Daan Speth
LightNews LightNews
daanspeth.bsky.social
Daan Speth
@daanspeth.bsky.social
1.5K followers 1.6K following 180 posts
Computational microbiologist. Senior scientist at @cemess.bsky.social, @univie.ac.at.

Microbial ecology, mostly of nitrogen cycle microbes, and data driven physiology.

Maintainer of the GlobDB genome database https://globdb.org
Posts Replies Media Videos
Pinned
daanspeth.bsky.social
Daan Speth @daanspeth.bsky.social · Jun 10
I'm happy to announce the latest release of the GlobDB, available at globdb.org.

The GlobDB is a database of "species dereplicated" microbial genomes, and as of release 226 contains twice the number of species-representative genomes (306,260) than the latest GTDB release.
home | GlobDB
globdb.org
Reposted by Daan Speth
bacdive.bsky.social
This year's #BacDive workshop will take place on 24th November 2025, 3 - 5 PM CET online!

We are especially looking forward to the opportunity to answer your questions, and hear your feedback and ideas. 🦠🧬.

Write to training@bacdive.de to receive the Zoom login details 🖥️.
Agenda: 1. Introduction 2. The new website design 3. The new genome browser
November 13, 2025 at 9:35 AM
Reposted by Daan Speth
alegarritano.bsky.social
Here, we show that deep below, corals and feather stars don’t just share space – they share microbes. Endozoicomonadaceae + Nitrosopumilaceae inhabit both hosts in a “promiscuous” symbiosis that may fuel nitrogen cycling in the deep sea.
doi.org/10.1186/s401... 🌊🪸🧪 #Bioinformatics 🧬💻 #SymbioSky
November 13, 2025 at 6:11 AM
Reposted by Daan Speth
weiss-lab.bsky.social
The Center for Microscopy and Image Analysis at the University of Zurich is seeking a new Head:

jobs.uzh.ch/job-vacancie...

It is super fun to work with them, tons of expertise and cutting edge instrumentation in ❄️🔬
Application deadline: December 15, 2025.
UZH: Head of the Center for Microscopy and Image Analysis (Core Facility)
The Center for Microscopy and Image Analysis (ZMB) is a nationally and internationally recognized Core Facility at the University of Zurich (UZH), providing access to state-of-the-art light and electr...
jobs.uzh.ch
November 12, 2025 at 6:42 PM
Reposted by Daan Speth
bejalab.bsky.social
1/6
PhD /PostDoc positions available. Exploration of physiological functions of the cell fusogen Fusexin1 in Archaea.
In a collaborative project between the Albers lab (Freiburg) and the Podbilewicz lab (Technion) starting in January 2026.
November 12, 2025 at 7:53 AM
Reposted by Daan Speth
aylwyn-scally.bsky.social
Come and join us here in Cambridge! Applications open for a new faculty position, for a researcher in computational and/or theoretical biology, based jointly in Genetics and Mathematics. Happy to answer questions about research, teaching and working here.

www.cam.ac.uk/jobs/faculty...
Faculty Position in Computational Biology
Applications are invited for an Assistant/ Associate Professorship in Computational Biology to commence on 1 April 2026 or shortly thereafter. This is a joint post between the Department of Applied
www.cam.ac.uk
November 11, 2025 at 9:05 PM
Reposted by Daan Speth
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 Daan Speth
acritschristoph.bsky.social
This is a great thread. But three points.

1. Agree: profit in publishing is the central issue, but it needed the APC to go into overdrive. The mistake of the 2010s OA movement was to shift culture around access and not profit. This damanged sci publishing bc APCs incentivize quantity over quality
hansonmark.bsky.social Mark A. Hanson @hansonmark.bsky.social · 2d
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 5:28 PM
Reposted by Daan Speth
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 Daan Speth
amydwillis.bsky.social
With much gratitude to everyone who supported the wonderful #STAMPS summer course at the MBL, I share that STAMPS will not be offered in 2026.

💔😿
November 11, 2025 at 1:05 AM
daanspeth.bsky.social
@dominikluecking.bsky.social
sullivan-lab.bsky.social Sullivan Lab at OSU @sullivan-lab.bsky.social · 6d
🚨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 7:59 PM
Reposted by Daan Speth
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
Reposted by Daan Speth
bananabenana.bsky.social
For the sake of the entire #biology 🧪🧬🦠🧫🔬💊and #medsky science 🩺community, I think @enasequence.bsky.social and the #bioinformatics community needs to prioritise development of new tools and functionality in-line with #NCBI and #Genbank, before it potentially goes down sometime in the near future.
November 5, 2025 at 11:54 PM
daanspeth.bsky.social
@loyteam.bsky.social in case you didn’t come across this one yet #microsky
November 7, 2025 at 7:55 PM
Reposted by Daan Speth
emmseveri.bsky.social
#microsky finally a TRAP transporter that is *not* the Neu5Ac-transporting SiaPQM ;-)

www.cell.com/structure/fu...
Structural basis of isethionate transport by a TRAP transporter from a sulfate-reducing bacterium
Newton-Vesty et al. used a megabody fiducial to determine the cryo-EM structure of an isethionate TRAP transporter, revealing the substrate and Na+-binding sites. Transport is dependent on Na+ and the...
www.cell.com
November 6, 2025 at 1:29 AM
Reposted by Daan Speth
cbibberson.bsky.social
Re-boosting! The Dept. of Microbiology 🧫 at the University of Tennessee is hiring two 9-month faculty! Come join a vibrant and growing department located in the foothills of the Smoky Mountains! #microsky
cbibberson.bsky.social Carolyn Ibberson @cbibberson.bsky.social · 20d
Come join us in Knoxville!

The Dept. of Microbiology 🧫🦠 at the University of Tennessee is hiring 2 Assistant Professors (tenure track, 9-month appt.).

Microbial Drivers of Chronic Disease: apply.interfolio.com/173153Quantitative Microbe-Plant-Environment Interactions: apply.interfolio.com/173345
Job ad for Quantitative Microbe-Plant-Environment interactions position Job ad for microbial drivers of chronic disease position
November 6, 2025 at 1:07 PM
Reposted by Daan Speth
microyunha.bsky.social
We're thrilled to announce SeqHub, an AI-enabled platform for biological sequence analysis. SeqHub brings together sequence search, genome annotation, and data sharing in one place.
October 28, 2025 at 1:47 PM
Reposted by Daan Speth
apcamargo.bsky.social
🚨New preprint out!
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8)
www.biorxiv.org/content/10.1...
November 6, 2025 at 5:26 PM
Reposted by Daan Speth
emmseveri.bsky.social
#microsky #phagesky CRISPR-cas galore

www.nature.com/articles/s41...
An updated evolutionary classification of CRISPR–Cas systems including rare variants - Nature Microbiology
An exploration of previously undescribed variants from the long tail of the CRISPR–Cas distribution.
www.nature.com
November 6, 2025 at 4:46 PM
Reposted by Daan Speth
amydwillis.bsky.social
Are you looking for a #tenuretrack or #openrank job in #biostatistics or #statistics? @fredhutch.org is hiring! Seattle is a wonderful place to grow your career; the bio/stat & science scene here is world-class; and you will work w/ amazing UW Biostat students. Apply!
apply.interfolio.com/176402
Apply - Interfolio {{$ctrl.$state.data.pageTitle}} - Apply - Interfolio
apply.interfolio.com
November 4, 2025 at 6:57 PM
Reposted by Daan Speth
fpbase.org
The FPbase spectra viewer just had it's biggest software refactor in 6 years. It *should* be largely invisible to the end user (hopefully just faster and less buggy). Please let me know if you find any issues as you use it!

www.fpbase.org/spectra/
FPbase Fluorescence Spectra Viewer
An interactive fluorescence spectra viewer to evaluate the spectral properties of fluorescent proteins, organic dyes, filters, and detectors.
www.fpbase.org
November 4, 2025 at 3:03 PM
Reposted by Daan Speth
taylorpriest.bsky.social
GcMeta - a new global resource of metagenome-assembled genomes and their encoded functions with an easy to use, interactive and searchable website academic.oup.com/nar/advance-...
gcMeta 2025: a global repository of metagenome-assembled genomes enabling cross-ecosystem microbial discovery and function research
Abstract. The rapid growth of metagenomic sequencing has generated an unprecedented wealth of metagenome-assembled genomes (MAGs), transforming opportuniti
academic.oup.com
November 3, 2025 at 9:01 AM
Reposted by Daan Speth
stcmicrobeblog.bsky.social
Ray: Just a note to say STC is officially back up and running!! You can view our new home via smallthingsconsidered.blog
smallthingsconsidered.blog
November 3, 2025 at 1:10 AM
Reposted by Daan Speth
rebeleinlab.bsky.social
Our latest work on the nitrogenase-like methylthio-alkane reductase, which specifically reduces reduces carbon-sulfide bonds is now out @natcatal.nature.com: doi.org/10.1038/s419.... We find for the first time large #nitrogenase metalloclusters (P- and L-cluster) outside nitrogenases.
October 23, 2025 at 10:09 AM
Reposted by Daan Speth
tsbschm.bsky.social
Great to see this finally published!

Metalog: curated and harmonised contextual data for global metagenomics samples

now out in @narjournal.bsky.social

academic.oup.com/nar/advance-...
Metalog: curated and harmonised contextual data for global metagenomics samples
Abstract. Metagenomic sequencing enables the in-depth study of microbes and their functions in humans, animals, and the environment. While sequencing data
academic.oup.com
October 31, 2025 at 3:16 PM
Reposted by Daan Speth
dsmzd3.bsky.social
📣 Open position:

We are looking for a new #ScientificLead for the #SILVA database 🧬🖥️, who will be responsible for guiding the development of this important resource and for curating the #SILVA taxonomy🌳.

Read and share!

👉 www.dsmz.de/dsmz/career/...

🧪🦠🌱🦋💽
October 31, 2025 at 5:41 PM