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Reposted

Chao Yang @chaooo.bsky.social · Aug 27

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

Nature Ecology & Evolution @natecoevo.nature.com · Aug 27

Combination of large-scale phylogenomic analysis, mouse lethality experiments and bacterial growth assays shows sheds light on how a pandemic clone of Vibrio parahaemolyticus was able to spread worldwide

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

Wave succession in the pandemic clone of Vibrio parahaemolyticus driven by gene loss - Nature Ecology & Evolution

A combination of large-scale phylogenomic analysis, mouse lethality experiments and bacterial growth assays shows that gene loss in the putrescine utilization pathway has enhanced biofilm formation an...

www.nature.com

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danielfalush.bsky.social @danielfalush.bsky.social · Jun 30

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.

danielfalush.bsky.social @danielfalush.bsky.social · Jun 30

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 · Jun 30

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 · Jun 30

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 · Jun 30

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 · Jun 30

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 · Jun 30

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 · Jun 18

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 · Jun 18

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 · Jun 17

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 · Mar 24

follow me Graham!

danielfalush.bsky.social @danielfalush.bsky.social · Feb 28

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

danielfalush.bsky.social @danielfalush.bsky.social · Feb 28

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 · Feb 28

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 · Feb 28

And the first bacterial ecospecies threesome, in Streptococcus oralis.

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danielfalush.bsky.social @danielfalush.bsky.social · Feb 28

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

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danielfalush.bsky.social @danielfalush.bsky.social · Feb 28

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 · Feb 28

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 · Feb 28

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 · Feb 28

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 · Feb 28

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 · Feb 28

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...

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 ...

www.biorxiv.org

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Reposted

Guillaume Méric @gmeric.bsky.social · Feb 27

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...

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 ...

www.biorxiv.org

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danielfalush.bsky.social @danielfalush.bsky.social · Jan 27

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 :).