Xabier Vázquez-Campos

Phenotypic and genomic characterization of Bathyarchaeum tardum gen. nov., sp. nov., a cultivated representative of the archaeal class Bathyarchaeia
#microbiology #archaea
www.frontiersin.org/journals/mic...

Systematic benchmarking of basecalling models for RNA modification detection with highly-multiplexed nanopore sequencing Nanopore direct RNA sequencing (DRS) holds promise for advancing our understanding of the epitranscriptome by detecting RNA modifications in native RNA molecules. Recently, Oxford Nanopore Technologie...

Fresh preprint from the
@novoalab.bsky.social !😀📌 Do you want to barcode up to 96 #RNA samples in your #nanopore flowcells? How well do RNA #modification-aware models perform? What if there is #noBasecallingModel for your modification-of-interest? Find it out here!😊 www.biorxiv.org/content/10.1...

GitHub - lh3/longdust: Identify long STRs, VNTRs, satellite DNA and other low-complexity regions in a genome Identify long STRs, VNTRs, satellite DNA and other low-complexity regions in a genome - lh3/longdust

Longdust, a new tool to identify highly repetitive STRs, VNTRs, satellite DNA and other low-complexity regions (LCRs). Similar to SDUST but for long regions.
github.com/lh3/longdust

Figure 3 from the preprint https://doi.org/10.31223/X59T74 showing microbial strategies for biomining and bioremediation across space and Earth applications. See the article for a full caption.

🪐🌎 "A search for life in the universe advances life on Earth" preprint doi.org/10.31223/X59...

@cubouldearth.bsky.social alum @tacaro.bsky.social (Postdoc Caltech) is a co-author, helping show how astrobiology research improves life on earth through sustainability technology, remediation, & biotech

Manipulation of the nucleotide pool in human, bacterial and plant immunity - Nature Reviews Immunology Modification of the nucleotide pool is emerging as key to innate immunity in animals, plants and bacteria. This Review explains how immune pathways conserved from bacteria to humans manipulate the nuc...

We wrote a review on the free nucleotide pool as a central playground in human, bacterial, and plant immunity – now out in Nature Reviews in Immunology

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

Was fun to write this piece with Dina Hochhauser!

Here is a thread to explain the premises

1/

Unwelcome guests: characterizing the ecological niche of insertion sequences within prokaryotic genomes www.biorxiv.org/content/10.1... #jcampubs

Phylogenomics of Asgard archaea reveals a unique blend of prokaryotic-like horizontal transfer and eukaryotic-like gene duplication. Asgard archaea hold a pivotal position in the tree of life as the closest known relatives to eukaryotes and are therefore crucial for understanding eukaryogenesis. Earlier genomic analyses revealed th...

Phylogenomics of Asgard archaea reveals a unique blend of prokaryotic-like horizontal transfer and eukaryotic-like gene duplication.

Papier très intéressant qui cite mon preprint sur le système KJE des chaperonnes. Fait plaisir de voir ce genre de travail

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

Biologist folk (especially in evolutionary biology and/or ecology, but it don’t matter):

Can you give me your favorite examples of trade offs in biology? Organism or system don’t matter. Primary literature or reviews preferred.

Microbial metal physiology: ions to ecosystems Nature Reviews Microbiology - Metal ions are required for all cells, and their homeostasis relies on ancient mechanisms that facilitate their import, distribution and storage. In this Review,...

Metal ions are universally required for life, and many of the foundational principles of metal homeostasis have emerged from studies of microbial systems. In this review, I provide a introductory overview targeted to those new to the field.
#MicroSky #Metals

rdcu.be/eycU2

New online! Hunting archaeal viruses

Figure 2. Contact-dependent predation relies on specific adaptations of the predator cell envelope. (a) Envelope-spanning multiprotein machineries, including type IV pili (T4P, in shades of pink) and secretion systems (shades of brown and orange), participate in various predatory mechanisms. For clarity, subcomplexes (such as the OM secretin of T4P) are represented as single objects rather than complex oligomeric assemblies; for further details about molecular composition, structural architecture, and annotations of these systems, we refer the reader to Refs. 14••, 42••, 43 (Kil and Tad systems), 39, 44 (T4aP), 35, 45 (T4aSS), 30••, 46 (T9SS and grappling hook), 30••, 47 (T6SS), and 32, 15••, 42••, 48 (T3SS*). (i) Tight adherence (Tad) and type IVa (T4a) pili located at the prey-contacting cell pole are essential for B. bacteriovorus predation, but their precise function is unclear. (ii) L. enzymogenes contact-dependent killing of prey involves a type IVa secretion system (T4aSS), hypothesised to deliver toxic effectors into prey cells. (iii) In liquid environments, prey capture by Aureispira sp. CCB-QB1 depends on grappling hooks consisting of a GhpA heptamer, a T9SS substrate. Subsequent prey killing and lysis is proposed to rely on the contraction of an unusual T6SS harbouring antenna-like structures of unknown function. (iv) M. xanthus prey killing and lysis are mediated by the interplay of a Tad-like system, termed the Kil system, and a needle-less type III secretion system complex (T3SS*, lacking components usually required for toxic effectors delivery). Both systems localise at prey contact sites and are hypothesised to form a complex for the delivery of toxic effectors into prey cells via specialised Tips located at the extremity of the Kil pilus. (b) During epibiotic predation, B. exovorus uses its nonflagellated pole to form a stable junction with the prey OM. (i) Representative Cryo-EM image showing B. exovorus attached to the C. crescentus prey surface (…

Figure 1. Contact-dependent predation strategies among bacteria. (a–d) Physical contacts between predator (light blue) and prey (dark grey) cells are highlighted with orange halos. A characterised prey–predator pair was selected to illustrate each predation strategy. All represented prey cells are diderm bacteria; the periplasm is indicated when relevant. Plain arrows indicate transitions between key predation steps. Dashed arrows represent active cell movement. Indicative scale bars are included on each panel. (a) Epibiotic predation. Bdellovibrio exovorus firmly attaches to the surface of prey, including Caulobacterales species (Caulobacter crescentus is depicted here) and consumes their contents from outside (prey shown in pale grey). (b) Endobiotic predation. Upon contact with a broad range of proteobacteria, such as Escherichia coli, Bdellovibrio bacteriovorus transiently attaches to the prey surface before invading its periplasm and digesting the prey from inside. (c) Ixotrophy. Multicellular filaments of Aureispira sp. CCB-QB1 capture, immobilise, and lyse their prey, which include Vibrio (e.g. Vibrio campbellii) and Cyanobacteria species. (d) Group attack. Myxococcus xanthus uses social motility to efficiently invade prey colonies (e.g. E. coli). M. xanthus kill and lyse prey cells in a contact-dependent manner. M. xanthus can also prey on monoderm species, but efficient prey lysis requires bacteriolytic factors secreted in the environment in addition to direct contact 14••, 15••, 16. (c,d) Prey lysis upon contact is depicted with dashed lines.

a compendium of vampires and pirates
(and their armories). actually more of an encyclopedia...

by @coralietesseur.bsky.social (drawings made by hand!⭐), @ysantin.bsky.social & @lalouxlab.bsky.social

read! > www.sciencedirect.com/science/arti...
#MicroSky

An Asgard archaeon from a modern analog of ancient microbial mats It has been proposed that eukaryotic cells evolved via symbiosis between sulfate-reducing bacteria and hydrogen-producing archaea. Here we describe a highly enriched culture of a novel Asgard archaeon...

📣 New paper alert!
One of the most exciting projects we've done in recent years is now out on BioRxiv: "An Asgard archaeon from a modern analog of ancient microbial mats".

Glimpse into early complex life! ❄️🦠 🔬🧬

www.biorxiv.org/content/10.1.... A thread...

An Asgard archaeon from a modern analog of ancient microbial mats 👀 www.biorxiv.org/content/10.1... #jcampubs

Microbial Databases, Software Tools, and Web Services Publish your microbial database or software tool in MRA to gain recognition, citations, and community trust.

Call for manuscript submissions on publicly available databases, software tools, and web-based services that can be used as a resource for the microbiology community. Happy to answer any questions.
journals.asm.org/journal/mra/...

once upon a time "...the bacterial ribosome was thought to be composed of a fixed set of ribosomal proteins (RPs) and ribosomal RNA (rRNA), ensuring precise translation"

ribosomologists take note: the role of heterogeneity of the ribosomes in the bacterial stress response 👇

#RNASky #MicroSky

An Asgard archaeon from a modern analog of ancient microbial mats https://www.biorxiv.org/content/10.1101/2025.07.22.663070v1

Unusual protein found in a Loki Asgard Archaea.

Check out this weird protein we found in a Loki Asgard archaea.🧬🧶Only found relatives in other Lokis. 🤔

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

Wild cell structures in a new Asgard, Nerearchaeum marumarumayae. www.biorxiv.org/content/10.1...

a cartoon of two spidermans standing in front of a nypd van ALT: a cartoon of two spidermans standing in front of a nypd van

"Researchers value null results, but struggle to publish them"
-Nature

www.nature.com/articles/d41...

A dinoflagellate-infecting giant virus with a micron-length tail Viral infection is a ubiquitous source of marine plankton mortality, but relatively few viruses that infect phytoplankton have been characterized. Here we describe a virus, PelV-1, with unusual morpho...

Excited that this is out as a preprint! ❇️

We are introducing a novel dinoflagellate giant virus that holds so many mysteries!

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

🚨 FIRST PAPER ALERT 🚨

My first research paper I've been involved with is out now as a preprint 🦠🥳🦠

#archaea #microsky #PhD

So excited to finally show the world a project years in the making. A huge group effort with lots of expertise leading to a unique #Asgard syntrophy story. Very fortunate to have been involved in cultivating and analysing this wonderful organism ❤️

An Asgard archaeon from a modern analog of ancient microbial mats It has been proposed that eukaryotic cells evolved via symbiosis between sulfate-reducing bacteria and hydrogen-producing archaea. Here we describe a highly enriched culture of a novel Asgard archaeon...

This was fun! Folding whole proteomes… looking at tomogram, looking at genomes🤩 lots to discover!🧬🧶

@snobsi.bsky.social @juliameltzer.bsky.social @kmichie.bsky.social @debnathghosal.bsky.social @brendanburns999.bsky.social @iduggin.bsky.social (and a quite few others I can't find in bluesky)

An Asgard archaeon from a modern analog of ancient microbial mats It has been proposed that eukaryotic cells evolved via symbiosis between sulfate-reducing bacteria and hydrogen-producing archaea. Here we describe a highly enriched culture of a novel Asgard archaeon...

Our new preprint with a new #Asgard from stromatolites (and its Desulfobacterota companion). Complete circularised genomes of both, cool #cryoem images, protein modelling, etc

Big group effort with a lot of people involved
#archaeasky #archaea
www.biorxiv.org/content/10.1...

Are any of my followers aware of microbes that code for aerobic metabolism but can not grow aerobically?

That is are there physiologically obligate anaerobes that contain genetic machinery for oxidative metabolism?

#microsky

Detecting Foldback Artifacts in Long Reads https://www.biorxiv.org/content/10.1101/2025.07.15.664946v1

Wow, this is something. Interested to read this to see where time is lost (fixing AI errors, hallucinations, repetitions, and slop?). This is why we need hard data, because human brains perceive a lot of things that aren’t actually true.

Interpreting UniFrac with Absolute Abundance: A Conceptual and Practical Guide www.biorxiv.org/content/10.1... #jcampubs

The MicrobeAtlas database: Global trends and insights into Earth’s microbial ecosystems www.biorxiv.org/content/10.1... #jcampubs