Andrea Telatin

A human gut metagenome-assembled genome catalogue spanning 41 countries supports genome-scale metabolic models - Nature Microbiology HRGM2 is a catalogue of 155,211 high-quality metagenome-assembled genomes spanning 41 countries that allows improved genome-scale metabolic modelling and functional characterization of human gut micro...

#Resource

HRGM2 - a catalogue of 155,211 high-quality metagenome-assembled genomes spanning 41 countries that allows improved genome-scale metabolic modelling and functional characterization of human gut microbes.

#MicroSky #MicrobiomeSky 🦠💻

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

@mrclmb.bsky.social alumnus Tony Hyman to become new @embl.org director general

Optimized k-mer search across millions of bacterial genomes on laptops https://www.biorxiv.org/content/10.1101/2025.11.23.690050v1

The study gave dna and cells to the labs. In both cases library preparation was done and in the latter also extraction. So the variability has multiple sources :)

Ring validations are important. @quadraminstitute.bsky.social took part of this study from dna to analysis

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.

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/...

Quick thread on the BBC and the political and societal significance of recent developments:

One of the main reasons the UK has historically been so much less polarised than the US, is that Britain has a shared source of information, consumed and trusted by most people regardless of their politics.

So it turns out... the US air travel system was incredibly, deeply dependent on federal funding to just run day-to-day all this time, to the benefit of private airline shareholders, when everyone thinks that state-run trains are leeching off the government. Weird!

A social card with a digital illustration of of AI and the text "Research Scientist (Bioinformatics) to develop and apply computational methods for metaproteomics and multi-omics to advance precision microbiome research. Salary : £37,500 to £41,500, Contract length: 2 years, Apply by 9 November 2025"

⏰ Closing soon! We’re looking for a Research Scientist (Bioinformatics) to join the Laboratory of Dr Kai Cheng in our Food, Microbiome and Health programme

💷 £37,500 to £41,500
🗓️ Apply by 9 November 2025
➡️ buff.ly/DqLnYek

Escherichia coli with a 57-codon genetic code The near-universal genetic code uses 64 codons to encode the 20 canonical amino acids and protein synthesis. Here, we designed and generated Escherichia coli with a 4-megabase synthetic genome in whic...

Escherichia coli with a 57-codon genetic code | Science www.science.org/doi/10.1126/...

I saw you running in Newmarket road :)

To clarify: This is a tool that uses google scholar. Not a google tool

U.S. Biotech Future Is Now Made in China This past year, oncologists across the United States faced an agonizing choice: Which cancer patients would receive their full, life-saving chemotherapy regimen and which would face delays or substand

U.S. Biotech Future Is Now Made in China www.realclearworld.com/articles/202...

From genotype to phenotype with 1,086 near telomere-to-telomere yeast genomes www.nature.com/articles/s41... 🧬🖥️🧪 github.com/HaploTeam/10...

Estimating the potential economic and health impact of integrated genomic surveillance in a hospital setting Integrated genomic surveillance, combining whole genome sequencing (WGS) of bacterial isolates with patient movement data, promises improved detection…

"WGS-informed prevention could hypothetically generate net savings of €1.35 million annually if transmission was stopped once a clonal isolate was detected in a second patient."

I think that translates to ~1.5 million US dollars

🚨🔊 Fully funded PhD!! 🚨🔊

Are you interested in wildlife gut microbiomes? Love birds, fieldwork and bioinformatics? Want to join a collaborative and supportive team? Looking for training to become an independent scientist?

Please apply!

Informal enquiries welcome!

www.uea.ac.uk/course/phd-d...

Interested in modelling metabolism from food -> gut microbiome -> blood ? 5 days left to apply for a fully funded position to investigate this. 👇👇👇

New blog post!

metaMDBG (@gaetanbenoit.bsky.social) and Myloasm (@jimshaw.bsky.social) have had recent releases, so I updated the benchmarks from the Autocycler paper:
rrwick.github.io/2025/09/23/a...

Both tools improved considerably! Time to update your conda environments 😄

If you are UK-based and working on any aspect of microbiomes (human, plant, insect, soil, animal, ...), please do sign up to Microbiome-Net for details of networking, funding and training opportunities.

forms.office.com/pages/respon...

Head of Bioinformatics - MRC Laboratory of Medical Sciences We are recruiting for a Head of Bioinformatics to lead our Bioinformatics facility

Come be our head of bioinformatics at @mrc-lms.bsky.social !

Our bioinformatics team are closely involved with lots of interesting science and we love working with them. Topics inc. development, cancer, metabolism, aging, TEs (my favourite of course 😜) #TEsky lms.mrc.ac.uk/work/vacanci...

Lib Dems: We have 12x Reform's MPs, can we have the same coverage?

BBC: But Reform has 2x your poll rating. If there were an election tomorrow, they'd be running the country.

Lib Dems: So you're putting their people and policies under scrutiny, right?

BBC:

Lib Dems: Right?

OpenAI admits AI hallucinations are mathematically inevitable, not just engineering flaws In a landmark study, OpenAI researchers reveal that large language models will always produce plausible but false outputs, even with perfect data, due to fundamental statistical and computational limi...

"In a landmark study, OpenAI researchers reveal that large language models will always produce plausible but false outputs, even with perfect data, due to fundamental statistical and computational limits."

www.computerworld.com/article/4059...

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

We want to explore the metabolic interactions among gut bacteria, when the human host eats different foods - maybe this explain partly the Enterosignature structure?
Please do apply for our bioinformatic post to explore this question in metagenomes: jobs.quadram.ac.uk/Details.asp?...

This is a bonkers chart used by OpenAI to advertise the capabilities of GPT-5. The y-axis reads "Accuracy (%)." The size of the bars does not match the labels, though.

The AI hype is so wild that we know see charts like this and think that "must have made by AI".
Or are marketing teams worse than AI nowadays?

YouTube video by Perimeter Institute for Theoretical Physics Veritasium: What Everyone Gets Wrong About AI and Learning – Derek Muller Explains

Yes. Check this out youtu.be/0xS68sl2D70?...

🧪 Just out in Bioinformatics Advances: “Structure-based metabolite function prediction using graph neural networks”   

Explore the full study here: https://doi.org/10.1093/bioadv/vbaf174

Authors include: @alisaadatv.bsky.social, @jannahastings.bsky.social

Headline from the Daily Mail, 11 April 1927: "Stop the Flapper-Vote Folly!"

The right-wing press is going mad over votes at 16 ("a naked attempt to twist democracy in Labour’s favour", an "election-rigging move"...)

Oddly, they said the same 100 years ago when the voting age for women fell from 30 to 21.

Let's revisit the Mail's campaign to"Stop the Flapper Vote Folly"...

Happy Independence Day ⭐️

happy Transposon Day @yaasircheema.bsky.social and co :)