With bacterial strains of the same species exhibiting remarkably different characteristics, it is vital biotic developers accurately characterise what strains are present in their product. This enables developers to maximise the biotics’ therapeutic potential, provide consumers with transparent information, comply with regulatory requirements, and retain intellectual property alike.
Widely used short read analysis can fail to resolve these differences because the genomic variation between strains is often so slight, leading to low resolution analysis.
A Fluorescent Light in the Dark
In an exciting new pre-print, Perseus Biomics, a Belgium-based biotechnology start-up, present their technology, DynaMAP (Dynamic Microbiome Abundance Profiling), as a solution for the problem of achieving high resolution microbiome analysis.
The technology, which leverages optical mapping of fluorocoded DNA to resolve bacteria at a strain level, demonstrated it can distinguish between strains that have 99.5% average nucleotide identity (ANI) similarity – a feat that can be unreliable using traditional short-read NGS.
‘By imaging a bacterium’s genome structure instead of reading every nucleotide, DynaMAP quickly and easily reveals strain-defining features in complex samples’
explains Arno Bouwens, R&D Director Perseus Biomics
Answering the Unanswerable From Biotics to Biomarkers
DynaMAP’s use cases are wide-reaching, from biotic development to biomarkers, with the technology already being implemented across several exciting projects.
Biotic developers are leveraging its strain-tracking capabilities to monitor the impact of their probiotic strain on the composition of the gut microbiota. Many probiotic strains are from the same species as those found in the natural gut microbiota making DynaMAP an indispensable tool in their studies.
In the biomarker development space, Perseus’ clients are utilizing DynaMAP’s high sensitivity to identify specific microbial signatures associated with various conditions down to the strain level. For instance, the OPADE Project are using the technology to develop predictive biomarkers to improve diagnosis and treatment of patients with major depressive disorders.
Additionally, this strain tracking capability is not just limited to in vivo use cases, with fermented food and probiotic manufacturers also using DynaMAP to monitor the strain composition of their fermenters and for QC.
In fact, ‘DynaFERM’ is a collaboration between Puratos and Perseus Biomics to monitor the yeast and bacteria strains found in their industrially produced sourdough batches. The high resolution, fast turnaround nature of DynaMAP means the presence of unwanted strains can be quickly detected, minimising contamination and limiting waste of compromised batches. The technology will also ensure better taste and product quality.
A Path to Clinical Integration
The pre-print comes at a point when the limitations of NGS analysis are being acknowledged as one potential bottleneck for the adoption of microbiome analysis in the clinic.
A frontiers editorial entitled “Integration of NGS in clinical and public health microbiology workflows: applications, compliance, quality considerations” cited NGS’ lack of standards and computationally intensive workflows, as barriers to its greater use.1
DynaMAP could represent a technology that fills the unmet need in the microbiome analysis field – bridging the gap between the lab and the clinic by being user-friendly, scalable, and delivering same day results.
How Does DynaMAP Work?
DynaMAP combines the power of advanced fluorocoding and optical mapping to enable rapid detection of bacteria in a sample with a one-day turnaround time. The process begins with DNA extraction, which produces long DNA fragments ready to be analysed. The fragments are then tagged by a site-specific enzymatic labelling reaction and combed onto a flat surface. Single-molecule fluorescence microscopy creates a unique optical map for each fragment and a finely-tuned pattern-matching algorithm compares these maps with reference databases to confirm the strains. This outcome is achieved without the need for DNA amplification or library preparation, creating an unbiased workflow.
Unprecedented Precision in Microbiome Analysis
In the new paper, scientists used controlled bacterial strain mixtures to validate DynaMAP’s capabilities through a round of tests.
DNA Mix Shows Near-Perfect Species Detection
In the first test, DynaMAP was evaluated using a mixture of DNA from five bacterial species in equal proportions. The system showed consistent species recovery with relative abundances between 17-23% (expected 20%), and when tested against a larger database of nearly 5,000 genomes, maintained remarkably low false positive rates of just 0.034%.
Accurate Bacterial & Yeast Profiling
In the second experiment, DynaMAP was tested on the ZymoBIOMICS microbial community standard D6300, containing various bacteria and yeasts. Through five repeat experiments, the system accurately measured bacterial abundances with no gram-strain bias, though some species were underrepresented due to resistance factors. The system showed a detection limit of 0.1% and demonstrated strong correlation with SMS-based analysis, showing only 1-5% variation in relative abundances.
Precise Strain-level Resolution
Following the strong results in the second test, DynaMAP was tested for its ability to distinguish between closely related strains. To do this, an alignment test was conducted using the ZymoBIOMICS standard against a comprehensive strain database (containing up to 4,428 strains for E. coli). The results demonstrated DynaMAP could distinguish between strains with up to 99.5% average nucleotide identity (ANI) similarity.
Real-World Ready: Human Microbiome Analysis
In the final experiment, DynaMAP’s performance was tested on faecal microbiomes from five human stool samples. Comparative analysis with SMS showed comparable abundance measurements and precision levels.
Taking to the Stage
If you’re interested in learning more about this paradigm-shifting technology, Arno Bouwens, R&D Director of Perseus Biomics, is set to present at the upcoming Microbiome Times Partnering Forum – taking place March 18th-19th. Bouwens’ talk entitled “DynaMAP: Precision Metagenomics Beyond Sequencing” will explore the results of the pre-print, together with an exclusive sneak peek of the benchtop device Perseus Biomics is developing.
Citation
- Yang, S. et al. (2024) ‘Editorial: Integration of NGS in clinical and Public Health Microbiology workflows: Applications, compliance, quality considerations’, Frontiers in Public Health, 12. doi:10.3389/fpubh.2024.1357098.