Advancing microbial genomics at Institut Pasteur with the PromethION 2 Integrated

At Institut Pasteur (Pasteur Institute), the Biomics team supports research into infectious diseases across a broad spectrum of organisms — from bacteria and viruses to fungi and parasites. To keep pace with evolving research needs, the group recently added the PromethION 2 Integrated (P2i) device into their workflows. We spoke to Chloé Baum (Institut Pasteur, France) about why they chose the P2i and how it is reshaping the support the team can provide.

Could you briefly introduce yourself and your background?

I’m a molecular biologist specialising in next-generation sequencing (NGS) technologies. After completing a joint PhD between New England Biolabs in the USA and Genoscope in France, where I focused on new sequencing approaches for studying microbial communities, I joined Biomics, the sequencing core facility at Institut Pasteur.

I now lead the wet-lab team, managing NGS services while implementing Oxford Nanopore sequencing for diverse research projects. My role combines technology development, service provision, and scientific consulting.

What kind of research projects does your team support?

Our mission is to provide researchers at Institut Pasteur with access to cutting-edge sequencing technology and help them use sequencing approaches tailored to their questions. Biomics supports research across infectious diseases, which means our work spans everything from genome assembly and metagenomics to pathogen surveillance and transcriptomics.

In recent years, demand for custom projects and experimental design support has grown. Our researchers are starting to dive deeper with their questions, so routine sequencing is no longer always the answer they need.

Why did you decide to incorporate Oxford Nanopore sequencing into your workflows?

For us as a core facility, Oxford Nanopore sequencing complements our Illumina short-read sequencing workflows. For example, for small genome assembly, we advise a nanopore-only approach. You don’t need to correct with short reads.

Oxford Nanopore sequencing has also expanded the range of applications we can support, such as direct RNA projects. For RNA viruses like dengue and chikungunya, which have short genomes (~10 kb), we can capture the full-length genome in a single read. It’s incredible.

Learn more about direct RNA sequencing projects from Chloé’s London Calling (2025) presentation.

Another application we are receiving more requests for is modification analysis of RNA or DNA. This opens exciting opportunities to better understand microbial biology, host-pathogen interactions, and gene regulation without requiring additional experimental workflows.

When it comes to offering sequencing that can capture long reads, Oxford Nanopore Technologies was the answer for us rather than PacBio. We liked the flexibility, portability, and simple setup. In addition, nanopore sequencing is widely used across the Pasteur Network in different countries, as it is more accessible for remote locations and for labs that are not core facilities. Therefore, we can support a wider range of researchers with this platform.

What prompted you to move from your previous configuration to the PromethION 2 Integrated (P2i)?

Before acquiring the P2i, we operated a PromethION 2 Solo connected to a GridION device. That setup wasn’t ideal for our needs as a core facility because we needed access to both devices separately, and our data output exceeded storage capacity.

The P2i combines sequencing and computing in a single device, making it far more user-friendly and autonomous for our researchers, with less time troubleshooting for me. The P2i has increased accessibility, while also boosting our overall sequencing capacity.

Have your workflows changed since implementing the P2i?

The P2i allows us to easily scale projects, for example, multiplexing up to 96 bacterial genomes on a single PromethION Flow Cell, which is a huge gain. At the same time, it maintains the flexibility we need to accommodate a diversity of project types. This is key when you work on a range of organisms, as they have different genome sizes and different methylation statuses, and we regularly come across the unexpected, so we must adapt.

Can you share how you have used Adaptive Sampling?

Adaptive Sampling has been invaluable. It enriches target organisms directly from complex samples without extra wet-lab steps.

We’ve used it to target specific pathogens for food safety analysis and assemble genomes from intracellular bacteria that couldn’t be isolated otherwise (either by enriching the target or depleting the host genome). We’ve also combined it with capture approaches to reduce the time to answer. As Adaptive Sampling is integrated into MinKNOW and there is great guidance documentation, it is now easy to pick up and apply this approach to the range of projects we receive.

How do you see Oxford Nanopore technology shaping the future of microbiology and infectious disease research?

I think it will continue to have a major impact on microbiology and infectious disease research by making sequencing more accessible and portable. Many institutes in the Pasteur Network operate in settings where rapid genomic insights are critical. The portability, ease of deployment, and real-time sequencing capabilities make in-field sequencing a reality, reducing turnaround times for critical decisions.

I also expect continued improvements not only in throughput and accuracy, but also in flow cell quality and stability. I hope to see ongoing development of solutions tailored to the needs of the microbiology community, where rapid, comprehensive, and cost-effective sequencing can have a major scientific and public health impact.

And finally — what excites you most about future developments?

I am particularly excited about the development of direct RNA sequencing, especially with the recent release of the Direct RNA Barcoding Kit. It makes the technique more cost-effective and scalable for microbiology applications and routine projects. Also, being able to analyse methylation and other modifications alongside DNA and RNA sequence data, all in one go, is something I can’t wait to fully explore.

See the bigger picture with PromethION 2 Integrated. Compact yet powerful, the P2i is designed for labs that need high-output sequencing without complexity.

See what’s possible. Discover more with PromethION 2 Integrated.

Oxford Nanopore Technologies products are not intended for use for health assessment or to diagnose, treat, mitigate, cure, or prevent any disease or condition.