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Eduardo Rocha

@epcrocha.bsky.social
3K followers 579 following 123 posts

Scientist, genomics, evolution, microbiology, computational biology, Institut Pasteur/CNRS, Paris

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Eduardo Rocha @epcrocha.bsky.social · 22/09/2026
Lots of discussions on TA's role. These are often addictive, but this has a limited impact in stabilising genomic regions in the long term. And TAs also don't really distribute like anti-phage systems (which does not mean they aren't). The mystery goes on!
comparison of TA and defense systems distributions
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Eduardo Rocha @epcrocha.bsky.social · 22/09/2026
Do addictive systems stabilise the neighbouring chromosomal regions? In the long term, not really. TAs are in chromosomal hotspots with high gene turnover and we find that neighbouring genes get lost by mechanisms independent of TA loss. TAs also get pseudogenised and lost (starting with Toxins)
presence and absence of TA systems
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Eduardo Rocha @epcrocha.bsky.social · 22/09/2026
We experimentally validated 50 of the TAs and they varied a lot in their ability to impose a post-segregational killing phenotype. Still, most of the functional ones did show such a significant addiction score, which contributes to explain their abundance.
functional, addictive TA systems
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Eduardo Rocha @epcrocha.bsky.social · 22/09/2026
We start with a genome having 80 TA systems of type II (yes, 80, same genome): Photorhabdus laumondii TT01. What could 80 such systems be doing in the same genome? Defend from phages? Stabilise the chromosome? Being selfish ?
distribution of TAs in selected genomes
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Eduardo Rocha @epcrocha.bsky.social · 17/03/2026
When a novel function emerges in a lineage it would often be in the best interest of the individuals to keep the innovation private. Yet, again, mobile genetic elements capturing the novel function will increase their reproductive rate and will inevitably spread it across species.
lifecycle of functional innovation by horizontal gene transfer
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Eduardo Rocha @epcrocha.bsky.social · 17/03/2026
HGT is driven by mobile genetic elements. Yet, the elements themselves are often co-opted for other functions by the host genome. Many of the best understood cases of functional innovation come from domestication of (parts of) mobile elements.
domestication of mobile genetic elements
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Eduardo Rocha @epcrocha.bsky.social · 17/03/2026
Gene acquisition by HGT or duplication processes are very different, because HGT often involves novel genes. Even when they are homologous to existing genes, they are often quite different. This affects the subsequent evolutionary process.
Gene duplication versus gene acquisition by HGT
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Eduardo Rocha @epcrocha.bsky.social · 14/10/2025
We also observe a vibrant zoo of mobile genetic elements, specialised in what diversity they generate. Plasmids drive transfer of pathogenicity, temperate phages of antiphage junctions. Unexpected & intriguing agents include novel phage-plasmids (linear and circular) and plasmid-phage-satellites.
Gene content and phylogenetic placement of novel satellite–plasmid elements
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Eduardo Rocha @epcrocha.bsky.social · 14/10/2025
Our results show the importance of spatial segregation of the agents (bacteria, temperate and virulent phages) in different compartments (water column, locations within oysters) in the stability of this dynamical system. No obvious predator-prey cycles here.
Predator–prey dynamics during the 2021 sampling season
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Eduardo Rocha @epcrocha.bsky.social · 14/10/2025
Two intensive sampling periods of oyster-associated vibrio and their phage, 4 years apart, and many surprises. Despite being washed by the Atlantic, wide tides, and vibrio (almost?) disappearing most of the year, we can find the exact same virulent phages 4 years later (down to 0 SNP)! preprint👇
Lytic phages form modular isolation networks and exhibit long-term genetic stability
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Eduardo Rocha @epcrocha.bsky.social · 23/07/2025
Plasmid mobility can evolve rapidly. Some plasmids evolve faster than others and carry preferentially certain cargo functions, such as antibiotic resistance, other change in terms of mobility from helpers to hitchers, from phages to conjugative, others may simply die out. 8/9
the evolution of plasmid mobility
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Eduardo Rocha @epcrocha.bsky.social · 23/07/2025
Plasmids can be targeted by bacteria and other MGEs (including other plasmids) for destruction by multiple defense systems. But they can also fight back creating a diversity of positive and negative interactions with cells and other MGEs. 7/9
plasmids strike back
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Eduardo Rocha @epcrocha.bsky.social · 23/07/2025
Some plasmids seem to be able to pick their hosts (and/or being picked by their hosts). This involves molecular interactions promoting targeted conjugation or phage-plasmid infection. 6/9
plasmids pick their hosts
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Eduardo Rocha @epcrocha.bsky.social · 23/07/2025
Other plasmids are also phages, others are satellites of phages. This brings balance to the world of mobile genetic elements, both phages and conjugative elements can be of type integrative (in the chromosome) or plasmids. Advantages and disadvantages of these types are open to understanding. 5/9
Phage-plasmids versus conjugative plasmids
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Eduardo Rocha @epcrocha.bsky.social · 23/07/2025
Most plasmids require other plasmids to transfer between cells (hitchers) or enjoy some sort of lazy mobility. This is only now being quantified and understood in detail. 4/9
mechanisms of hitchers and lazy plasmids to transfer between cells.
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Eduardo Rocha @epcrocha.bsky.social · 23/07/2025
Now that there are tens of thousands of completely sequenced plasmids, one gets the opportunity not only to understand their diversity but also study their molecular biology at the light of their ecology and impact on microbial populations. 3/9
statistics on plasmids
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Eduardo Rocha @epcrocha.bsky.social · 23/07/2025
Conjugation is now understood in exquisite detail in a few systems, but many questions remain: What exactly happens in the recipient cell? How does it occur in some major clades (Cyanobacteria, Archaea)? What is the cost of the process (for donors and recipients)? 2/9
conjugation history and distribution of ralaxases and conjugative systems
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Eduardo Rocha @epcrocha.bsky.social · 23/07/2025
Here's our new broad review on the extended mobility of plasmids, about all mechanisms driving and limiting their transfer. From conjugation to conduction, phage-plasmids to hitchers, molecular to evolutionary dynamics, ecology to biotech. The state of affairs. 1/9 academic.oup.com/nar/article/...
graphical abstract of the article the extended mobility of plasmids
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Eduardo Rocha @epcrocha.bsky.social · 09/05/2025
WARNING: We have a postdoc position to work on the follow-up of this work. If you're interested, the deadline is tomorrow !!! (but I'll wait a few more days for interested candidates). research.pasteur.fr/fr/job/postd...
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Eduardo Rocha @epcrocha.bsky.social · 16/04/2025
New postdoc position in our lab (2 y+): evolutionary genomics of integrons and MGEs with focus on vibrio-phage interactions. Great environment @pasteur.fr for science, career building. Super collaborators @celineloot.bsky.social @amazeld.bsky.social @fredoleroux.bsky.social 3 weeks to apply!
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Eduardo Rocha @epcrocha.bsky.social · 14/04/2025
The Paired Difference Index revealed variations in the ability to infect the best host (relative to all others). Inversely, a vibrio clade lost the phage receptor and became resistant to all phages. Together, we show that the most generalist phages tend to infect the most generalist vibrios.
phage-vibrio interaction matrix
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Eduardo Rocha @epcrocha.bsky.social · 14/04/2025
Genomes are co-linear, w/high diversity regions: their pan-genome includes numerous defence and counter-defence systems (≥58, viperins, DNA modification, etc). This variability is caused by homologous recombination, which shifted a clade host spectrum (switch of receptor, narrower host range).
organisation of the phage genomes
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Eduardo Rocha @epcrocha.bsky.social · 14/04/2025
New paper @isme-microbes.bsky.social : Among a sample of 1044 vibrio phages, we found 17 new Schizotequatrovirus with large genomes (>250kb), a broad host range, and yet a low frequency in our samples (?!). #MicroSky #PhageSky
morphological and genomic distinctions of the phage
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Eduardo Rocha @epcrocha.bsky.social · 27/01/2025
Under our assumptions recombination accounts for up to 25% and 8% of all gene gains. We then looked closely at recombination tracts and their genomic context to identify these events. Transformation seems to favour shorter events and would account for ~6% (Ab) and 1% (Lp) of gene gains.
contexts of recombination in flanking core genes are associated with gene gains
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Eduardo Rocha @epcrocha.bsky.social · 27/01/2025
We showed before (doi.org/10.1371/jour...) that transformation varies a lot in A. baumannii and L. pneumophila. We now use this variation to identify recombination events putatively caused by transformation. Transformation slightly favours gene losses over gains, with little impact on genome size.
Transformation rates, genome size in A. baumannii
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Eduardo Rocha @epcrocha.bsky.social · 27/01/2025
The contribution of natural transformation for the acquisition of novel genes has been notoriously difficult to quantify because it relies on recombination (which is affected by other processes). Here's a first estimate : doi.org/10.1101/2025... (for the very busy: 1-6% of gene gains) #MicroSky
Transformation, Recombination and horizontal transfer
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Eduardo Rocha @epcrocha.bsky.social · 01/01/2024
Happy 2024!
A beach picture
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Eduardo Rocha @epcrocha.bsky.social · 07/11/2023
Finding similar results across large panels of 2 very different species suggests commonalities in how intragenomic conflicts drive transformation rates (which may be selected for many reasons) & shape bacterial evolution. Many thanks to co-authors, esp. amazing Fanny Mazzamurro & @labxc.bsky.social
models for the evolution of natural transformation
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Eduardo Rocha @epcrocha.bsky.social · 07/11/2023
Intragenomic conflicts explain the fewer MGEs in transformable strains. GWAS confirmed systematic negative associations between transformation & plasmids (Lp), prophages (Ab) & transposable elements (both). It fits the chromosome curing model but reveals additional intra-genomic conflicts.
GWAS showing the association between MGEs and low transformation rates
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Eduardo Rocha @epcrocha.bsky.social · 07/11/2023
We find that transformation rates evolve by large quick changes as a jump process across six orders of magnitude. Transformation is associated with (slightly) larger recombination rates, clear loss of linkage disequilibrium, and fewer restriction-modification systems.
Transformation rates across the two bacterial species
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Eduardo Rocha @epcrocha.bsky.social · 31/10/2023
3/3 These acquisitions may provide low-level resistance or tolerance to quinolones. We propose they give bacteria time to acquire the high-resistance point mutations (that fix exceedingly fast). Thanks to all co-authors, and esp. Charles Coluzzi (not here yet) ! academic.oup.com/mbe/article/...
Functions acquired before emergence of resistance to quinolones.
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Eduardo Rocha @epcrocha.bsky.social · 31/10/2023
2/3 We found many events of gene transfer syst. preceding mutations giving resistance to quinolones. Accounting genetic linkage, we obtained groups of co-integration events, many being mobile genetic elements. Hence, MGEs spread resistance, but may also "prepare" genetic backgrounds for resistance.
groups of genes associated with subsequent acquisition of mutations to quinolones
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Eduardo Rocha @epcrocha.bsky.social · 31/10/2023
1st post on a ms just out in #MBE. We have been playing with the idea that horizontal gene transfer by shaping genetic backgrounds can affect patterns of adaptation by point mutations (or other changes) in core genes. We apply a recent method to identify significant chronologies HGT -> mutation. 1/3
Establishing chronologies
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