Multiplex qPCR Kit for F. Prausnitzii Phylogroup Differentiation

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Solution Overview

Problem

Current methods for diagnosing inflammatory bowel disease (IBD) lack accuracy and specificity, particularly in distinguishing between Crohn's disease and ulcerative colitis, and there is a need for improved methods to quantify Faecalibacterium prausnitzii phylogroups for disease diagnosis and treatment prediction.

Innovation Solution

A novel multiplex quantitative polymerase chain reaction (qPCR) method using species-specific primers and hydrolysis probes designed for the 16S rRNA gene of Faecalibacterium prausnitzii phylogroups I and II, allowing for accurate quantification and differentiation of these groups in intestinal samples.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Measurement precision

If conventional diagnostic methods are used for IBD, then the diagnostic process is simple, but the diagnostic accuracy and specificity are insufficient

Engineering Contradiction:

Improvediagnostic accuracyVSAvoiddiagnostic method complexity

Core Design Contradiction:

Measurement precisionVSDevice complexity

Solution Approach 1:

The diagnostic method is segmented into multiple independent components: species-specific primers for F. prausnitzii detection, phylogroup-specific probes for differentiation (PHGI vs PHGII), and quantitative analysis modules. This segmentation allows each component to be optimized independently while maintaining overall diagnostic accuracy and enabling modular implementation that balances precision with manageable complexity.

Inventive Principle:

Principle #1Segmentation

Solution Approach 2:

The invention changes the parameter of measurement from general bacterial presence to specific phylogroup differentiation within F. prausnitzii. By introducing phylogroup-specific probes that target distinct genetic sequences, the method transforms a single-parameter detection into a multi-parameter analysis system, thereby improving diagnostic specificity without proportionally increasing operational complexity.

Inventive Principle:

Principle #35Parameter changes

2Measurement precision

If F. prausnitzii quantification is performed using existing methods, then the procedure is straightforward, but the ability to distinguish between phylogroups I and II is insufficient

Engineering Contradiction:

Improvephylogroup differentiation accuracyVSAvoiddetection complexity

Core Design Contradiction:

Measurement precisionVSDifficulty of detecting and measuring

Solution Approach 1:

The invention introduces phylogroup-specific probes as intermediary elements that mediate between the target DNA and the detection system. These probes act as selective intermediaries that bind to phylogroup-specific sequences, enabling differentiation between PHGI and PHGII. The intermediaries translate genetic sequence differences into detectable signals, improving phylogroup identification accuracy while maintaining procedural simplicity through standardized probe hybridization protocols.

Inventive Principle:

Principle #24Intermediary (Mediator)

3Adaptability or versatility

If IBD diagnosis relies on current biomarkers, then the diagnostic workflow is simple, but the ability to predict therapeutic efficacy is limited

Engineering Contradiction:

Improvetreatment prediction capabilityVSAvoidbiomarker analysis complexity

Core Design Contradiction:

Adaptability or versatilityVSDevice complexity

Solution Approach 1:

The F. prausnitzii quantification method serves multiple functions: it detects bacterial presence, differentiates phylogroups, diagnoses IBD, and predicts therapeutic response. This multi-functionality is achieved through a single integrated assay that provides comprehensive information from one sample analysis, reducing the need for multiple separate tests and thereby managing complexity while enhancing adaptability across different clinical decision-making scenarios.

Inventive Principle:

Principle #6Universality (Multi-functionality)

Applied Scientific Principles

This section explains which scientific principles are used to turn an abstract innovation direction into a practical engineering solution.

Function Achieved in This Case

Enables precise quantification of Faecalibacterium prausnitzii phylogroups, serving as biomarkers for intestinal disease detection, differential diagnosis, and predicting therapeutic efficacy, improving diagnostic accuracy and treatment outcomes for IBD.

Implementation Method 1

Methodology Applied

Scientific EffectPolymerase chain reaction (PCR):

Implementation Method 2

species-specific primers and hydrolysis probes designed for the 16S rRNA gene

Methodology Applied

Scientific EffectHybridization:

Data Source

PatentUS12516386B2Kit for the quantification of <i>Faecalibacterium prausnitzii </i>phylogroup I and/or phylogroup II members and the use thereof as biomarkers

Publication Date: 2026.01.06 GOODGUT SL

AI summary

The present invention relates to a novel method for an accurate quantification in intestinal samples of Faecalibacterium prausnitzii phylogroup I members (PHGI) and/or Faecalibacterium prausnitzii phylogroup II members (PHGII). It further relates to a method for detecting intestinal diseases, including the screening, diagnosis, differential diagnosis, and/or monitoring of disease activity or progression in a human subject comprising determining the abundance of PHGI and/or PHGII in an intestinal sample from said subject. Moreover, it relates to a method for the prediction of the efficacy of a drug in the therapeutic treatment of an intestinal disease in a human subject comprising determining the abundance of PHGI and/or PHGII in an intestinal sample from said subject.