Bacteria chromosomes contain Genomic Islands that provide virulence, antibiotic resistance, MGE-defence,... They transfer between cells, but the mechanism of most remains elusive.
Here we explore the conjugative capacity of these mysterious Genomic Islands.
www.biorxiv.org/content/10.6...
Preprint alert๐ข! โจEver wondered how much bacterial parasites influence evolutionary outcomes of their host?
โก๏ธ We co-evolved two bacterial strains in conditions in which the costs and benefits of prophage carriage varied
Here is what we found. โจwww.biorxiv.org/content/10.6...
โจ#MicroSky #PhageSky
๐งต
๐จOur new article is out in #PLOS Pathogens!
What drives nestedness in phagesโbacteria interactions network in an agro-ecosystem? ๐ฑ
๐ journals.plos.org/plospathogen...
#Phagesky @inrae-pv.bsky.social @phimresearch.bsky.social @phagedirectory.bsky.social
(Yes, that's a phage in those kinetics!)
No Genetics? Try ASOs โ A non-genetic approach to silence genes at the phage-host interface. We use it to study jumbo phage biology and anti-phage defence.
@jorg-vogel-lab.bsky.social @helmholtz-hiri.bsky.social
@uni-wuerzburg.de @helmholtzhzi.bsky.social
published now in @nature.com
At last ! A tool specifically for phage-plasmid hunters. Check tyPPing by @karinailchenko.bsky.social and @eugenpfeifer.bsky.social
If you look for phage-plasmids, you absolutely have to try tyPPing!
Results and user guide on bioRxiv, GitHub+Zenodo
Check out: bsky.app/profile/kari...
Super proud (!) of the work by @karinailchenko.bsky.social & happy + many thanks to awesome collaboration with @epcrocha.bsky.social and R Bonnin.
๐จ New preprint! ๐งฌ
๐๐ก๐๐ ๐-๐ฉ๐ฅ๐๐ฌ๐ฆ๐ข๐๐ฌ (๐-๐๐ฌ) are fascinating elements: both ๐ญ๐๐ฆ๐ฉ๐๐ซ๐๐ญ๐ ๐ฉ๐ก๐๐ ๐๐ฌ and ๐ฉ๐ฅ๐๐ฌ๐ฆ๐ข๐๐ฌ โก๏ธ tricky to detect.
We present ๐ญ๐ฒ๐๐๐ข๐ง๐ โ the first ๐ข๐๐๐ง๐ญ๐ข๐๐ข๐๐๐ญ๐ข๐จ๐ง ๐๐ง๐ ๐๐ฅ๐๐ฌ๐ฌ๐ข๐๐ข๐๐๐ญ๐ข๐จ๐ง ๐ญ๐จ๐จ๐ฅ ๐ ๏ธdesigned specifically for P-Ps:
โ
Accurate
โ
Sensitive
โ
Easy to use
๐ www.biorxiv.org/content/10.1...
New preprint out! ๐งฌ๐ฆ ๐ฑ
What shapes #phageโbacteria #networks in #plant environments?
- Ecological origins of bacteria and phages?
- Phage taxonomy?
- Bacterial phylogeny?
- #Prophages? #Defence-systems?
๐ here: www.biorxiv.org/content/10.1...
Discover which of these actually shape the network ๐
After many years in the making, here is our host range #phage paper with #ecology, #evolution and #biocontrol perspectives published in Molecular Ecology! @phimresearch.bsky.socialโฌ @inrae-pv.bsky.socialโฌ #PVBMT #JulianGarneau onlinelibrary.wiley.com/doi/10.1111/...
These are our key findings:
Habemus paper! Our story on integron-encoded anti-phage defenses is now out in @science.org! 16 new systems, small versions of known ones, and a lot more in this highly-collaborative study.
Many thanks to everyone involved, especially my supervisor @epcrocha.bsky.social
bsky.app/profile/bapt...
Overall, our findings underscore the complex interplay within the gut microbiome, where antibiotics not only affect bacteria but also reshape the associated phage communities, and in turn again influence the bacterial populations.
We look forward to get further interesting insights in future works!
We believe that its phages are the key players!
By targeting these dominant bacteria, these phages create opportunities for other bacterial species to re-colonize, ultimately helping to regain diversity in the gut!
We believe that "Kill-the-Winner" dynamics are at play: Antibiotics create a disturbance allowing certain bacteria to flourish.
Parabacteroides distasonis is one of those, and typically thrives after cephalosporin treatment.
What wasn't fully understood was why it loses its dominance.
3rd: Despite the initial loss of some phage species, we saw a temporary and significant increase in the number of dominant, virulent phages. But why?
2nd: Gut phages are unique to each individual (nothing new) and here we show that your unique phage "fingerprint" largely persists even after strong perturbations. So, in a way, your phages remain truly yours!
We studied the dynamics of gut phage populations in healthy individuals who received antibiotic treatment: 3rd Gen Cephalosporins.
1st: Antibiotics๐do not only just affect bacteria๐ฆ but also their viruses. We observed a 20% decrease in the richness+diversity, but (lucky us) it recovers over time!
Excited ๐ฅณ to share our latest work on gut phages!
Big thanks to @epcrocha.bsky.social, Erick D, Camille d'H, @fplazaonate.bsky.social, Quentin LB, and all others involved for support and contributions! ๐
Out in Cell Reports @cp-cellreports.bsky.social
doi.org/10.1016/j.ce...
Here's what we found ๐ค
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/...
This work sheds light on the underappreciated role of phages in post-antibiotic gut microbiome recovery. We think this is just the beginning!
More infos here: github.com/EpfeiferNutr...
and๐
doi.org/10.5281/zeno...
A great example:
Parabacteroides distasonis known to bloom after treatment๐ฆ โก๏ธ๐and only when its phages were absent.
But when they (phages) were around and burst ๐ P. distasonis bacteria were hardly detectable ๐ฆ โก๏ธ๐ชซ
๐งWe believe these phages help gut recovery! ๐ก๏ธ
They prevent bacterial blooms of (e.g., antibiotic-resistant) species that would otherwise dominate the gut.
๐ฅ Most surprising: some phages thrived the day after treatment! More than on any other day.
๐ BUT: these phages were virulentand NOT induced prophages. So, what is their role ๐ค?
So, what happens to gut phages after antibiotics?๐ค 20% of them vanished after treatment ๐, but over time, recovery occurred
๐The response was highly individual-specific, reinforcing the uniqueness of each personโs microbio- and phageome!
We found >6400 phage species๐งฎ, lots of high quality๐, most predicted to be temperate, ca. 1900๐ ones, and (super exciting!) a lot are also phage-plasmids!
๐งWe fine-tuned the analysis of the phageome part taken from the CEREMI trial๐
Briefly: 22 volunteers (healthy background) received antibiotic treatment๐ typical for a clinical setting. Their ๐ฉ were analyzed over a period up to 180 days after treatment for phages and bacteria
Excited๐จto share our first work on the human gut phageome doi.org/10.1101/2025...
Always inspiring to work with @epcrocha.bsky.social , Erick D, Camille d'H and everyone else within this super dynamic consortium
@inrae-france.bsky.social+@pasteur.fr+@inserm.fr! Many thanks for this great journey!๐
New preprint. Large genomes vibriophages have it all: multiple functions, autonomy (full set of tRNA genes!), anti-defenses, broad host range. Yet, they remain rare, pinpointing the limits of generalists. Great collaboration with @fredoleroux.bsky.social led by Charles Bernard in our lab.
