The president speaks genocide The words, the law, the future

“A whole civilization will die tonight, never to be brought back again.”
These are the words of the president of the United States, today.
The president speaks genocide. And so we too must speak. Not only about crimes, but about their legal punishment.
snyder.substack.com/p/the-presid...

#Archaea #ArchaeaSky #MicroSky

exceptional work, hiro & team 👏👏👏
it's wonderful to see 𝘓. 𝘰𝘴𝘴𝘪𝘧𝘦𝘳𝘶𝘮 dancing. live videos reveal so much more than stills!

ALT source: www.biorxiv.org/content/10.1...

Kurzgesagt – In a Nutshell Animation videos explaining things with optimistic nihilism since 12,013. We’re a team of illustrators, animators, number crunchers and one dog who aim to spark curiosity about science and the world ...

Big news, friends! I just joined the team at Kurzgesagt – In a Nutshell @kurzgesagt.org as a Researcher & Fact-Checker 🐦💻🔍

Basically I get to nerd out over science with wildly creative people every day. Dream job 💚

Go watch their stuff if you haven’t already!
www.youtube.com/@kurzgesagt

(EPSRC DTP) How do the interactions between temperate and lytic phages shape microbial communities? at The University of Manchester on FindAPhD.com PhD Project - (EPSRC DTP) How do the interactions between temperate and lytic phages shape microbial communities? at The University of Manchester, listed on FindAPhD.com

www.findaphd.com/phds/project...

Genome duplication in a long-term multicellularity evolution experiment - Nature In the Multicellularity Long Term Evolution Experiment, diploid yeast evolve to be tetraploid under selection for larger multicellular size, revealing how whole-genome duplication can arise due to its...

1/46 Hey folks, we have a new paper out on the MuLTEE. Strap in and I’ll tell you the story of how this “little paper on polyploidy” turned into the most data rich paper our lab has produced, largely thanks to the leadership and work ethic of @kaitong25.bsky.social.

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

Come join our fun community @ox.ac.uk! Two postdoc positions available in the fabulous Slack and Foster labs www.fosterlab.uk/vacancies

We are recruiting @ox.ac.uk @dunnschool.bsky.social for a joint project between Kevin Foster's group and mine! Cluster hire of two postdocs interested in:
1) Mucosal immunology and oral vaccine development
my.corehr.com/pls/uoxrecru...
2) Microbiology
my.corehr.com/pls/uoxrecru...

Please share!

very awesome paper, btw!

@contamclub.bsky.social

A winter’s contamination - tragedy in three acts

Order of amino acid recruitment into the genetic code resolved by last universal common ancestor’s protein domains | PNAS The current “consensus” order in which amino acids were added to the genetic code is based on potentially biased criteria, such as the absence of s...

We identified protein domains in LUCA (Last Universal Common Ancestor). Their distinctive amino acid usage reveals the order amino acids were added to the genetic code, based mostly on size. Older proteins hint at earlier alternative codes. 1/15 @seekingluca.bsky.social www.pnas.org/doi/10.1073/...

Funny! this brings back memories of when Nüsslein-Vollhard told a fellow female graduate student that she wouldn’t hire a postdoc who wastes time putting on makeup everyday.
The one piece of advice by a Nobel laureate that didn’t improve my science, but my morning routine.

For anyone interested in #evolution #virulence #gutmicrobiome I have a new perspective with Bruce Levin and Fernando Baquero just out @pnas.org

www.pnas.org/doi/abs/10.1...

This is exactly right. Population genetics has a reification of simple models problem. And we are weirdly non-Bayesian in that we do not check our simple - clearly too simple! - models against the priors generated through direct observation in ecology and other fields.

(1/6) Our new short paper on incidental bacterial domestication between patient isolation and creation of frozen stock. Geno/phenotype changes are obscured by rich media and more prevalent than we previously thought.

#MicroSky

Here it’s the brain affecting the gut microbiota- via the Brunner’s gland, which nerves stimulate to produce mucus, home for the Lactobacilli. Links physiological state to immunity. Amazing work by Ivan de Araujo and Hao Chang. doi.org/10.1016/j.ce...

🦠🧫@maxplanckcampus.bsky.social

IS jumping?

Evolutionary biologists teaching intro courses: "Hardy-Weinberg is the null model of evolution."

Evolutionary biologists studying bacteria/archaea/asexual eukaryotes:

#evolution

Excited to share our new paper out in Science! We combined simulations, experiments, and field data to show how dispersal simultaneously stabilizes species and genetic diversity, which results in persistent eco-evo dynamics. doi.org/10.1126/scie...

Putting my stake in the ground as an enjoyer (and user) of the term 'prokaryote'. It's an efficient way to talk about two groups of organisms which are very often talked about in the same breath! Nobody gets mad about 'fish' because it's paraphyletic! 🧪

Obsession with methods in microbial ecology Striving towards bare minimum technique awesomeness

In my latest newsletter I write about the obsession with methods in microbial ecology, and I share my admiration of simple, but elegant experimental approaches.

🧪🦠
What do you think?

open.substack.com/pub/matthias...

Bacterial ecology and evolution converge on seasonal and decadal scales Ecology and evolution are distinct theories, but the short lifespans and large population sizes of microbes allow evolution to unfold along contemporary ecological time scales. To document this in a natural system, we collected a two-decade, 471-metagenome time series from a single site in a freshwater lake, which we refer to as the TYMEFLIES dataset. This massive sampling and sequencing effort resulted in the reconstruction of 30,389 metagenomic-assembled genomes (MAGs) over 50% complete, which dereplicated into 2,855 distinct genomes (>96% nucleotide sequence identity). We found both ecological and evolutionary processes occurred at seasonal time scales. There were recurring annual patterns at the species level in abundances, nucleotide diversities (π), and single nucleotide variant (SNV) profiles for the majority of all taxa. During annual blooms, we observed both higher and lower nucleotide diversity, indicating that both ecological differentiation and competition drove evolutionary dynamics. Overlayed upon seasonal patterns, we observed long-term change in 20% of the species' SNV profiles including gradual changes, step changes, and disturbances followed by resilience. Most abrupt changes occurred in a single species, suggesting evolutionary drivers are highly specific. Nevertheless, seven members of the abundant Nanopelagicaceae family experienced abrupt change in 2012, an unusually hot and dry year. This shift coincided with increased numbers of genes under selection involved in amino acid and nucleic acid metabolism, suggesting fundamental organic nitrogen compounds drive strain differentiation in the most globally abundant freshwater family. Overall, we observed seasonal and decadal trends in both interspecific ecological and intraspecific evolutionary processes. The convergence of microbial ecology and evolution on the same time scales demonstrates that understanding microbiomes requires a new unified approach that views ecology and evolution as a single continuum. ### Competing Interest Statement The authors have declared no competing interest.

Been dreaming of this paper for a decade. 1 PhD and 1 postdoc later, here it is!

What do ecology and evolution look like in a 20-year microbiome time series? They blur together

@quendi.bsky.social @archaeal.bsky.social @uslter.bsky.social @sarilog.bsky.social 🧪🖥️🧬

www.biorxiv.org/content/10.1...

Large-scale duplication events underpin population-level flexibility in tRNA gene copy number in Pse... Abstract. The complement of tRNA genes within a genome is typically considered to be a (relatively) stable characteristic of an organism. Here, we demonstrate t

This is a very cool piece of work from Jenna Gallie et al - Large-scale duplication events underpin population-level flexibility in tRNA gene copy number in Pseudomonas fluorescens academic.oup.com/nar/advance-...

Interesting! Their theory seems to hinge on constant recombination (which in the face of niche overlaps forces low-diversity populations to increase their niche breadths instead of e.g. diversifying into more narrow but multimodal distributions). No such homogenizing recombination in Bacteria (?)

Ahhh to be a microbiologist in these exciting times when evolution and ecology talk to each other… absolutely brilliant talks at @meehubs.bsky.social

This is it, people - join my lab at the University of Southampton!
* PhD position in interdisciplinary microbiology starting October 2024 *
southcoastbiosciencesdtp.ac.uk/project/inva...
Contact n.nikolic@exeter.ac.uk for more info

Apply southcoastbiosciencesdtp.ac.uk/apply/
Deadline: 8 Jan 2024

Finally - hit me up if you see a job opening that you think could be a good fit for a (micro)biologist with a knack for science communication, data visualization, open science, and writing! Targeting Germany/Switzerland especially 🙌 8/8

OK this is the mind-blowing image of the week for me: the total global biomass of mammals.

Wild animals are a tiny proportion.

From a paper by Ron Milo Lab at Weizmann Institute, via a great Oxford lecture by @marionkoopmans.bsky.social

www.pnas.org/doi/10.1073/...

What makes a temperate phage an effective bacterial weapon? bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

Proud supervisor as PhD student Matt Thomas submits his first first-author publication, collab with Mike Brockhurst exploring what makes a temperate phage an effective bacterial weapon www.biorxiv.org/content/10.1...