Manuel Kleiner

Spatial structure: shaping the ecology and evolution of microbial communities Spatial structure naturally emerges in microbial communities, shaping growth, interactions, and evolution, and revealing how microscale processes scale up

Most microbes don't live in shaking flasks; spatial structure shapes how microbes interact and evolve at every scale, as we discuss in our recent review @jeroenmeijer.bsky.social @simonvanvliet.bsky.social @bedutilh.bsky.social @bramvandijk.bsky.social and others
academic.oup.com/femsre/artic... 🧵👇

🆕 Vacancy! We’re looking for a motivated Research Scientist to join the laboratory of Dr @lizsayavedra.bsky.social in our Food, Microbiome and Health programme.

💷 £37,500 to £45,350
🗓️ Apply by 22 March 2026
➡️ buff.ly/VwXSgWQ

If you are interested in investigating horizontal gene transfer by phages and virus-like particles using computational approaches, this postdoc position in the Callahan Lab could be for you

jobs.ncsu.edu/postings/226...

Diagram illustrating early genome erosion during the transition from a free-living Sodalis bacterium to two host-associated endosymbionts inside the long-tailed mealybug. Circular genomes show intact genes in blue and pseudogenes in red, highlighting increased pseudogene accumulation in symbiotic forms. Caption asks: “What are the downstream molecular consequences of early genome erosion?”

Happy to share a preprint—the last chapter of my dissertation with @mcsymbiont.bsky.social and Co—on what happens when bacterial endosymbionts accumulate huge numbers of pseudogenes during early genome reduction.

www.biorxiv.org/content/10.6...

Check out our new preprint using 30 SynComs covering a phylogenetic diversity gradient, we uncover many interesting strain and community features involved in seed to seedling bacterial transmission 🧫🌱
@emersys-irhs.bsky.social in the SUCSEED project @inrae-dpt-spe.bsky.social

Thrilled to host @manuelkleiner.bsky.social for a week at @bengurionuniv.bsky.social for a MetaProteomics workshop!
No better start than a seminar on "Advanced Metaproteomic Approaches To Investigate Functional Host-Microbiota Interactions." 🧬

Back-scratching bovine leads scientists to reassess intelligence of cows Brown Swiss in Austria has been discovered using tools in multiple ways – something only ever seen in humans and chimpanzees

COW TOOLS COW TOOLS COW TOOLS

The microbial keystone concept is a very cool topic in microbiome ecology. This review summarises mechanisms, prediction methods and implications, with "keystoneness" being highly context/time dependent + new methods approaches suggested. Very nice read!
www.nature.com/articles/s41...

Subsurface Life on Earth as a Key to Unlock Extraterrestrial Mysteries This paper discusses current research on subsurface microbiology. Exploring Earth's deep and extreme subsurface environments provides critical insights into life's limits and adaptability. Subsurface...

🌏 Happy 🔭 New 🧪 Year 🦠 2026 ✨

If you feel like an easy read about subsurface microbiomes and astrobiology:

Here is an opinion I wrote with @emvidal.bsky.social @geobiomaggie.bsky.social @drbradbrad.bsky.social and Melody Lindsay

enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...

As I browse around, I keep an eye out for (what I think) are surprising facts.

This 2021 paper estimated that the USA, China and the UK spend USD 2.5 billion on peer review, based on the contribution made by researchers.
🧵

If you work on Dark Oxygen --> come to #AbSciCon2026 this year. 17-22 May, Madison

Join our session on ""Dark Oxygen" Production: where does it happen, how does it work, and what does it mean for astrobiology?"

Submit your abstract until January 14

More info here: agu.confex.com/agu/abscicon...

The Bezzle gives some good insights into how it is done
bluecypressbooks.com/book/9781250...

Dear US researchers: break the outrage addiction. I survived the besieging of science. So can you As I watch US researchers respond to threats against science, I’m reminded of when scientists in Brazil navigated a similar storm.

This column in a word: boss-up, y’all. It is not a warm and fuzzy hug, or an outrage sing-along. It’s a clear reflection of the present, a wake up call, and a preview of the future. We aren’t going to complain Trump away. It’s survival time. www.nature.com/articles/d41...

Troubleshooting common errors in assemblies of long-read metagenomes - Nature Biotechnology Long-read sequence assemblies from metagenomes contain frequent errors.

Troubleshooting common errors in assemblies of long-read metagenomes - @merenbey.bsky.social @banfieldlab.bsky.social go.nature.com/44P7nSm

#metaproteomics

Interested in learning how #metaproteomics workflows work and what you can use them for. I am part of a team giving a three day workshop on metaproteomics at Ben Gurion University in late January 2026. Details and registration here lifewp.bgu.ac.il/wp/psme/

Bacteriophages are normally classified as either virulent or temperate. Reality is, of course, more complicated!
Here we show many bacterial isolates contain non-temperate phages that can persist through restreaking.
Thanks to all co-authors for such a great collaboration!

I’m old enough to remember when CBS News would never have surrendered to a demagogic president or any other politician. Remember Edward R. Murrow?

We are recruiting a Lab Manager/Research Specialist
jobs.ncsu.edu/postings/225...
Please re-post, thank you

Evaluation of statistical approaches for differential metaproteomics Metaproteomics characterizes and compares molecular phenotypes of organisms in communities by comprehensively analyzing their protein expression profiles using statistical methods. However, not all st...

Super excited to have this paper out. We developed a complex set of ground truth samples to test more than 110 statistical approaches for differential #metaproteomics
We can now give clear guidance on what tests perform well. Thank you Tjorven Hinzke and
@benoitkunath.bsky.social for the leadership

The direct causal evidence of ultra-processed foods for adverse health outcomes is accruing
nature.com/articles/s41...

The most precious commodity you have is your attention. You don’t have to waste it on poor-faith debates or arguments with strangers if you don’t think they’ll be productive. You can prioritize the things that matter to you and make your life richer.

Assessing the diversity and functional profile of the “microbial proteome” in fermented foods Fermented foods are staples in diets worldwide and are known for their health benefits. Microorganisms are the key to fermented food production as they convert raw substrates into digestible, nutritio...

In fermented foods microbes convert some of the food substrate into microbial protein. We found that in some fermented foods up to 10% of the total protein is microbial and that some of these microbial proteins have functions that might explain some of the beneficial effects of fermented foods.

I Set A Trap To Catch My Students Cheating With AI. The Results Were Shocking. "Students are not just undermining their ability to learn, but to someday lead."

"essays produced by ChatGPT are soulless, boring abominations. Words, phrases and punctuation rarely used by the average college student are pervasive." www.huffpost.com/entry/histor...

Universal rules govern plasmid copy number - Nature Communications Plasmids exhibit a broad range of sizes and copies per cell, and these two parameters appear to be negatively correlated. Here, Ramiro-Martínez et al. analyse the copy number of thousands of diverse b...

Curious about plasmid biology? Our latest paper is out now in Nature Communications! 🚨

doi.org/10.1038/s414...

We analyzed thousands of diverse bacterial plasmids to shed light for the first time on a key aspect of plasmid biology: plasmid copy number. 1/7 👇

Diving through the purple sulfur bacteria layer of Fayetteville Green Lake with our ROV last month. This is the most intense density of PSB that I've seen in many years!

If you are interested in #metaproteomics think about joining the 7th International Metaproteomics Symposium next June in Germany www.hs-anhalt.de/landingsites...
I have been at several and they were always awesome

Identifying rare and active species that drive carbon turnover in complex microbiotas - Nature Microbiology By combining bioorthogonal non-canonical amino acid tagging, metaproteomics and stable isotope probing, we identified a rare and uncharacterized bacterium with a glycine-mediated metabolism for syntro...

Our latest Research Briefing is out, on using metaproteomics and stable isotope labelling to uncover rare species involved in carbon turnover www.nature.com/articles/s41...

q.e.d Science Critical Thinking AI for constructive criticism and science evaluation

Here's the link to the system, try it! qedscience.com
@qedscience.bsky.social

This is gaining traction in anti-COVID vax circles but none of them have clocked that it comes from a dataset spanning 2000-2020. The shots are so powerful they transcend time.