Another week, another paper that we liked so much, we made a brief comment on

You should take a look! It's only a short thread 🧵

#Phage #Phagesky

While more experimental evidence is warranted, this work motivated a vivid discussion in our team!
It also reminds us that we are still far from understanding #phage biology even after >100 years of research.

Figure 2. Comparing the metabolic condition effect on phage adsorption rate. The y-axis of both panels represents the relative effect of growth in arsenate and azide (low metabolic condition) on the adsorption rate, η′, compared to the adsorption rate in the high metabolic condition, η, for hosts grown in glucose. Panel A displays this effect for each phage (x-axis), while panel B illustrates the relationship between the effect and the adsorption rate in glucose, η. The dashed line represents a fitted model on the metabolic state sensitive phages that examines and quantifies the correlation between η′/η and η. Taken from Anastasios Marantos Kim Sneppen Stanley BrownNamiko Mitarai2025Viral commitment to infection depends on host metabolismeLife14:RP107825 https://doi.org/10.7554/eLife.107825.1

❓ - The authors showed a decreased adsorption of phages in bacteria that are not actively growing. What does this imply for phage replication in the environment where bacteria are not actively replicating ?

❓ - However, some time points were over the doubling time of E. coli, while bacterial density was considered stable.

✅ - To circumvent the issue of different adsorption times for each phage authors used a standard mass-action kinetics model to make the result time-independent

Figure 1. Taken from Anastasios MarantosKim SneppenStanley BrownNamiko Mitarai2025Viral commitment to infection depends on host metabolismeLife14:RP107825 https://doi.org/10.7554/eLife.107825.1

📝 - This work aimed to compare the adsorption rate of 5 different E. coli phages (λ, ϕ80, M13, T6 and T5), under two different conditions: high and low metabolic activity.

The authors described how, for 4 out of 5 phages, the ratio of adsorption is higher under high metabolic activity

We recently came across this study (published on @elife.bsky.social ) and it caught our eye, so we decided to make a brief #phagesky comment on it
📝Premise
✅What we liked
❓Questions it raised for us
elifesciences.org/reviewed-pre...

All images are taken from the paper

We recently had a nice lab discussion about this work and wanted to share some of it on a short thread here 🧵

BTW, word on the street is that prophages are pretty cool 😎

#Phage #Phagesky

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

Figure 4A The number of induced prophages per sample (condition in rows and isolates in columns). The isolate phylum is shown along the top bar. Actinomycetota is shown in yellow, Fusobacteriota in black, Bacillota in blue, Pseudomonadota in red and Bacteroidota in teal. Cropped and highlighted (red squares) for emphasis on differences in phage induction results by different concentrations of the same stimuli Modified from from Dahlman, S., Avellaneda-Franco, L., Rutten, E.L. et al. Isolation, engineering and ecology of temperate phages from the human gut. Nature 647, 698–705 (2025). https://doi.org/10.1038/s41586-025-09614-7

❓- Given that prophage induction appears dose- and context-dependent, i.e: variable cue exposure leads to some non-overlapping induction profiles, we’re left to wonder, how many molecular mechanisms are behind prophage dynamics in the gut?

>100 years on, phages continue to surprise!!

❓- CaCo2 cells are a great start towards a gut context! — but could other gut cell populations act as inducers of different prophage subsets?

This also opens the path for exploring the spatial dimension (mucosa vs lumen vs crypts) given the cellular diversity between them

Figure 4A The number of induced prophages per sample (condition in rows and isolates in columns). The isolate phylum is shown along the top bar. Actinomycetota is shown in yellow, Fusobacteriota in black, Bacillota in blue, Pseudomonadota in red and Bacteroidota in teal. Cropped for emphasis on phage induction results by different stimuli Taken from Dahlman, S., Avellaneda-Franco, L., Rutten, E.L. et al. Isolation, engineering and ecology of temperate phages from the human gut. Nature 647, 698–705 (2025). https://doi.org/10.1038/s41586-025-09614-7

✅- Interesting results stemmed from

1) The choice of gut-relevant induction conditions such as human cellular products (CaCo2)

2) Detection of DGRs targeting non-tail genes in the induced phages, likely related to phage counter-defense genes

Figure 1A Schematic of the methods used. (1) Induction of pure-culture bacterial isolates with standard induction agents. (2) Bacterial synthetic community co-cultured with and without Caco2 cell monolayer. (3) Induction of bacterial isolate pure cultures with cell culture medium, Caco2 cells or cell products Cropped for emphasis on experimental design Taken from Dahlman, S., Avellaneda-Franco, L., Rutten, E.L. et al. Isolation, engineering and ecology of temperate phages from the human gut. Nature 647, 698–705 (2025). https://doi.org/10.1038/s41586-025-09614-7

📝 - Using multiple stimuli, Dahlman and co. induced 134 temperate phages, representing 18% of the predicted prophages, in a collection of 252 human gut bacteria

The authors characterize the induced phages and provide insight into factors governing the induction (or lack thereof) of prophages

Isolation, engineering and ecology of temperate phages from the human gut - Nature Human host-associated cellular products may act as induction agents for bacteriophages.

From time to time, we like to comment on recent papers that catch our attention

We found this one from Dahlman et al., @jeremyjbarr.bsky.social lab, very interesting indeed

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

📝- Premise
✅- What we liked
❓- Questions and prospective

(Images are taken from the paper)

The BBH lab has a new Doctor!!🚨🚨

Caroline Henrot, a member of our lab since 2022, defended her thesis last friday @pasteur.fr

This work focused on the induction of prophages, and other bacterial interactions, in the gut microbiota. It was performed in collaboration with @inrae-france.bsky.social

We have a new lab member at the BBH!

Meet Brice Gastineau, a Master 2 student who'll be joining us for the next 7 months. He'll be working with our Lung team 🫁, particularly with the lung-on-chip model

Welcome to the lab!

Today was Microbiology PhDay at @pasteur.fr where we highlighted the work of two of our PhD candidates

Solène Ecomard and Ngoc-Minh-Chau Nguyen participated with their posters on Tail fiber and Lung-on-chip, showing some of the good work performed by them at the BBH 👏

First post of 2026 for the BBH and it's a good one. This week, one of our PhD candidates, Caroline Henrot, took a big step in her journey by submitting her thesis document 🎉

Stay tuned for more news on her and her work, performed in collaboration with @inrae-france.bsky.social, throughout the year!

🚨New paper alert🚨

We were very pleased to see the publication of this work, product of our collaboration with the fine folks at @helmholtzmunich.bsky.social and @tum.de

That's a wrap on 2025 from the BBH lab!!!

www.tandfonline.com/doi/full/10....

Last friday one of our lab's Postdocs, Nandita Sharma, presented her "Work in progress" talk at @pasteur.fr

Her results deal with the role of bacterial competition in the microbiota and the factors at play determining its outcome. Really cool stuff that we'll be sharing in the near future

THIS WAS GREAT FUN!! The team was watching last night and we really enjoyed getting to be a part of it

Thanks to the production team for highlighting the BBH lab work, among other @pasteur.fr groups

If you missed it last night, no worries, you can check it out here

www.france.tv/documentaire...

We mentioned this a while back, so we thought we'd show you another photo from that day, taken from a different angle 😎

This documentary, featuring the boss, will premiere TONIGHT!!! at 21h in France 5

www.francetvpro.fr/contenu-de-p...

www.francetelevisions.fr/et-vous/notr...

We were at the "Phages in Nancy" meeting last week and had a very fun time!

You can read all about it on this tread 🧵

#phagesky

Thanks a lot to the organizers for a great meeting !!

See you all next year in Toulouse 😎

We mentioned that we had 5 posters, right?

Well, we saved this one for last because Ngoc-Minh-Chau Nguyen rocked the house and ended up leaving with a prize!!! 🏆

She was VERY lively while presenting her results so we were glad to see her work be recognized by the jury

bsky.app/profile/phag...

Eventually things got competitive, as we tried to assemble the lego phage

It took us a while to put the whole thing together but look, we're not structural virologists, ok?

Of course, not everything was work, the team also participated in the fun time at the gala dinner

Although, as soon as the boss saw this little lego phage, we were back to the classroom 🤓

Caroline Henrot, presenting her talk "Prophage-inducing bacteriocins are frequent in Escherichia coli intestinal isolates" at the "Phages in Nancy" conference

Caroline Henrot, presenting her talk "Prophage-inducing bacteriocins are frequent in Escherichia coli intestinal isolates" at the "Phages in Nancy" conference

Nicolas Dufour, presenting his talk "Phagothérapie et infection pulmonaire : état des lieux et défis à relever" at the “Phages, MICI, Phagothérapie & Co” session, attached to the "Phages in Nancy" conference

Nicolas Dufour, presenting his talk "Phagothérapie et infection pulmonaire : état des lieux et défis à relever" at the “Phages, MICI, Phagothérapie & Co” session, attached to the "Phages in Nancy" conference

We were also able to present two talks, one by Caroline Henrot and another by Nicolas Dufour (in the “Phages, MICI, Phagothérapie & Co” session)

Fun fact: Caroline is actually from Nancy so she had to represent in her hometown and she did a very good job!!

Postdoc Nandita Sharma, presenting her poster "Interspecies competition between Citrobacter rodentium and Escherichia coli involves prophages" at the Phages in Nancy conference

Camille Sivelle, presenting her poster "Explorations on the mechanisms that bacteria deploy to survive a bacteriophage cocktail challenge" at the "Phages in Nancy" conference

Solene Ecomard presenting her poster "Structure-function relationships between bacteriophage tail fibers and host range: investigations with Nankovirus and Pakpunavirus infecting Pseudomonas aeruginosa" at the "Phages in Nancy" conference

Jose Alejandro Bohorquez presenting his poster "Interaction between bacteriophages and innate immunity as a determinant for the efficacy of phage therapy" at the "Phages in Nancy" conference

Our group was able to participate with 5 posters by members of our "gut" and "lung" teams

There was lively discussion around them and we were happy to share our results

You'll notice we only shared 4 posters in here ............ I wonder why🤔

We were glad to take part in the "Phages in Nancy" meeting last week, organized by site.phages.fr and hosted by Xavier Bellanger

We'll share some of the highlights in this thread 🧵

TL,DR We had a good time visiting some of our Portuguese colleagues this week, where we talked #phage and ran into some old and new faces

Our visit had it all: good science, good food and even an unexpected seismic drill

You can read all about it on this thread 🧵