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Reposted by @danielfalush.bsky.social

Louis-Marie Bobay @lbobay.bsky.social · 18/11/2025

Our latest paper is out with @adiop.bsky.social and @gmdouglas.bsky.social. We analyzed the extent of homologous recombination between bacterial species (introgression) and how it affects species borders (it can vary a lot depending on the approach used to classify species!). rdcu.be/eQAMf

rdcu.be

Introgression impacts the evolution of bacteria, but species borders are rarely fuzzy

Nature Communications - It is commonly thought that bacterial species borders tend to be fuzzy, due to frequent exchange of DNA. Here, Diop et al. quantify the patterns of gene flow between core...

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danielfalush.bsky.social @danielfalush.bsky.social · 31/10/2025

We are hiring! Postdoc position exploring the ecological niche of the Molassodon ecospecies of Vibrio parahaemolyticus, that we @campy-bara.bsky.social have previously shown has a distinct "hunt, kill, devour phenotype in the laboratory. details here: www.simm.cas.cn/web/rcdw/rcz... please share.

simm.cas.cn

病原菌定量基因组学研究组（DANIEL FALUSH组）博士后招聘启事----中国科学院上海药物研究所

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Reposted by @danielfalush.bsky.social

Chao Yang @chaooo.bsky.social · 27/08/2025

Our “Less is more” story is out! 🚀 We reveal how gene loss shaped the adaptive evolution of pandemic Vibrio parahaemolyticus, highlight a potentially general mechanism across bacteria. Huge thanks @danielfalush.bsky.social @campy-bara.bsky.social @jaimemurtaza.bsky.social & all coauthors

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danielfalush.bsky.social @danielfalush.bsky.social · 30/06/2025

What's left to discover: What are the viscous liquids in which Molassodon hunts, kills and devours bacterial prey? We now have many more tools to help us find out, and to understand the trade offs for different bacterial strategies. All comments welcome, thank you for reading.

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danielfalush.bsky.social @danielfalush.bsky.social · 30/06/2025

We also identify a convergent intermediate form and are also able to provide details about the molecular and evolutionary assembly of the Molassodon genotype, revealing a key role for lateral flagella glycosylation.

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danielfalush.bsky.social @danielfalush.bsky.social · 30/06/2025

Upregulated genes provide clues about the ecological advantage of fast swimming in viscous liquids. A Type 6 secretion system and nutrient uptake genes are upregulated, allowing the bacteria to kill and devour bacterial prey.

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danielfalush.bsky.social @danielfalush.bsky.social · 30/06/2025

We use TNseq and RNA seq to show that 2/3 of ecospecies loci are either essential for this enhanced swimming or are unregulated along with it.

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danielfalush.bsky.social @danielfalush.bsky.social · 30/06/2025

Bacterial ecospecies are powerful tools for molecular biological, evolutionary and ecological investigation because all of the differentiated genes are working together. Molassodon have abandoned swarming on surfaces and instead use their lateral flagella to swim faster in viscous liquids.

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danielfalush.bsky.social @danielfalush.bsky.social · 30/06/2025

Bacterial ecospecies are complex adaptations on an otherwise freely recombining background. Molassodon has evolved via introgression of accessory genes and a few core genes from other Vibrio species, as well as point mutation.

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danielfalush.bsky.social @danielfalush.bsky.social · 30/06/2025

Molassodon! Excited to post my research group's first laboratory project. We identify a phenotype and a putative ecological strategy for the Molassodon ecospecies of Vibrio parahamolyticus, thanks to the hard work of our lab team led by @campy-bara.bsky.social www.biorxiv.org/content/10.1...

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danielfalush.bsky.social @danielfalush.bsky.social · 18/06/2025

There is every chance to make a recovery from these cuts and to leave science in a healthier place than it was, for example if the opposition to them galvanizes a common sense of purpose across American society - don't lose sight of that!

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danielfalush.bsky.social @danielfalush.bsky.social · 18/06/2025

We have lived within a period of unprecedented stability and.. should keep some sense of perspective about this. Second World War and cultural revolution caused incomparably greater upheaval, for example, silly to compare, but many things were better than ever a couple of human generations later.

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danielfalush.bsky.social @danielfalush.bsky.social · 17/06/2025

I agree it's terrible, my sympathies, but I do think that hyperbolae, "multiple generations" are not helpful. In my parents lifetime, I can think of much worse things that have happened and been recovered from.

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danielfalush.bsky.social @danielfalush.bsky.social · 28/02/2025

Thank you for reading our thread, please read the preprint too! your comments on all aspects are extremely welcome.

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danielfalush.bsky.social @danielfalush.bsky.social · 28/02/2025

Fascinatingly, their convergence in ecospecies differentiation between the two streptococcus species, involving the same genes and gene categories (cell division related), despite independent origins. Different genera find different but predictable paths for adaptive differentiation.

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danielfalush.bsky.social @danielfalush.bsky.social · 28/02/2025

The first two bacterial ecospecies we discovered, in Heliocobacter pylori and vibrio parahaemolyticus are characterized by high differentiation restricted to a small fraction of the genome. The streptococcal ones have progressed further, consistent with the older age of the species.

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danielfalush.bsky.social @danielfalush.bsky.social · 28/02/2025

And the first bacterial ecospecies threesome, in Streptococcus oralis.

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danielfalush.bsky.social @danielfalush.bsky.social · 28/02/2025

We illustrate this concretely by discovering a third bacterial ecospecies pair in Streptococcus mitis.

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danielfalush.bsky.social @danielfalush.bsky.social · 28/02/2025

Why? Well what happens is that for species which maintain large population sizes for long time periods, natural selection becomes increasingly important in structuring diversity and this generates long range LD.

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danielfalush.bsky.social @danielfalush.bsky.social · 28/02/2025

Last and not least, we provide an answer to the question of why panmictic bacterial species are rare. A well-mixed bacterial species should have low LD at all genetic distances, but there are no such species. Instead we find that the most diverse species have intermediate long-range LD.

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danielfalush.bsky.social @danielfalush.bsky.social · 28/02/2025

And there are curious findings too, like the fact that the genome fluidity of rod shaped bacteria is more than double that of spherical ones. What can you see in the data? Or what would you like to see? Let us know!

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danielfalush.bsky.social @danielfalush.bsky.social · 28/02/2025

We are able to use the population genetic data to address classic questions such as what determines the number of genes? It seems to be a balance between deletion bias and selection favoring increasing genome complexity.

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danielfalush.bsky.social @danielfalush.bsky.social · 28/02/2025

Why has it taken us so long to update it? Like fine wine, it has matured. Unlike fine wine, it has also grown in scale. We now analyze population genetic data from nearly 800 species, instead of twenty something and genomic data from 15000. Figure 1 presents an overview of genomic parameters.

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danielfalush.bsky.social @danielfalush.bsky.social · 28/02/2025

Delighted to present our Macrogenetics atlas of prokaryotes. www.biorxiv.org/content/10.1... This is a herculean effort from Chao Yang, which has a previous existence as a preprint first posted in 2018 "why panmictic bacteria are rare?" www.biorxiv.org/content/10.1...

biorxiv.org

Macrogenetic atlas of prokaryotes

Macrogenetics investigates the patterns and predictors of intraspecific genetic variation across diverse taxa, offering a framework to address longstanding evolutionary hypotheses. Here, we present a ...

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Reposted by @danielfalush.bsky.social

Guillaume Méric @gmeric.bsky.social · 27/02/2025

Very interesting new preprint from the Falush lab in Shanghai, describing an effort to parameterize a large number of microbial and population (phylo)genetic traits for >15k species, then examining their interactions. Loads to dig up & possibly quite impactful! 🔗 www.biorxiv.org/content/10.1...

biorxiv.org

Macrogenetic atlas of prokaryotes

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danielfalush.bsky.social @danielfalush.bsky.social · 27/01/2025

So the million dollar question, what is the trait? Is there a trait? We don't know. The top loading genes provide some hints (number 1 is a fimbria locus). Really interested to hear your thoughts and suggestions, thanks for reading and reposting :).

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danielfalush.bsky.social @danielfalush.bsky.social · 27/01/2025

We propose instead that the structure is due to diversifying selection on a quantitative trait. The trait is influenced by many genes, and the most extreme genotypes have a small advantage. For low recombination rates, the species splits into two. For intermediate rates get an ecocline.

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danielfalush.bsky.social @danielfalush.bsky.social · 27/01/2025

So what biological factors might explain this component of variation? Klebsiella recombines frequently, meaning that clonal relationships cannot obviously account for this species-wide structure. Population structure might, except you find the same lineages everywhere.

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danielfalush.bsky.social @danielfalush.bsky.social · 27/01/2025

Another way to visualize this is by looking at pairwise Linkage Disequilibrium (LD) between the most differentiated genes. This shows that PC1 captures the structure of association with PC1 values explaining pairwise LD between genes well.

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danielfalush.bsky.social @danielfalush.bsky.social · 27/01/2025

We think that this structure is due to a genome-wide component of variation, which can be captured for example using Principal Components Analysis (PCA). A handful of loci in the genome contribute disproportionately to PC1 values, these loci are the most different between different ends of the tree.

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danielfalush.bsky.social @danielfalush.bsky.social · 27/01/2025

Have you never noticed the "backbone" in a tree of Klebsiella pneumoniae genomes? Did you ever wonder what might be causing it? If so, very interested to hear what you thought.

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danielfalush.bsky.social @danielfalush.bsky.social · 27/01/2025

Excited to share our preprint "A putative ecocline in Klebsiella pneumoniae" and super-interested to get your feedback. Really want to use the hive mind to get to the bottom of this phenomenon ASAP. www.biorxiv.org/content/10.1...

biorxiv.org

A putative ecocline in Klebsiella pneumoniae

Are quantitative traits important for bacteriology? The quantitative trait models used in animal and plant genetics assume that the trait takes continuous values and is influenced by many variants cir...

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