Eduardo Rocha
@epcrocha.bsky.social
Scientist, genomics, evolution, microbiology, computational biology, Pasteur Institute, Paris
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.
October 14, 2025 at 4:08 PM
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.
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.
October 14, 2025 at 4:08 PM
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.
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👇
October 14, 2025 at 4:08 PM
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👇
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
July 23, 2025 at 7:35 AM
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
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
July 23, 2025 at 7:35 AM
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
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
July 23, 2025 at 7:35 AM
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
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
July 23, 2025 at 7:35 AM
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
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
July 23, 2025 at 7:35 AM
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
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
July 23, 2025 at 7:35 AM
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
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
July 23, 2025 at 7:35 AM
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
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/...
July 23, 2025 at 7:35 AM
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/...
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...
May 9, 2025 at 1:07 PM
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...
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!
April 16, 2025 at 7:14 AM
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!
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.
April 14, 2025 at 8:36 AM
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.
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).
April 14, 2025 at 8:36 AM
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).
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
April 14, 2025 at 8:36 AM
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
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.
January 27, 2025 at 1:11 PM
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.
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.
January 27, 2025 at 1:11 PM
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.
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
January 27, 2025 at 1:11 PM
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
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
November 7, 2023 at 10:21 AM
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
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.
November 7, 2023 at 10:14 AM
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.
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.
November 7, 2023 at 10:13 AM
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.
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/...
October 31, 2023 at 4:33 PM
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/...
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.
October 31, 2023 at 4:28 PM
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.