Xabier Vázquez-Campos

Structure of an archaeal ribosome reveals a divergent active site and hibernation factor - Nature Microbiology Sequence and structural analyses reveal a divergent peptidyl transferase centre and a hibernation factor in archaea.

Out now:

Structure of an archaeal ribosome reveals a divergent active site and hibernation factor

@jhdcate.bsky.social @banfieldlab.bsky.social @diptinayak.bsky.social & co

#microsky

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

ISME Communications is expanding its scope to include Taxonomy and Nomenclature, recognizing their essential role in microbial ecology.
Read more: isme-microbes.org/taxonomy-and...
#microbes #taxonomy

Metal speciation and bioavailability in microbial growth media www.biorxiv.org/content/10.1... #jcampubs

A Systematic Investigation of Overfitting in Maximum Likelihood Phylogenetic Inference Maximum Likelihood (ML) tree inference reconstructs phylogenies from Multiple Sequence Alignments (MSAs). Since MSAs are inherently noisy, ML tools may experience overfitting, whereby the inferred top...

New preprint: ML tree inference tools such as IQ-Tree and RAxML-NG do typically not overfit the data during tree searches: www.biorxiv.org/content/10.1...

Alice: fast and haplotype-aware assembly of high-fidelity reads based on MSR sketching We introduce Mapping-friendly Sequence Reduction (MSR) sketches, a sketching method for high-fidelity (HiFi) long reads, and Alice, an assembler that operates directly on these sketches. MSR produces ...

Our preprint on our new metagenomic HiFi assembler Alice is out 🥳 Based on a *new sketching method* (🧵1/6)
👉 Preprint www.biorxiv.org/content/10.1...
👉 Github github.com/rolandfaure/...

DFAST (sorta PGAP fromthe DDBJ)
Not overly complicated to add custom annotation sources (blastn, blastp, rps-blast, hmm-based...)

Welcome to the social media account of the International Microbiology Literacy Initiative (IMiLI). Nearly 1,000 researchers freely contribute to the IMiLI project integrating microbiology into education providing downloadable resources for all. Explore at imili.org

Apple is entering the protein folding arena.
SimpleFold: Folding Proteins is Simpler than You Think arxiv.org/abs/2509.18480 🧬🖥️🧪 github.com/apple/ml-sim...

Interested in removing particle-associated microbes from particles for eg flow cytometry, culturing, or other single-cell microbiology purposes? Led by graduating PhD stdnt Jordan Coelho:

Detergent-based separation of microbes from marine particles journals.asm.org/doi/10.1128/... #jcampubs 🌊

MicroMates: Oceanic Odyssey A card game where science meets adventure – dive into the invisible world of microorganims!

Check out MicroMates: Oceanic Odyssey by Minkor AB on @kickstarter.com www.kickstarter.com/projects/170...

Have you ever looked at some differentially occurring gene clusters in a microbial #pangenome and thought to yourself "I wonder if they contribute to any metabolic modules"?

With the most recent changes, the answer is a few clicks away in #anvio 😇

We can't have innovation if we block out those with new ideas or who challenge old ones. Reviewers can challenge without being assholes, and we need to acknowledge such behaviors exist and need to be expunged. 🧪

Extremely acidophilic filamentous fungi are more prevalent in diverse ecosystems than previously documented - Scientific Reports Scientific Reports - Extremely acidophilic filamentous fungi are more prevalent in diverse ecosystems than previously documented

Vietnam reveals a hidden treasure: 12 new species of acid-loving fungi and the rediscovery of Acontium velatum 🍄. Out of the 100 samples studied, most thrive at pH <1, heat & organic solvents —showing big biotech potential. Read the full study👉

EcoFoldDB: Protein Structure-Guided Functional Profiling of Ecologically Relevant Microbial Traits at the Metagenome Scale enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...

Compression of protein secondary structures enables ultra-fast and accurate structure searching Protein structure prediction has undergone a revolution with the advent of AI- based algorithms, such as AlphaFold and RoseTTAFold. As a result, over 200 million predicted protein structures have been...

"We show that, despite this compression factor, SSEs can be used as a highly effective tertiary structure comparison tool, with accuracy that approaches that of Foldseek, while offering a 200-fold speedup. "

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

Naiavirus: an enveloped giant virus with a pleomorphic, flexible tail - Nature Communications Rodrigues and Queiroz et al. report the discovery of Naiavirus, the largest enveloped virus, isolated from a Brazil biome. With an oval capsid and flexible tail, its giant genome holds many novel gene...

Naiavirus: an enveloped giant virus with a pleomorphic, flexible tail
nature.com/articles/s41467-025-63463-6

agtools: a software framework to manipulate assembly graphs https://www.biorxiv.org/content/10.1101/2025.09.14.676178v1

X-Mapper 🦠🧬🧪 - a sequence aligner developed for microbes, now on Bioconda! 🚀
• 11–24× fewer suboptimal alignments (same for human genome)
• 3–579× lower inconsistency
• improves on ~30% of reads aligned to non-target species
github.com/mathjeff/map...
bioconda.github.io/recipes/x-ma...
#microsky

A review on microbial-biofilm mediated mechanisms in marine microplastics degradation - Antonie van Leeuwenhoek Although the buildup of plastic in the marine environment is a long-standing problem, it has only lately been realized how relevant this pollution may be to the ocean. Microplastic fragments are an em...

A review on microbial-biofilm mediated mechanisms in marine microplastics degradation link.springer.com/article/10.1... #jcampubs

Aquatic fungal diversity assessment through metagenomics is still limited to current databases aslopubs.onlinelibrary.wiley.com/doi/10.1002/... #jcampubs

Why Do Filamentous Actinomycetota Produce Such a Vast Array of Specialized Metabolites? www.annualreviews.org/content/jour... #jcampubs

A deep-sea hydrothermal vent worm detoxifies arsenic and sulfur by intracellular biomineralization of orpiment (As2S3)
#microbiology #DeepSea
@plosbiology.org
journals.plos.org/plosbiology/...

Translational coupling of neighboring genes in prokaryotes | Journal of Bacteriology Prokaryotic genes are arranged in operons, with functionally related genes often located adjacent to one another (1). There are several ways in which the operonic organization of genes facilitates the...

Check out our new paper: a review of translational coupling, the phenomenon where translation of one prokaryotic gene can promote translation of the gene downstream. We cover the history, and delve into the mechanism, which is still not fully understood. journals.asm.org/doi/10.1128/...

“Launching the IUCN Microbial Conservation Specialist Group as a global safeguard for microbial biodiversity”- paper published and group assembled! I'm delighted to announce the publication of "Launching the IUCN Microbial Conservation Specialist Group as a global safeguard for microbial biodiversity" -- a short publication in Nature, written by the new IUCN Microbe Group, of which I am a part! The paper introduces the need for a Specialist Group focused on microorganisms, microbial communities, and the connection between microbes and health of environments and all other organisms.

“Launching the IUCN Microbial Conservation Specialist Group as a global safeguard for microbial biodiversity”- paper published and group assembled!

I'm delighted to announce the publication of "Launching the IUCN Microbial Conservation Specialist Group as a global safeguard for microbial…

Looking for a new approach to studying or eliminating phages? Check out our study introducing anti-phage ASOs (antisense oligos) out in @Nature today. nature.com/articles/s4158…

Atomic resolution structures of the methane-activating enzyme in anaerobic methanotrophy reveal extensive post-translational modifications
#microbiology #methane #archaea
@natcomms.nature.com
www.nature.com/articles/s41...

Phage defence-system abundances vary across environments and increase with viral density royalsocietypublishing.org/doi/full/10.... #jcampubs

Dissecting microbial communities with single-cell transcriptome analysis Revealing insights into the function of microbial communities requires moving beyond measuring bulk taxonomic composition to detecting interactions between subpopulations. Following the transformative...

Dissecting microbial communities with single-cell transcriptome analysis www.science.org/doi/abs/10.1... #jcampubs

Phage-encoded homing endonucleases attenuate bacterial immunity The arms race between bacteria and bacteriophages (phages) gave rise to multiple layers of antagonistic mechanisms, many of which remain unexplored. Here, we investigated the anti-phage defense system...

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

#phagesky #phage

Why do bacteria accumulate antiphage defence systems? royalsocietypublishing.org/doi/abs/10.1... #jcampubs