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daniel falush

@DanielFalush

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Statistical genetics of bacteria, humans etc. Hiring at all levels - do get in touch.

Institute Pasteur Shanghai
Joined September 2014
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@DanielFalush
daniel falush
9 months
Our paper "An Ancient ecospecies of Helicobacter pylori" was published yesterday in Nature. Thanks to Elise, Roberto, Sarah and our collaborators in Oita, Gothenburg and elsewhere for their hard work.
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nature.com
Nature - ‘Hardy’ Helicobacter pylori ecospecies shares the ancestry of ‘Ubiquitous’ H. pylori from the same region in most of the genome but has nearly fixed...
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@DanielFalush
daniel falush
23 days
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
daniel falush
23 days
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
daniel falush
23 days
Unregulated genes provide clues about the ecological advantage of fast swimming in viscous liquids. A Type 6 secretion system and nutrient uptake genes are unregulated, allowing the bacteria to kill and devour bacterial prey.
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@DanielFalush
daniel falush
23 days
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
daniel falush
23 days
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
daniel falush
23 days
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
daniel falush
23 days
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 Sarah
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@DanielFalush
daniel falush
26 days
RT @leo_speidel: Postdoc position in my group in Tokyo! .Please get in touch if you are interested. And happy to discuss projects - rang….
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riken.jp
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@DanielFalush
daniel falush
5 months
Thank you for reading our thread, please read the preprint too! your comments on all aspects are extremely welcome.
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@DanielFalush
daniel falush
5 months
So in summary our atlas provides a new way of systematizing prokaryotic life, suggesting that diverse species form ecologically selected clusters.
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@DanielFalush
daniel falush
5 months
The convergence in ecospecies differentiation between the two streptococcus species, involving the same genes and gene categories (cell division related), suggest that particular genera find predictable paths for adaptive differentiation.
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@DanielFalush
daniel falush
5 months
The first two bacterial ecospecies, 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
daniel falush
5 months
And the first bacterial ecospecies threesome, in Streptococcus oralis.
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@DanielFalush
daniel falush
5 months
We illustrate this concretely by discovering a third bacterial ecospecies pair in Streptococcus mitis.
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@DanielFalush
daniel falush
5 months
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
daniel falush
5 months
Finally, 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
daniel falush
5 months
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
daniel falush
5 months
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
daniel falush
5 months
Why has it taken us so long to update it? Like fine wine, it has matured. 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
daniel falush
5 months
Delighted to present our Macrogenetics atlas of prokaryotes. 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?"
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biorxiv.org
Background Bacteria typically have more structured populations than higher eukaryotes, but this difference is surprising given high recombination rates, enormous population sizes and effective...
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