Oligonucleotide Primer Set for Enterococcus faecalis EF-2001 Detection

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Solution Overview

Problem

Current methods lack the ability to rapidly and specifically distinguish the Enterococcus faecalis EF-2001 strain from closely related bacterial strains, which is crucial for identifying probiotic versus pathogenic bacteria, given its biological modulating activities and potential health impacts.

Innovation Solution

A primer set comprising specific oligonucleotide pairs (e.g., SEQ ID NOs: 1-30) is designed to amplify chromosomal DNA regions unique to Enterococcus faecalis EF-2001, enabling rapid and specific detection through PCR, and a method involving heat treatment to produce a heat-treated lactic acid bacterium composition.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Measurement precision

If conventional detection methods are used, then general lactic acid bacterium detection is possible, but specific identification of Enterococcus faecalis EF-2001 strain cannot be achieved

Engineering Contradiction:

Improvedetection specificityVSAvoiddetection method complexity

Core Design Contradiction:

Measurement precisionVSDevice complexity

Solution Approach 1:

The detection system is segmented into multiple primer sets, each targeting specific chromosomal regions (contigs 1, 4, 7, 11, 13, 16, 22, 25, 31, 43) of the EF-2001 strain. This segmentation allows specific identification through multiple independent detection channels, improving measurement precision without requiring a single complex detection system.

Inventive Principle:

Principle #1Segmentation

Solution Approach 2:

The patent creates digital copies of specific chromosomal DNA regions through PCR amplification using designed primer pairs. These amplified DNA copies serve as detectable markers that specifically identify the EF-2001 strain, enabling precise detection without directly analyzing the entire genome, thus reducing detection complexity.

Inventive Principle:

Principle #26Copying

2Productivity

If rapid detection is implemented, then identification speed is improved, but detection accuracy may be compromised

Engineering Contradiction:

Improvedetection speedVSAvoididentification accuracy

Core Design Contradiction:

ProductivityVSMeasurement precision

Solution Approach 1:

The primer sets are pre-designed and pre-optimized to target conserved chromosomal regions of the EF-2001 strain. This preliminary design ensures that when rapid PCR detection is performed, the primers immediately bind to specific targets, achieving both high speed and high accuracy simultaneously without requiring complex real-time analysis.

Inventive Principle:

Principle #10Preliminary action

Solution Approach 2:

The patent replaces complex multi-step identification systems with a simplified PCR-based detection mechanism. By substituting mechanical/biological identification processes with molecular amplification and detection, the system achieves rapid results while maintaining high accuracy through specific primer binding to unique chromosomal sequences.

Inventive Principle:

Principle #28Mechanics substitution (Replace mechanical system)

3Reliability

If probiotic strain identification is prioritized, then health safety is improved, but detection complexity increases

Engineering Contradiction:

Improvestrain identification reliabilityVSAvoiddetection system complexity

Core Design Contradiction:

ReliabilityVSDevice complexity

Solution Approach 1:

The detection system applies local quality by designing primers that target specific local chromosomal regions (contigs 1, 4, 7, 11, 13, 16, 22, 25, 31, 43) unique to the EF-2001 strain. Each primer pair is optimized for its specific target region, enabling reliable strain identification through localized detection rather than comprehensive genome analysis, thus reducing overall system complexity.

Inventive Principle:

Principle #3Local quality

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

The primer set allows for the specific identification of Enterococcus faecalis EF-2001 strain without cross-reacting with related strains, and the heat-treated composition enhances TNF-α production, facilitating the detection and utilization of this strain in probiotic and food applications.

Implementation Method 1

Methodology Applied

Scientific EffectPCR amplification:

Implementation Method 2

a method involving heat treatment to produce a heat-treated lactic acid bacterium composition

Methodology Applied

Scientific EffectHeat treatment: Heat Treatment

Data Source

PatentUS20240318265A1Lactic acid bacterium detection primer set, and detection method using said primer set

Publication Date: 2024.09.26 NIHON BERUMU CO LTD

AI summary

The present invention provides: a primer set capable of identifying lactic acid bacterium EF-2001 strain specifically; and a detection method using the primer set.According to the present invention, a primer set for use in the detection of lactic acid bacterium EF-2001 strain is provided, which comprises oligonucleotides comprising a combination of SEQ ID NOs: 1 and 2, SEQ ID NOs: 4 and 5, SEQ ID NOs: 7 and 8, SEQ ID NOs: 10 and 11, SEQ ID NOs: 13 and 14, SEQ ID NOs: 16 and 17, SEQ ID NOs: 19 and 20, SEQ ID NOs: 22 and 23, SEQ ID NOs: 25 and 26, and/or SEQ ID NOs: 28 and 29, or oligonucleotides comprising a combination of SEQ ID NOs: 1 and 3, SEQ ID NOs: 4 and 6, SEQ ID NOs: 7 and 9, SEQ ID NOs: 10 and 12, SEQ ID NOs: 13 and 15, SEQ ID NOs: 16 and 18, SEQ ID NOs: 19 and 21, SEQ ID NOs: 22 and 24, SEQ ID NOs: 25 and 27, and/or SEQ ID NOs: 28 and 30.