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Alejandro Manzano Marín

@amanzanom.bsky.social

1.8K followers 440 following 290 posts

Senior Scientist 👨🏽‍🔬 @dome-vienna.bsky.social, @univie.ac.at
🇲🇽🇪🇺(🇦🇹🇫🇷🇪🇸) Symbionts, bacteria, insects, leeches, viruses, bioinformatics, evolution, genomics. Opinions are my very own.

#SymbioSky

https://besymblab.univie.ac.at/
https://ecoevo.social/@amanzanom

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Alejandro Manzano Marín @amanzanom.bsky.social · Apr 22

After many years in the making (and an eternal cycle of adding new data....) our work on the discordance among phylogenomic datasets in #aphids is out!

@dome-vienna.bsky.social @inrae-france.bsky.social 🧪 #EvolSky

doi.org/10.1101/2024...

Phylogenetic trees displaying incongruence between reconstructions based on aphid and endosymbiotic bacteriasequences

Alejandro Manzano Marín

@amanzanom.bsky.social

We have #leech #cocoons!

The hard work of @pegah-kalatehjari.bsky.social already paying off. Soon to come, baby leeches @dome-vienna.bsky.social

@fwf-at.bsky.social @univie.ac.at

November 27, 2025 at 10:27 AM

Alejandro Manzano Marín

@amanzanom.bsky.social

Really cool #review

Natural and artificial variations of the standard #geneticCode

Of course with mention of #endosymbiont lineages

doi.org/10.1016/j.cu...

November 21, 2025 at 10:37 AM

Reposted by Alejandro Manzano Marín

The Probst Lab

@probstlab.bsky.social

We are excited to share @probstlab.bsky.social's latest publication on the diversity of CRISPR-Cas spacers, led by @katharinasures.bsky.social !! 🧬

Have a read!! ➡️ doi.org/10.1093/gbe/...

@emilruff.bsky.social @alexjaffe.bsky.social @geomicrosoares.bsky.social & others not in Bluesky!

Acquisition of Spacers from Foreign Prokaryotic Genomes by CRISPR-Cas Systems in Natural Environments

Abstract. Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) systems of bacteria and archaea provide immunities

doi.org

November 17, 2025 at 12:09 PM

Reposted by Alejandro Manzano Marín

Mark A. Hanson

@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 Alejandro Manzano Marín

Dan Brockington

@danbrockington.bsky.social

Profits from scientific publishing are eye-watering, costing us billions. In ‘The Drain of Scientific Publishing’ (arxiv.org/abs/2511.04820), (building on ‘The Strain of Scientific Publishing’ doi.org/10.1162/qss_a_00327) we show how it is harmful – and unnecessary.

The Drain of Scientific Publishing

The domination of scientific publishing in the Global North by major commercial publishers is harmful to science. We need the most powerful members of the research community, funders, governments and ...

arxiv.org

November 12, 2025 at 11:41 AM

Reposted by Alejandro Manzano Marín

Sullivan Lab at OSU

@sullivan-lab.bsky.social

🚨vConTACT3 preprint live!🚨(Peer Review soon...!)

vConTACT3 delivers a unified, scalable, and transparent framework for genome-based virus taxonomy — helping translate big viral data into systematic classification.

🔗 Read the preprint: doi.org/10.1101/2025...

Improvements details below 👇

Scalable and systematic hierarchical virus taxonomy with vConTACT3

Viruses are key players in diverse ecosystems, but studying their impacts is technically and taxonomically challenging. Taxonomic complexities derive from undersampling, diverse DNA and RNA genomes wi...

doi.org

November 7, 2025 at 4:36 PM

Alejandro Manzano Marín

@amanzanom.bsky.social

.... 2nd work

2) Parallel #evolution of #Bacteroidota as Long-Term #endosymbionts of #insects

by Jinyeong Choi, Cong Liu, Pradeep Palanichamy, Yumiko Masukagami, Hirotaka Tanaka, Takumasa Kondo, Matthew E. Gruwell, @filiphusnik.bsky.social

doi.org/10.1101/2025...

#SymbioSky @oistedu.bsky.social

Parallel Evolution of Bacteroidota as Long-Term Endosymbionts of Insects

Symbiotic relationships transform diverse aspects of both symbiont and host biology. The most visible changes include a massive reduction of the endosymbiont genome and the development of novel host o...

doi.org

November 5, 2025 at 9:39 AM

Alejandro Manzano Marín

@amanzanom.bsky.social

Two great works by @filiphusnik.bsky.social group @oistedu.bsky.social on scale insect's #symbioses.

1) Genomic diversity and functional potential of facultative bacterial #symbionts across #scaleInsects

by Pradeep Palanichamy, Jinyeong Choi, Arno Hagenbeek

doi.org/10.1101/2025...

#SymbioSky

Genomic diversity and functional potential of facultative bacterial symbionts across scale insects

Microbial symbionts play pivotal roles in the physiology, ecology, and evolution of insects. While obligate symbionts have been extensively characterized in insects feeding on nutritionally poor diets...

doi.org

November 5, 2025 at 9:34 AM

Reposted by Alejandro Manzano Marín

Ramya Ganesan

@chaintist.bsky.social

Had to draw a cartoon for this fascinating finding!
Defensive fungal symbiosis on insect hindlegs: www.science.org/doi/10.1126/...
#SymbioSky

A cartoon/ digital drawing summarising the findings of the paper "Defensive fungal symbiosis on insect hindlegs" by T. Nishino et al published in 2025. On the top left, a female Megymenum gracilicorne bug shows off symbiotic organs on the hind legs where she carries Ascomycota fungi. These were previously assumed to be Tympanal organs in these bugs but only females had them?; that didnt make a whole lot of sense to the authors...To the right of the bug is a row of eggs lying side by side. The paper shows that the bugs deposit the symbiotic fungi on the egg surface after egg-laying. Next on the image, fungal conidia grow on the egg surface. The eggs are pinkish in colour. A few fungi wear sunglasses like they are body guards. The paper shows that they protect the eggs from Trissolcus brevinotaulus, a parasitoid wasp, that likes to lay its eggs inside the developing bug's eggs. There are two wasps in this cartoon "eyeing" the fungi and looking frustrated. Eggs turn from whitish to pinkish within 10-days because they are reflecting the body colour of the nymph within the eggs.

November 1, 2025 at 4:59 PM

Reposted by Alejandro Manzano Marín

Mark A. Hanson

@hansonmark.bsky.social

PhD studentship for interested chinese nationals funded by the China Scholarship Council!

Come work with us to investigate how innate immunity works in an important agricultural pest, and disentangle how the immune system evolves. 🇬🇧🇨🇳

For more info, see: bit.ly/4ntrsEe
#Drosophila #Aphid #Immunity

An advertisement for a PhD doing aphid immunity work

October 28, 2025 at 1:44 PM

Reposted by Alejandro Manzano Marín

Javier Santoyo

@jsantoyo.bsky.social

Commentary: a review of technical considerations for planning an RNA-Sequencing experiment. #RNAseq #TechnicalConsidertions #ExperimentDesign #LibraryPrep #DataAnalysis #BMCgenomics 🧪🧬 🖥️
bmcgenomics.biomedcentral.com/articles/10....

October 27, 2025 at 3:31 PM

Alejandro Manzano Marín

@amanzanom.bsky.social

The Endosymbiont consortia of two #Cixiidae #Planthoppers reveal an ancient #Symbiosis with ‘Candidatus #Mirabilia symbiotica’

#SymbioSky

doi.org/10.1111/1758...

The Endosymbiont Consortia of Two Cixiidae Planthoppers Reveal an Ancient Symbiosis With ‘Candidatus Mirabilia Symbiotica’

Many insects harbour ancient beneficial endosymbionts that produce essential nutrients. Two planthopper species from the Cixiidae family harbour different tripartite endosymbiont consortia, including...

doi.org

October 16, 2025 at 12:43 PM

Reposted by Alejandro Manzano Marín

MEEhubs

@meehubs.bsky.social

We’re back! ✨ The next #MeeHubs26 is coming with 7 hubs across the globe and incredible lineups at each. Can’t wait to share more soon! meehubs.org

Home

meehubs.org

October 7, 2025 at 2:30 PM

Reposted by Alejandro Manzano Marín

Roni Odai

@rodai.bsky.social

Viral AlphaFold Database (VAD) is live in Science Advances

~27,000 predicted viral protein monomers & homodimers

Conserved folds across bacteria, archaea & eukaryotic viruses

New toxin–antitoxin system KreTA uncovered

Vast “functional darkness” remains uncharted

www.science.org/doi/10.1126/...

The Viral AlphaFold Database of monomers and homodimers reveals conserved protein folds in viruses of bacteria, archaea, and eukaryotes

VAD is a Viral AlphaFold Database of protein monomers and homodimers from viruses infecting hosts across the tree of life.

www.science.org

October 2, 2025 at 8:48 AM

Reposted by Alejandro Manzano Marín

Jack Tamisiea

@jack-tamisiea.bsky.social

437 million years ago in what is now Wisconsin, the earliest known leeches were terrorizing trilobites. Instead of sucking blood, these critters were likely engulfing invertebrates whole or vacuuming out their insides!

Latest for @nytimes.com on a fantastic #fossil: www.nytimes.com/2025/10/01/s...

This Leech Had an Appetite for Something Other Than Blood

www.nytimes.com

October 1, 2025 at 8:00 PM

Reposted by Alejandro Manzano Marín

Tami Lieberman

@contaminatedsci.bsky.social

Precisely calling mutations across hundreds of bacterial isolates has been hard, requiring manual filtering and expertise.

Until now, using AccuSNV.

Herui Liao trained an ML model based on our previous meticulously called SNVs.
www.biorxiv.org/content/10.1...

High-accuracy SNV calling for bacterial isolates using deep learning with AccuSNV

Accurate detection of mutations within bacterial species is critical for fundamental studies of microbial evolution, reconstructing transmission events, and identifying antimicrobial resistance mutati...

www.biorxiv.org

September 29, 2025 at 7:45 PM

Reposted by Alejandro Manzano Marín

Peer Community Journal

@peercomjournal.bsky.social

Last Friday, we published the 500th article of Peer Community Journal! 🥳

September 29, 2025 at 7:37 AM

Alejandro Manzano Marín

@amanzanom.bsky.social

Hey #SymbioSky! (@symbionticism.bsky.social, @amelialindsey.bsky.social, @shropshirejd.bsky.social???)

I'm preparing material for a lecture on phages of beneficial endosymbionts. Looking for an up-to-date review on #phageWO and/or #Wolbachia....

September 29, 2025 at 8:13 AM

Alejandro Manzano Marín

@amanzanom.bsky.social

#Symbionts with eroded genomes adjust gene expression according to host life-stage and environment

#SymbioSky

@kaltenpoth-lab.bsky.social

doi.org/10.1038/s443...

Symbionts with eroded genomes adjust gene expression according to host life-stage and environment | EMBO reports

imageimageThe symbionts of Donaciinae, despite having severely eroded genomes of around 0.5 Mbp, exhibit specific transcriptional responses that allow them to react to changes both within and across h...

doi.org

September 19, 2025 at 2:12 PM

Alejandro Manzano Marín

@amanzanom.bsky.social

Evolution and comparative #genomics of #tick- #associated Francisella #endosymbionts: insights into metabolic pathways and historical biogeographic patterns

#SymbioSky

doi.org/10.1101/2025...

Evolution and comparative genomics of tick-associated Francisella endosymbionts: insights into metabolic pathways and historical biogeographic patterns

Ticks (Ixodida) are the second most important vectors of infectious diseases in vertebrates, after mosquitoes. They also maintain mutualistic relationships with bacteria, such as endosymbionts that pr...

doi.org

September 19, 2025 at 2:11 PM

Alejandro Manzano Marín

@amanzanom.bsky.social

The facultative intracellular #symbiont #Lariskella is neutral for lifetime fitness and spreads through #cytoplasmicIncompatibility in the leaffooted bug, Leptoglossus zonatus

#SymbioSky

doi.org/10.3389/fmic...