Xabier Vázquez-Campos
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xabivc.bsky.social
Xabier Vázquez-Campos
@xabivc.bsky.social
180 followers 260 following 41 posts
Nearly-dry wet-lab microbiologist 😅

Biologist, (env.) microbiologist, bioinformatician. First gen.
Posts Replies Media Videos
Reposted by Xabier Vázquez-Campos
phylogenomics.bsky.social
Science is awesome ... www.cell.com/trends/biote... #violacein #pigments
One-pot production of colored bacterial cellulose
Zhou et al. report the one-pot production of colored bacterial cellulose (BC) as a sustainable alternative to petroleum-based fabrics. Metabolic engineering enhanced colorant yields, while co-culture ...
www.cell.com
November 16, 2025 at 5:04 AM
Reposted by Xabier Vázquez-Campos
wentsunghwang.bsky.social
#Archaea, #DPANN, #phylogenetic_reconciliation
New preprint online!
www.biorxiv.org/content/10.1...
Phylogenetic reconciliation supports a methanogenic ancestor of the Archaea and a derived origin for host-associated lineages
The phylogeny of the Archaea continues to be revisited and revised as new groups are discovered and phylogenetic methods improve, but key questions about their early evolution remain. It has been sugg...
www.biorxiv.org
November 13, 2025 at 7:28 PM
Reposted by Xabier Vázquez-Campos
jcamthrash.bsky.social
Introgression impacts the evolution of bacteria, but species borders are rarely fuzzy www.nature.com/articles/s41... #jcampubs
Introgression impacts the evolution of bacteria, but species borders are rarely fuzzy - Nature Communications
It is commonly thought that bacterial species borders tend to be fuzzy, due to frequent exchange of DNA. Here, Diop et al. quantify the patterns of gene flow between core genomes across 50 major bacte...
www.nature.com
November 13, 2025 at 7:40 PM
Reposted by Xabier Vázquez-Campos
jcamthrash.bsky.social
Augmenting microbial phylogenomic signal with tailored marker gene sets www.nature.com/articles/s41... #jcampubs
Augmenting microbial phylogenomic signal with tailored marker gene sets - Nature Communications
Marker genes used in microbial phylogenomics are limited to fixed gene sets selected from complete genomes. TMarSel is a flexible yet robust method for selecting any number of markers from genomes or ...
www.nature.com
November 13, 2025 at 8:54 PM
Reposted by Xabier Vázquez-Campos
jcamthrash.bsky.social
Assembly, architecture and functional roles of microbial surface layers www.nature.com/articles/s41... #jcampubs
Assembly, architecture and functional roles of microbial surface layers - Nature Reviews Microbiology
Surface layers (S-layers) are ubiquitous protein assemblies that coat prokaryotic cells, with their functional roles increasingly coming into focus. In this Review, Isbilir and colleagues discuss rece...
www.nature.com
November 13, 2025 at 7:44 PM
Reposted by Xabier Vázquez-Campos
jlsteenwyk.bsky.social
NEW pub in @science.org 🥳

Is it sponges (panels A & B) or comb jellies (C & D) that root the animal tree of life?

For over 15 years, #phylogenomic studies have been divided.

We provide new evidence suggesting that...

🔗: www.science.org/doi/10.1126/...
November 13, 2025 at 8:34 PM
Reposted by Xabier Vázquez-Campos
hansonmark.bsky.social
We wrote the Strain on scientific publishing to highlight the problems of time & trust. With a fantastic group of co-authors, we present The Drain of Scientific Publishing:

a 🧵 1/n

Drain: arxiv.org/abs/2511.04820
Strain: direct.mit.edu/qss/article/...
Oligopoly: direct.mit.edu/qss/article/...
A table showing profit margins of major publishers. A snippet of text related to this table is below. 1. The four-fold drain 1.1 Money Currently, academic publishing is dominated by profit-oriented, multinational companies for whom scientific knowledge is a commodity to be sold back to the academic community who created it. The dominant four are Elsevier, Springer Nature, Wiley and Taylor & Francis, which collectively generated over US$7.1 billion in revenue from journal publishing in 2024 alone, and over US$12 billion in profits between 2019 and 2024 (Table 1A). Their profit margins have always been over 30% in the last five years, and for the largest publisher (Elsevier) always over 37%. Against many comparators, across many sectors, scientific publishing is one of the most consistently profitable industries (Table S1). These financial arrangements make a substantial difference to science budgets. In 2024, 46% of Elsevier revenues and 53% of Taylor & Francis revenues were generated in North America, meaning that North American researchers were charged over US$2.27 billion by just two for-profit publishers. The Canadian research councils and the US National Science Foundation were allocated US$9.3 billion in that year. A figure detailing the drain on researcher time. 1. The four-fold drain 1.2 Time The number of papers published each year is growing faster than the scientific workforce, with the number of papers per researcher almost doubling between 1996 and 2022 (Figure 1A). This reflects the fact that publishers’ commercial desire to publish (sell) more material has aligned well with the competitive prestige culture in which publications help secure jobs, grants, promotions, and awards. To the extent that this growth is driven by a pressure for profit, rather than scholarly imperatives, it distorts the way researchers spend their time. The publishing system depends on unpaid reviewer labour, estimated to be over 130 million unpaid hours annually in 2020 alone (9). Researchers have complained about the demands of peer-review for decades, but the scale of the problem is now worse, with editors reporting widespread difficulties recruiting reviewers. The growth in publications involves not only the authors’ time, but that of academic editors and reviewers who are dealing with so many review demands. Even more seriously, the imperative to produce ever more articles reshapes the nature of scientific inquiry. Evidence across multiple fields shows that more papers result in ‘ossification’, not new ideas (10). It may seem paradoxical that more papers can slow progress until one considers how it affects researchers’ time. While rewards remain tied to volume, prestige, and impact of publications, researchers will be nudged away from riskier, local, interdisciplinary, and long-term work. The result is a treadmill of constant activity with limited progress whereas core scholarly practices – such as reading, reflecting and engaging with others’ contributions – is de-prioritized. What looks like productivity often masks intellectual exhaustion built on a demoralizing, narrowing scientific vision. A table of profit margins across industries. The section of text related to this table is below: 1. The four-fold drain 1.1 Money Currently, academic publishing is dominated by profit-oriented, multinational companies for whom scientific knowledge is a commodity to be sold back to the academic community who created it. The dominant four are Elsevier, Springer Nature, Wiley and Taylor & Francis, which collectively generated over US$7.1 billion in revenue from journal publishing in 2024 alone, and over US$12 billion in profits between 2019 and 2024 (Table 1A). Their profit margins have always been over 30% in the last five years, and for the largest publisher (Elsevier) always over 37%. Against many comparators, across many sectors, scientific publishing is one of the most consistently profitable industries (Table S1). These financial arrangements make a substantial difference to science budgets. In 2024, 46% of Elsevier revenues and 53% of Taylor & Francis revenues were generated in North America, meaning that North American researchers were charged over US$2.27 billion by just two for-profit publishers. The Canadian research councils and the US National Science Foundation were allocated US$9.3 billion in that year. The costs of inaction are plain: wasted public funds, lost researcher time, compromised scientific integrity and eroded public trust. Today, the system rewards commercial publishers first, and science second. Without bold action from the funders we risk continuing to pour resources into a system that prioritizes profit over the advancement of scientific knowledge.
November 11, 2025 at 11:52 AM
Reposted by Xabier Vázquez-Campos
stevenjrobbins.bsky.social
Metagenomics colleagues!

I'm looking for studies where both Illumina and ONT sequencing were performed on the same samples from soil, human, ruminent, and other sample types for comparison. Bonus if those studies include PacBio data.

Please help and share!
November 11, 2025 at 8:21 PM
Reposted by Xabier Vázquez-Campos
dzunkovam.bsky.social
Our Springer Nature book is just published! Big thanks to the co-editor Chris Rinke
@chrisrinke.bsky.social and to all book contributors, coming from @i2sysbio.es, @jgi.doe.gov and many other institutes I couldn't find on BlueSky
link.springer.com/book/10.1007...
#microsky #singlecell #genomics 🧪🦠
Single-Cell Omics in Microbiome Research
This volume introduces single-cell microbial (gen)omics as an innovative approach to study microbial diversity and symbiosis
link.springer.com
November 10, 2025 at 4:30 PM
Reposted by Xabier Vázquez-Campos
jcamthrash.bsky.social
The cell envelope of diderm bacteria: a unified scaffold, not a stack of layers www.sciencedirect.com/science/arti... #jcampubs
November 10, 2025 at 4:39 PM
Reposted by Xabier Vázquez-Campos
jcamthrash.bsky.social
The Hidden Viral Network: How Viruses Shape Microbial Adaptability and Biogeochemical Cycling in the Polyextreme Mars‐Analog Qaidam Basin Desert enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/... #jcampubs
The Hidden Viral Network: How Viruses Shape Microbial Adaptability and Biogeochemical Cycling in the Polyextreme Mars‐Analog Qaidam Basin Desert
Our study unveils the largely unexplored soil virosphere and virus-host interactions in the hyperarid Mars-analog desert of the Qaidam Basin. The findings underscore the vital ecological role of viru....
enviromicro-journals.onlinelibrary.wiley.com
November 10, 2025 at 4:40 PM
Reposted by Xabier Vázquez-Campos
jcamthrash.bsky.social
A century of research on Planctomycetota bacterial phylum, previously known as Planctomycetes academic.oup.com/femsre/advan... #jcampubs
November 10, 2025 at 4:43 PM
Reposted by Xabier Vázquez-Campos
gabaldonlab.bsky.social
#Review: “Quest for Orthologs in the era of Data Deluge and AI: Challenges and Innovations in Orthology Prediction and Data Integration” in JME

We reflect on how data explosion, new structural/AI tools, and complex features impact how we think about orthology link.springer.com/article/10.1...
Quest for Orthologs in the era of Data Deluge and AI: Challenges and Innovations in Orthology Prediction and Data Integration - Journal of Molecular Evolution
The rapid advancement of DNA sequencing technologies and computational algorithms has led to an unprecedented surge in genomic data, driven by several large-scale sequencing projects worldwide. Orthol...
link.springer.com
November 7, 2025 at 1:42 PM
Reposted by Xabier Vázquez-Campos
kmichie.bsky.social
This is amazing work lead by Tom (@tlitfin.bsky.social) in my team. Always trying to get more for less and making computing efficient. So satisfying making science resources go further. Boltz2 is great for protein structure prediction and hopefully LMI4Boltz extends its use. Code on GitHub… 🧶🧬
LMI4Boltz: Optimizing VRAM utilization to predict large macromolecular complexes with consumer grade hardware
AlphaFold2 has revolutionized structural biology by enabling the prediction of protein structures approaching experimental quality. AlphaFold3 extends this framework to support modelling broad biomole...
www.biorxiv.org
October 31, 2025 at 9:40 PM
Reposted by Xabier Vázquez-Campos
msmjetten.bsky.social
Nickel: Geochemistry, biochemistry and its role in chemical and biological evolutions
www.sciencedirect.com/science/arti...
Nickel: Geochemistry, biochemistry and its role in chemical and biological evolutions
Nickel is a versatile element that plays critical roles in Earth's geological and biological evolution, from the depths of the magmatic mantle to the …
www.sciencedirect.com
November 9, 2025 at 5:47 PM
Reposted by Xabier Vázquez-Campos
elisabethbik.bsky.social
Reformation of science publishing: the Stockholm Declaration
A call to action for universities, academies, science organizations and funders to unite and join this effort.
Bernhard Sabel and Dan Larhammar

royalsocietypublishing.org/doi/10.1098/...
Reformation of science publishing: the Stockholm Declaration | Royal Society Open Science
Science relies on integrity and trustworthiness. But scientists under career pressure are lured to purchase fake publications from ‘paper mills’ that use AI-generated data, text and image fabrication....
royalsocietypublishing.org
November 9, 2025 at 8:43 PM
Reposted by Xabier Vázquez-Campos
soreklab.bsky.social
Preprint: Bacteria sense virus-induced genome degradation via methylated mononucleotides

tinyurl.com/ch3damp

We show how molecular byproducts released during virus-induced cell exploitation are used as signals to trigger host immunity

Revealed by the amazing Ilya Osterman. See his thread below👇
November 6, 2025 at 10:39 AM
Reposted by Xabier Vázquez-Campos
jcamthrash.bsky.social
Widespread horizontal transfer and strong selection enhance microbial adaptation in Antarctic soils www.biorxiv.org/content/10.1... #jcampubs
November 5, 2025 at 4:25 PM
Reposted by Xabier Vázquez-Campos
cyanoney.bsky.social
Single-particle genomics uncovers abundant non-canonical marine viruses from nanolitre volumes

Very cool paper and method. I was looking forward to this coming out of preprint (short thread below on why)

www.nature.com/articles/s41...
Single-particle genomics uncovers abundant non-canonical marine viruses from nanolitre volumes - Nature Microbiology
Environmental micro-compartment genomics provides efficient and high-throughput single-particle DNA sequencing that captures overlooked members of microbial communities.
www.nature.com
November 5, 2025 at 3:34 PM
Reposted by Xabier Vázquez-Campos
jcamthrash.bsky.social
Metabolic diversity of the Ferrovales and potential contributions to iron oxidation www.biorxiv.org/content/10.1... #jcampubs
November 4, 2025 at 1:53 PM
Reposted by Xabier Vázquez-Campos
biorxiv-microbiol.bsky.social
A membrane-bound nuclease directly cleaves phage DNA during genome injection https://www.biorxiv.org/content/10.1101/2025.11.03.685801v1
November 3, 2025 at 4:16 PM
Reposted by Xabier Vázquez-Campos
jcamthrash.bsky.social
Direct carbon monoxide fixation via the bacterial and archaeal Wood–Ljungdahl pathways www.biorxiv.org/content/10.1... #jcampubs
November 1, 2025 at 6:28 AM
Reposted by Xabier Vázquez-Campos
jcamthrash.bsky.social
Subcellular organization of the archaeal cell www.sciencedirect.com/science/arti... #jcampubs
November 1, 2025 at 6:35 AM
Reposted by Xabier Vázquez-Campos
evgenii-protasov.bsky.social
Reduction of NAD and NMN on mineral surfaces with H2 reveals a functional role for the AMP moiety in a prebiotic context
#LifeOrigin #chemistry
www.nature.com/articles/s42...
Reduction of NAD and NMN on mineral surfaces with H2 reveals a functional role for the AMP moiety in a prebiotic context - Communications Chemistry
The evolutionary role of adenosine monophosphate (AMP) in cofactors like NAD remains poorly understood. Here, the authors reveal that the AMP moiety protects NAD from overreduction in hydrothermal and...
www.nature.com
November 3, 2025 at 8:57 PM
Reposted by Xabier Vázquez-Campos
precursorcell.bsky.social
This is going to be one of the biggest, most important features of AlphaFold @alphafold.bsky.social if further improved! Glycobiochemistry needs this bestfriend! #glycotime

academic.oup.com/glycob/artic...
Modeling glycans with AlphaFold 3: capabilities, caveats, and limitations
Abstract. Glycans are complex carbohydrates that exhibit extraordinary structural complexity and stereochemical diversity while playing essential roles in
academic.oup.com
October 31, 2025 at 8:51 PM