Bacteriophage Lab of Institut Pasteur

@phagepasteur.bsky.social

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Our team is studying bacteriophages that are viruses infecting bacteria. Since 2006, Laurent Debarbieux has reignited a research lab about phage therapy following the pionnering work of Félix d'Herelle started in early 20th century.

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
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
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
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
F´elix d’H´erelle, 1873–1949. Contributor: HistoricImages / Alamy Stock Photo
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
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
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
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
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
Ngoc-Minh-Chau Nguyen receiving a prize for her poster titled "From mouse to man: building models to quantify the dynamic interactions between bacteriophages and bacteria on the pulmonary epithelium" 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
Postdoc Nandita Sharma, presenting her poster "Interspecies competition between Citrobacter rodentium and Escherichia coli involves prophages" at the Phages in Nancy conference
Fig 2. L'equipe BBH
Fig 1. LE CHEF
Figure 2. The BBH lab team (mostly)
Figure 1. The boss