Precision Microbiome Profiling: understanding the microbiome to deliver precision medicine

The impact of the microbiome on a person’s health and disease is only slowly being fully realized. Here Bio-Me introduce themselves and their work to factor in the microbiome to the delivery of precision medicine.

Technology developments often lead to new conceptual understandings of nature that drive science forward. DNA sequencing is an example of this, a technology that led us to the concept of Precision Medicine: the promise that we can utilize information stored in DNA to develop better medicines and to administer treatments tailored to the patient. So far Precision Medicine has yet to fully deliver on this promise. Complex diseases (e.g. cancer and diabetes) continue to pose major challenges to current medicine. We still tend to stratify and treat patients as large homogenous groups. Why so? What is missing?

At the same time as the DNA sequencing technology was used to understand our genomes, it was also used to explore the diversity of microorganisms that coexist with us – the Microbiome. We are walking hosts for thousands of microorganisms, at least as many non-human cells as our own. These microorganisms play essential roles in determining the state of our health and in development of disease. Could this be the missing piece needed to deliver on the promise of Precision Medicine?

Precision Microbiome Profiling – PMP™

DNA sequencing was an excellent tool for developing our understanding of the microbiome. We now understand that our microbiomes interact with every organ in our body. Our gut microbiota provides the bootcamp for training and regulating our immune systems. Our microbiomes play significant roles in regulating our metabolism, nervous system, and it can determine response to drugs.

A technology was needed that could translate microbiome discoveries into clinical solutions for precision medicine and enable us to factor in the microbiome. PMP™ was developed with this end in mind, a qPCR platform for accurate microbiome tests that can aid in diagnosing and stratifying patients. Bio-Me identified five key criteria for a clinical microbiome technology:
• High resolution. PMP™ provides resolution at species/sub-species level.
• Short turnaround time. PMP™ Results can be available in hours.
• Precision. PMP™ requires very few sample processing/analysis steps and enables an unparalleled precision level.
• Quantitation. PMP™ provides the absolute number of genomes per ng of DNA of analyte.
• Simplified regulatory approval. qPCR is already widely used in clinical diagnostics.

Development of Microbiome biomarkers

Access to large-scale studies with high quality clinical data is the key to making robust observations and developing good biomarkers.

Researchers at University of Gothenburg recently identified Ruminococcus gnavus as a major independent predictor of several established features of the metabolic syndrome, such as body fat, serum triglycerides, and HbA1c1. In this study a total of 5215 fecal samples from the HUNT Biobank in Norway were analysed on Bio-Me’s PMP™ platform.

In a Norwegian study in pediatric Inflammatory Bowel Disease (IBD)2
quantification of approximately 100 well-characterized bacterial targets with PMP™ enabled discrimination between the following groups of subjects with high accuracy: IBD vs healthy, IBD vs symptomatic non-IBD, and Ulcerous Colitis vs Crohn’s disease. PMP™ also predicted the future need for biologic therapy.

So how does PMP™ compare to well-established DNA sequencing techniques? Preliminary data from Karolinska Institutet in Sweden show excellent alignment between PMP’s absolute quantification approach and the current gold standard Shotgun metagenomic sequencing. This confirms PMP™’s potential as a reliable clinical tool.

Adoption of the PMP™ platform

Partnering with credible drug developers is key in Bio-Me’s business model. One example is Siolta Therapeutics. Siolta develops a live biotherapeutic drug for prevention of infant allergic disease. PMP™ is used to stratify patients and monitor key microbiome biomarkers over the course of the treatment. Bio-Me will develop a companion microbiome test to support the future market introduction of Siolta’s drug. Bio-Me also collaborates with key institutions working to solve challenges in areas such as cancer immunotherapy, hematopoietic stem cell transplantation, myeloma, and colorectal cancer.

Concluding remarks

It is essential to increase our understanding of the microbiome to deliver on the promise of Precision Medicine. The medical community is picking up on this and researchers are now increasingly encouraged to factoring the microbiome into their work. Bio-Me serves academia, clinical researchers, and industry researchers all over the world from its laboratory in Oslo, Norway.

Bio-Me.com

1 Lancet 2022; June 1; https://doi.org/10.1016/S2213-8587(22)00113-9
2 Microorganisms 2022;10(7);1273: https://doi.org/10.3390/microorganisms10071273