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MDM lab

@mdmlab.bsky.social

Molecular Diversity of Microbes Lab at Institut Pasteur Focusing on bacterial immunity 🦠🧬🧫 // We ♥️ sharing our science with everyone // PI Aude Bernheim

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MDM lab @mdmlab.bsky.social · 23/11/2023

Congrats to the leading authors Baptiste Gaborieau, Hugo Vaysset, and @ftesson.bsky.social and to all the great team. www.biorxiv.org/content/10.1...

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MDM lab @mdmlab.bsky.social · 23/11/2023

Finally, we show the application of such predictions by establishing a pipeline to recommend tailored phage cocktails to target pathogenic strains from their genomes only🧬💻. We show higher efficiency of tailored cocktails on a collection of 100 pathogenic E. coli isolates.

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MDM lab @mdmlab.bsky.social · 23/11/2023

We then trained predictive algorithms to figure out which interactions we can accurately predict. We got an overall AUROC of 86%. We provide a roadmap for the future as it will allow us to focus on the 3,379 false negatives and 2,922 false positives that are not well predicted.

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MDM lab @mdmlab.bsky.social · 23/11/2023

On the phage side, the strain the phage was isolated on accounts for 53% of the variance (!). We show this is linked to the phage ability to adsorb which is driven by its Receptor Binding Proteins. Side note: Only ⅓ of out phages were able to infect Coli K-12

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MDM lab @mdmlab.bsky.social · 23/11/2023

Then came the team effort 🤩. We infected everyone against everyone generating a matrix >38000 interactions. This was done in triplicates with 3 concentrations. The matrix of interactions reveals complex (and beautiful !) patterns. How much of these do we understand ?

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MDM lab @mdmlab.bsky.social · 23/11/2023

We needed a dataset, diverse and at scale. We chose the Escherichia genus. We established 2 collections of 403 natural, diverse, Escherichia strains and 96 bacteriophages. We looked in their genomes 💻🧬 for traits related to infection (receptors, capsules, defense systems…).

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