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Bacteriophage Lab of Institut Pasteur @phagepasteur.bsky.social · 03/10/2026

The Boss is in Radio France ......... NOW!!!! You should tune in 📻 www.radiofrance.fr

Bacteriophage Lab of Institut Pasteur @phagepasteur.bsky.social · 02/10/2026

🔵⚪🔴Les détails sont tenus secrets mais allumez votre poste de radio sur Radio France ce samedi entre 11h et 12h, ça devrait vous intéresser 😏 #phage #BigBang

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Bacteriophage Lab of Institut Pasteur @phagepasteur.bsky.social · 28/09/2026

We commented on this work a few months ago so it was great to have him on site to ask him our follow up questions bsky.app/profile/phag...

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Bacteriophage Lab of Institut Pasteur @phagepasteur.bsky.social · 28/09/2026

We believe this face will be familiar to the #phage community in here The BBH lab is quite pleased to be hosting Jeremy Barr (@jeremyjbarr.bsky.social), from Monash University, for the upcoming months. We were off to a good start with his presentation on gut #microbiome last week @pasteur.fr

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Bacteriophage Lab of Institut Pasteur @phagepasteur.bsky.social · 23/09/2026

This review was performed by Devon Conti and Caroline Henrot, the two latest alumni from the BBH lab We're happy to see their effort come to fruition and we hope you find it informative and enjoyable #gut #phages

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Bacteriophage Lab of Institut Pasteur @phagepasteur.bsky.social · 23/09/2026

Bet that when you woke up this morning you thought "you know what would be nice? A review of #microbiome research performed with #OMM12 mice" 🐀 Well, have we got some good news for you The latest paper from the BBH lab was published TODAY 🚨 www.tandfonline.com/doi/full/10....

tandfonline.com

The OMM12 mice: a decade of dissecting host-microbiome interactions

Humans and their associated microbes form a multifaceted ecosystem. Gaining mechanistic insight into this system necessitates reductionist models integrating ecological and immunological dimensions...

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Bacteriophage Lab of Institut Pasteur @phagepasteur.bsky.social · 18/09/2026

2026 seemed to be the summer of #phage in the press 🎥 and we've been happy to participate This is a good way to get the message out there about phage #therapy and we're definitely noticing increased interest The Boss is scheduled for a couple more of these interviews. We'll keep you posted 😎

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Bacteriophage Lab of Institut Pasteur @phagepasteur.bsky.social · 17/09/2026

We'll be participating in this online course from @pasteuredu.bsky.social and so should you!! Enrollment is now open and the format provides several advantages in terms of language and timing Take a look at the program and join us to learn more about how #phage can be used against #AMR

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Bacteriophage Lab of Institut Pasteur @phagepasteur.bsky.social · 15/09/2026

New lab member at the BBH!! 🚨 Niamh Diver-Hall from the @uofgsii.bsky.social is joining our #gut team for the next year, as part of her Master's degree Her work will center in #phage defense and antidefense systems in gut bacteria 🦠 Welcome!!

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Bacteriophage Lab of Institut Pasteur @phagepasteur.bsky.social · 09/09/2026

The Boss was invited to participate in the #ERSCongress2026 🫁 congress this week in Barcelona He got to advocate for #phage therapy in front of a pretty sizeable crowd during the "Beyond antibiotics" session Thanks for the invite!! @europeanrespsoc.bsky.social

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Bacteriophage Lab of Institut Pasteur @phagepasteur.bsky.social · 03/08/2026

Well, we did it, folks! The BBH lab has a GitHub account 💻 We've been enjoying diving more into #Bioinformatics as of late and have decided to start sharing some of our tools through here, give us a follow! github.com/BBHphagelab

github.com

BBHphagelab - Overview

Bacterium Phage Host lab. BBHphagelab has 4 repositories available. Follow their code on GitHub.

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Bacteriophage Lab of Institut Pasteur @phagepasteur.bsky.social · 31/07/2026

Thanks to the folks at KU Leuven, particularly @hannelorelongin.bsky.social , for welcoming @moreautanais.bsky.social , one of our PhD candidates, this week! Tanaïs was happy to discuss all things "phageFACTor" but there was also time to enjoy some local views ...... and delicacies 🍟🍪

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Bacteriophage Lab of Institut Pasteur @phagepasteur.bsky.social · 10/07/2026

THAT'S A WRAP ON #VoM2026 FOR THE BBH LAB !!! We had a blast sharing all things #phage with all the teams present A HUGE congrats to the organizing committee for their amazing work all these days, they really knocked it out of the park #phagesky

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Bacteriophage Lab of Institut Pasteur @phagepasteur.bsky.social · 10/07/2026

The Viruses of Microbes conference is coming back to France!!! 🇫🇷 We're also happy to share that The Boss will be part of the organizing committee, led by the great team of Fréderic Laurent See you in Lyon in 2028!!

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Bacteriophage Lab of Institut Pasteur @phagepasteur.bsky.social · 10/07/2026

Well, the audience responded with something else, as well Alejandro's presentation was awarded the Intralytix award for "Best oral presentation" in the phage therapy category 🥳 A nice capper, recognizing the work of the BBH lab at #VoM2026

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Bacteriophage Lab of Institut Pasteur @phagepasteur.bsky.social · 09/07/2026

Perhaps also some representatives from the 2028 meeting in this photo? 👀👀👀

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Bacteriophage Lab of Institut Pasteur @phagepasteur.bsky.social · 09/07/2026

We were very happy to show some of our Immunophage synergy work at #VoM2026 during the Phage therapy session Our Postdoc @bohorquezalejo.bsky.social was able to summarize our work on this area and the audience responded with multiple, insightful questions

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Bacteriophage Lab of Institut Pasteur @phagepasteur.bsky.social · 08/07/2026

If you're in the mood for some (un)friendly bacterial competition, Nandita Sharma can tell you all about it and how prophages are involved 🦠 We keep hearing that prophages are cool, we'll keep you posted in any developments 😎 #phagesky #VoM2026

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Bacteriophage Lab of Institut Pasteur @phagepasteur.bsky.social · 08/07/2026

If immune response to phages is more of your cup of tea, we got you covered! Nicolas Dufour will be at poster number 93 to talk about phage-induced antibody response 🩸 #phagesky #VoM2026

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Bacteriophage Lab of Institut Pasteur @phagepasteur.bsky.social · 08/07/2026

Getting an early start for today's poster session at #VoM2026 First up, we have poster 17 by @ltanoeiro.bsky.social If you're interested in prophages or Campylobacter, you should come talk to him

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Bacteriophage Lab of Institut Pasteur @phagepasteur.bsky.social · 07/07/2026

On the same session, Marie Messika will be discussing her recent results on enteric phages at board 132 You don't wanna miss it #phagesky #VoM2026

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Bacteriophage Lab of Institut Pasteur @phagepasteur.bsky.social · 07/07/2026

If you happen to be at #VoM2026 the BBH lab has content for you on EVERY poster session 😎 On Tuesday, you can come by board 225 to check out Solène's work on tail fiber replacement See you at 2:30!!

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Bacteriophage Lab of Institut Pasteur @phagepasteur.bsky.social · 06/07/2026

The BBH is ready for #VoM2026 !!!! 🦠 We've been roaming the sites and taking in beautiful Prague The conference is off to a very good start with today's lectures + welcome reception We'll try to keep you updated on the proceedings

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Bacteriophage Lab of Institut Pasteur @phagepasteur.bsky.social · 01/07/2026

We’re happy to introduce phageFACTor (Functional Annotation and Curation Tool) 👩‍💻Developed by Tanaïs Moreau, our most recent PhD candidate, and building on Phold, we were able to improve annotation of prophage genes by as much as 50% 🧬 You should check it out github.com/TMs-code/pha...

In this example, we're showing the improvement in the percentage of annotated genes from prophage "Maintenon" from Clostridium innocuum (doi: 10.1186/s40168-023-01541-x) using the phageFACTor pipeline

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Bacteriophage Lab of Institut Pasteur @phagepasteur.bsky.social · 08/06/2026

Filipa Vale (IMED) and Alexander Harms (@ethz.ch) came by last week and we had some great discussions on all things #prophage and #phage It's not every week you have not one but TWO great scientists visiting you, so we had to celebrate with a nice apéro Hope to have you guys here more often!!

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Bacteriophage Lab of Institut Pasteur @phagepasteur.bsky.social · 03/06/2026

BTW, this collaboration has recently yielded some cool results 😎 We've been a bit slow to share but be on the lookout for our post about this in the coming days

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Bacteriophage Lab of Institut Pasteur @phagepasteur.bsky.social · 03/06/2026

We took a road trip yesterday to @inrae-france.bsky.social and had a pretty fun time sharing with our collaborators over there Despite having worked together for a while, some of us couldn't put faces to names over there, so it was a great opportunity to share with them Thanks for hosting us!

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Bacteriophage Lab of Institut Pasteur @phagepasteur.bsky.social · 26/05/2026

Once again, sharing part of the discussion that we had at the BBH about an interesting paper This time, it was this work performed at US San Diego about antibiotic/phage interaction in a single patient If you're interested, we've got a thread for you!! 🧵 #Phage #Phagesky

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Bacteriophage Lab of Institut Pasteur @phagepasteur.bsky.social · 26/05/2026

It also underscores the need for more studies like this one, joining clinical and laboratory approaches to better understand interactions between phage and bacteria within a patient More evidence will lead to better insight and, in turn, improved phage therapy outcome

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Bacteriophage Lab of Institut Pasteur @phagepasteur.bsky.social · 26/05/2026

Overall, though the results are hard to extrapolate (being a single case, as acknowledged by the authors) this work provides the basis for the exploration of the chemobiotherapy concept and raises interesting aspects of the phage antibiotic interaction in the host

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Bacteriophage Lab of Institut Pasteur @phagepasteur.bsky.social · 26/05/2026

❓- Immunological response to the phages was puzzling, since there seems to be a lack of anti-phage IgG in the patient, despite long-term exposure Why isn't there class switching in the host? Is cellular immunity reducing their activity?

Fig. 5: Intravenous phage efficacies are differentially tempered by antibody-mediated neutralization.

Taken from Luong, T., Kharrat, L., Champagne-Jorgensen, K. et al. Ecological partitioning enables phage–antibiotic cooperation in a human Pseudomonas infection. Nat Commun 17, 2615 (2026). https://doi.org/10.1038/s41467-026-69247-w

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Bacteriophage Lab of Institut Pasteur @phagepasteur.bsky.social · 26/05/2026

✅ - Sidenote: It doesn’t escape us that this is another successful outcome using a Pakpunavirus, named after the PAK_P1 phage isolated in the BBH >20 years ago!! 😎

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Bacteriophage Lab of Institut Pasteur @phagepasteur.bsky.social · 26/05/2026

✅ - This allowed for a peculiar scenario in which a bacterial population could be evaluated for a long period of time in a host environment The authors use a multidisciplinary approach that favours the interpretation of the bacteriological findings on a clinical context

Fig. 2: Co-therapy accelerates airway obstruction relief across functional and radiographic measures.
a, b Spirometric evidence of improved airway mechanics. a Forced vital capacity (FVC, green) and percent-predicted FVC (ppFVC, blue) over time. Dashed line indicates mean baseline FVC = 3.00 ± 0.12 L. b FEV₁/FVC ratio, representing the relationship between airflow and volume, expressed as percent change over time. The declining ratio during treatment reflects persistent small-airway damage limiting full recovery. c Quantitative computed tomography (qCT) chest images in the axial lung window after 2 days of ciprofloxacin alone (left) and one day post-coadministration (right). Reduced opacity in the left upper lobe indicates decreased inflammation. d Bar graphs showing reduced lobar air-trapping percentages following co-therapy. Values are reported for total lung (TL), right lung (RL), left lung (LL), right upper lobe (RUL), right lower lobe (RLL), left upper lobe (LUL), and left lower lobe (LLL). e Mid-maximal expiratory flow (MMEF, L s−1) derived from spirometry confirms partial small-airway clearance. f Principal-component analysis (PCA) biplot of 16 dimensionally reduced patient data sets integrating pulmonary, hematologic, and renal indices. Each circle represents a single day’s standardized data, colored by treatment phase; hierarchically defined clusters are circled. Arrows indicate variable loadings (see Table S5). Vector directionality and sample convergence toward baseline indicate an additive contribution of phage therapy relative to antibiotic monotherapy.

Taken from Luong, T., Kharrat, L., Champagne-Jorgensen, K. et al. Ecological partitioning enables phage–antibiotic cooperation in a human Pseudomonas infection. Nat Commun 17, 2615 (2026). https://doi.org/10.1038/s41467-026-69247-w

Fig. 3: Distinct phage and antibiotic timescales collapse multidrug-resistant Pseudomonas and restore a lower-burden chronic state.
a–c Quantification of bacterial dynamics in sputum. a Relative abundance of Pseudomonas in metagenomes. b Absolute abundance normalized to human reads, revealing bacterial load reductions otherwise obscured by dominance. c Layered area chart of mucoid (blue) and nonmucoid (yellow) subpopulations, expressed as colony-forming units (CFU) per mL of sputum. Persistent layering of mucoid behind nonmucoid counts indicates phenotype dominance. Vertical dashed lines mark key events: ciprofloxacin initiation (day –4), phage initiation (day 0), and end of co-therapy (day 14). d Heatmap of isolate susceptibilities to phages P1A, PYO2, and ciprofloxacin (CIP), separated by phenotype and collection day. Plaque formation indicates sensitivity (yellow); absence indicates resistance (maroon). Asterisks denote isolates analyzed by automated antibiotic susceptibility testing

Taken from Luong, T., Kharrat, L., Champagne-Jorgensen, K. et al. Ecological partitioning enables phage–antibiotic cooperation in a human Pseudomonas infection. Nat Commun 17, 2615 (2026). https://doi.org/10.1038/s41467-026-69247-w

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Bacteriophage Lab of Institut Pasteur @phagepasteur.bsky.social · 26/05/2026

📝 - Chemobiotherapy implies that "phages and antibiotics act as coordinated but nonsynergistic selective forces whose effects are constrained and partitioned by microbial ecology and host immune modulation within a heterogeneous infection landscape" This case is used as a practical example of it

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Bacteriophage Lab of Institut Pasteur @phagepasteur.bsky.social · 26/05/2026

📝 - Authors use the case of a cystic fibrosis patient infected with P. aeruginosa and treated with a combination of antibiotics + phage to explore chemobiotherapy, a concept previously used in the cancer field (with some differences) This entailed the evaluation of the patient for >100 days !!!

Figure 1. a Timeline of clinical events (gray) and intravenous (IV) antimicrobial treatments (colored) for pulmonary exacerbation in an elderly patient with CF. Time is shown relative to the first IV phage dose (vertical dashed line, day 0); the second dashed line marks the end of all IV therapies (day 15). First-line colistin + ceftazidime was discontinued early due to acute kidney injury (AKI). b Posterior-to-anterior chest x-rays at hospitalization (left) and immediately before co-therapy (right) show persistent left-upper-lobe consolidation (yellow arrow). The reduced but unresolved opacity underscores the need for continued treatment. c Heatmap of minimum inhibitory concentrations (MICs) for patient sputum isolates (values in Table S2). Mucoid colonies (top) were largely susceptible, whereas nonmucoid colonies (bottom) were extensively drug-resistant. ND indicates MIC not determined d Forced expiratory volume in 1 s (FEV₁, green) and percent-predicted FEV₁ (ppFEV₁, blue) over time. The dashed line denotes the mean baseline FEV₁ (1.49 ± 0.06 L).

Taken from Luong, T., Kharrat, L., Champagne-Jorgensen, K. et al. Ecological partitioning enables phage–antibiotic cooperation in a human Pseudomonas infection. Nat Commun 17, 2615 (2026). https://doi.org/10.1038/s41467-026-69247-w

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Bacteriophage Lab of Institut Pasteur @phagepasteur.bsky.social · 26/05/2026

This new paper by the folks over at UC San diego caught our eye, so we thought we'd give our two cents on it. As we've been doing in previous posts: 📝Premise ✅What we liked ❓Questions it raised for us www.nature.com/articles/s41... All images are taken from the original paper

nature.com

Ecological partitioning enables phage–antibiotic cooperation in a human Pseudomonas infection - Nature Communications

This case report presents a multi-omics case analysis of intravenous phage-antibiotic co-therapy in a patient with cystic fibrosis during an acute-on-chronic pulmonary exacerbation caused by multidrug...

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Bacteriophage Lab of Institut Pasteur @phagepasteur.bsky.social · 25/04/2026

#OTD in #Phage history: In 1873, the phage therapy pioneer Félix d’Hérelle was born!!! His amazing work at @pasteur.fr and other institutions laid the foundation in which groups like the BBH were founded You can read more about his fascinating life story here www.pasteur.fr/en/institut-...

F´elix d’H´erelle, 1873–1949. Contributor: HistoricImages / Alamy Stock Photo

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Bacteriophage Lab of Institut Pasteur @phagepasteur.bsky.social · 26/03/2026

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

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Bacteriophage Lab of Institut Pasteur @phagepasteur.bsky.social · 26/03/2026

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.

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Bacteriophage Lab of Institut Pasteur @phagepasteur.bsky.social · 26/03/2026

❓ - 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 ?

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

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Bacteriophage Lab of Institut Pasteur @phagepasteur.bsky.social · 26/03/2026

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

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Bacteriophage Lab of Institut Pasteur @phagepasteur.bsky.social · 26/03/2026

✅ - 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

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Bacteriophage Lab of Institut Pasteur @phagepasteur.bsky.social · 26/03/2026

📝 - 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

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

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Bacteriophage Lab of Institut Pasteur @phagepasteur.bsky.social · 26/03/2026

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

elifesciences.org

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Bacteriophage Lab of Institut Pasteur @phagepasteur.bsky.social · 19/03/2026

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...

nature.com

Isolation, engineering and ecology of temperate phages from the human gut - Nature

Human host-associated cellular products may act as induction agents for bacteriophages.

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Bacteriophage Lab of Institut Pasteur @phagepasteur.bsky.social · 19/03/2026

❓- 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!!

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

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Bacteriophage Lab of Institut Pasteur @phagepasteur.bsky.social · 19/03/2026

❓- 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

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Bacteriophage Lab of Institut Pasteur @phagepasteur.bsky.social · 19/03/2026

✅- 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

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