The Belgian start-up is looking to revolutionize the microbiome profiling through advanced fluorocoding and optical mapping technology.
It leverages unique patterns of short nucleotide repeats (4-mers) along microbial genomes to create robust taxonomic barcodes.
This enables precise, strain-level taxonomic classification within three hours, without the need for DNA amplification or library preparation.
Arno Bouwens, R&D director at Perseus Biomics, told NutraIngredients, that “while sequencing has been groundbreaking in this field, we now believe it’s not the most efficient tool for this task.”
Revolutionizing microbiome analysis
The technology originated at the University KU Leuven, where the founding researchers initially used fluorescent molecules to analyze human DNA.
“After exploring bacterial phages, we realized the potential to identify bacterial species,” Bouwens said.
“We spent time developing methods to extract long DNA molecules and discovered we could distinguish strains that are 99.9% identical at the nucleotide level.
“This was surprising, as we weren’t using sequencing— yet we found that strains differ not only by sequence but also by genome structure, which was revealed by our technology’s ability to zoom out on the DNA molecule.”
Perseus Biomics was then founded in 2020, transitioning the technology from the university to a scalable system two years later.
“Now, we offer our technology as a service, providing microbiome data much faster than sequencing, which usually takes months,” Bouwens said.
Furthermore, next year will see the launch of the company’s benchtop device, which aims to make the technology accessible for users conducting tests on their own.
Patented optical DNA mapping technology
The tech company was adamant to address limitations in the microbiome field, explained Bouwens.
“Sequencing is like a hammer, where everything starts to look like a nail—it’s being used for many types of microbiome analysis, but we believe it’s not the best approach for all of them."
He explained that sequencing bacteria multiple times isn’t necessary, and without wanting to replace it, Bouwens believes his company’s solution is better for microbiome analysis and strain tracking.
Despite the perceived simplicity of the process, Perseus Biomics sits alone in this style of mapping.
“The optical mapping of DNA, though used in the Human Genome Project in the 90s, faced significant technical challenges that made it difficult to advance,” Bouwens added. “This process, which helped improve genome assembly, was largely unused after its initial application.”
Perseus Biomics identified two key challenges: the need to reliably linearize DNA molecules on a surface (using molecular combing) and extract long DNA molecules from samples.
“Solving both issues at once was a risky endeavor, but we took the gamble four years ago and eventually found a successful solutions,” Bouwens said. “Now the company holds patents for its DNA labeling technology, molecular combing process and associated algorithms.”
Probiotic applications
The technology is particularly beneficial for probiotic companies, as it simplifies tracking probiotic strains in the gut, a task that typically requires expensive sequencing, Bouwens said.
Perseus Biomics’ clients include companies developing probiotics such as AB-Biotics, which is using the DynaMAP technology to explore how its probiotics influence the gut microbiome and whether these probiotics survive and are detectable.
Other collaborators include companies in precision fermentation, even one company that makes sourdough bread and needs to identify the strains in their sourdough mixes to influence the bread’s taste.
Fast and affordable enterotyping
DynaMAP aims to revolutionize clinical applications by leveraging strain resolution technology, particularly in the development of a tool for microbiome enterotyping, which categorizes microbiome compositions.
“This tool could help identify dysbiotic enterotypes, linked to conditions like inflammatory bowel disease and multiple sclerosis,” Bouwens said.
“With an added software layer, we could offer a fast, affordable and efficient way to conduct enterotyping, avoiding the high costs and complexities of sequencing.”
This, he projects, may lead to an in vitro diagnostic tool, subject to certification. However, the top priority for now is to “get the technology out there and help people discover its applications.”
“We want to address the problems that people currently face with sequencing, especially the questions that existing technologies can’t answer,” Bouwens said.
He will be presenting DynaMAP on stage during the IPA World Congress + Probiota 2025, to be held in Copenhagen from Feb. 5 to 7.
