to test model fit. Here are some suggestions.

Living patescibacterial (CPR) cells are a rare sight! Meet Strigamonas methylophilicida, a parasite of methylotrophic proteobacteria we just described in our latest paper:

doi.org/10.1128/mbio...

Interested in microbial proteins and their diversity? 🖥️🧬🦠

We have recently released the Amino Acid Sequence Toolkit (AASTK). AASTK is designed to work with the GlobDB to create and work with datasets of protein sequences.

AASTK currently consists of 4 tools:
- CASM
- PASR
- CUGO
- Meta

1/

Tom Cavalier-Smith in Cornwall UK 23 August 2017, photo by Neal C-S

I am happy to share the unfinished but nevertheless fascinating autobiography of the late Thomas Cavalier-Smith, written in 2020, shortly before Tom passed away in 2021. I thank Ema Cavalier-Smith for sharing the text with me. I recently finished curating […]

[Original post on biologists.social]

Before he passed away in 2021, Tom Cavalier-Smith had drafted parts of his autobiography. It's now 'published' because Gáspár Jékely put a lot of effort in! Please enjoy and share: doi.org/10.5281/zeno...

This is great! Many thanks to Gáspár @jekely.biologists.social.ap.brid.gy for this effort.

Attached image

OrthoSNAP v1.6.0 is out. If you process large phylogenomic datasets, this release is built for your workflow. (1/3)

We are happy to welcome Xianzhe Gong to the team! His expertise in microbial metabolism and related fields will help us better characterize our collection of MAGs and cultured organisms from many different environments.

Playing with a new toy to study our favorite microbial mats.

Puri talking at the "Cell biology of eukaryogenesis" meeting organized by the @sbcf.bsky.social

First sampling of the year in a sunlit Parisian forest.

2026 kicks off with new faces in the lab!
We’re excited to welcome Dina Boukheloua, Eliott Tempez, and Pierre van Ettro, who will be working on endosymbionts in protists, archaeal genome evolution, and aquatic amoeba diversity. Welcome to the team!

With our old friends Sergey, Luis and Guifré, we have published a minireview in @currentbiology.bsky.social about aphelids, the sister group to fungi, including why we think they are not fungi but, nevertheless, key to understand early fungal evolution.

authors.elsevier.com/a/1mH793QW8S...

Near the end of the year, we are excited to welcome three new members to the team: Inés Ochoa (PhD student), and Charley McCarthy and Eva Zanditenas (postdocs). They will work on different projects using experimental and bioinformatics approaches.

Microbial eukaryotes keep challenging assumptions about eukaryotic cell and genome biology.

Our upcoming workshop explores the frontier of protist genomics and how it shapes cell biology, ecology and evolution.

Please save the date! Talks, posters and ECR events

Websites and details coming soon

SMBE2026 Symposium 12 | Reconstructing the deep Tree of Life: challenges and new approaches

SMBE2026 Symposium 12 | Reconstructing the deep Tree of Life: challenges and new approaches

📨 Abstract submission
smbe2026.org/abstracts

📋 Programme details
smbe2026.org/programme

#SMBE2026

Those interested in performing maximum likelihood phylogenomic analysis on data sets made up of eukaryotic nuclear genes using site heterogeneous mixture models like C60, I suggest you use the ELM model in IQ-TREE instead of the LG model /1

Discussing the origin and evolution of life in an ancient church during the meeting of the French Astrobiology Society

A Cell So Minimal That It Challenges Definitions of Life | Quanta Magazine The newly described microbe represents a world of parasitic, intercellular biodiversity only beginning to be revealed by genome sequencing.

According to the microbial ecologist Puri López-García, pictured here at a salt flat in the Chilean Andes, some 25% to 50% of all bacterial cells may be parasites of other cells.

Phylogeny-aware Simulations Suggest a Low Impact of Unsampled Lineages in the Inference of Gene Flow During Eukaryogenesis Abstract. The topologies of gene trees are broadly used to infer horizontal gene transfer events and characterize the potential donor and acceptor partners

Bernabeu, @microbiobits.bsky.social and @tonigabaldon.bsky.social use simulations to test for the robustness of inferred relative timings of gene transfers in the lineage leading to the ancestor of eukaryotes

🔗 doi.org/10.1093/gbe/evaf190

#genome #evolution

Dive into our November issue featuring:

🪆nested archaeal symbioses
🌱microbiota driven drought responses in plants
🏗️ BAM complex in Bacteroidota
💨microbial fermentative growth in the gut
🍸hospital-specific phage therapy cocktail

and much more..!

www.nature.com/nmicrobiol/v...

This paper has been a must! Great collaboration with @mkrupovic.bsky.social and @yifanzhou.bsky.social, a N&V by a legend of halophilic archaea tinyurl.com/yc3dcv72, and one picture of one of our expeditions to Dallol making the cover of the November issue of @natmicrobiol.nature.com

rdcu.be/eLtCH

How did life begin, and why does it matter? Scientists are tracing early microbial life–from LUCA to multicellularity–to unlock insights for biotech, climate science and even space exploration. Read the article: asm.org/articles/202...