Artificial Exogenous Reference Molecule for Microorganism Comparison
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Solution Overview
Problem
Current methods for detecting and comparing microorganisms across different species are limited by the need for separate amplification and sequencing processes, making it difficult to accurately compare the types and abundance of microorganisms in the same spatial region.
Innovation Solution
The development of artificial exogenous reference molecules that contain universal primer sequence regions for multiple species, allowing for simultaneous amplification and sequencing, and include specific recognition sequences to facilitate type and abundance comparison among different species.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If separate amplification and sequencing processes are used for different species of microorganisms, then each species can be detected with species-specific primers, but it becomes difficult to compare types and abundance among different species in the same spatial region
Solution Approach 1:
The patent introduces artificial exogenous reference molecules as intermediary substances that contain universal primer binding sites. These reference molecules serve as a common reference framework across different species, allowing sequencing reads from different species to be normalized and compared against the same reference standard, thereby enabling cross-species type and abundance comparison while maintaining species-specific detection accuracy
Solution Approach 2:
The patent changes the parameter of primer universality by designing artificial reference molecules with universal primer binding sites that can be recognized by primers across different species. This parameter change allows the amplification system to simultaneously target multiple species with a unified primer set, transforming the detection system from species-specific to multi-species compatible
2Productivity
If universal primers are designed according to conserved regions to amplify all microorganisms, then large-scale sequencing can be performed, but amplification efficiency varies across different batches making accurate comparison difficult
Solution Approach 1:
The patent creates artificial copies (reference molecules) that replicate the conserved region structures needed for universal primer binding. These synthetic reference molecules serve as standardized templates that can be added to each batch, providing a consistent reference point that compensates for batch-to-batch variations in amplification efficiency and enables reliable normalization across different sequencing runs
Solution Approach 2:
The patent performs preliminary action by adding known amounts of artificial exogenous reference molecules to samples before amplification. This pre-added reference material serves as an internal control that allows post-processing normalization of sequencing data, correcting for variations in amplification efficiency and batch effects that occur during the sequencing process
3Measurement precision
If traditional morphological and biochemical classification methods are used, then microorganisms can be identified, but the process is time-consuming, energy-consuming, and inaccurate for large-scale batch detection
Solution Approach 1:
The patent replaces the mechanical and biochemical classification processes with a molecular biology-based sequencing system. Instead of using microscopes, staining procedures, and biochemical tests, the invention uses DNA amplification and sequencing technologies to directly analyze genetic material, dramatically reducing detection time and labor while improving accuracy and enabling high-throughput batch processing
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 efficient and accurate comparison of microorganism types and abundance across different species by allowing the artificial exogenous reference molecules to participate in amplification reactions, providing a standardized method for data normalization and relative quantification.
Implementation Method 1
A principle of the large-scale sequencing is achieved mainly based on features of genetic sequences of microorganisms... universal primers are designed according to these conserved regions, thereby to obtain, by amplification, fragments of all the microorganisms of the same species
Data Source
AI summary
The present invention provides an artificial exogenous reference molecule for type and abundance comparison among different species of microorganisms. The artificial exogenous reference molecule includes several species detection regions and several linker sequence regions, where the species detection regions and the linker sequence regions are arranged alternately; at least two species detection regions are provided and are species detection regions for different species; and the linker sequence regions are random sequences different from species sequences to be detected. The species detection region includes a primer sequence region and a specific recognition region; the sequence length of the specific recognition region simulates the characteristic detection sequence length of the corresponding species to be detected; and the sequence of the specific recognition region has obviously specific difference from the DNA sequence of a genome in the species to be detected without homology. The artificial exogenous reference molecule provided by the present invention may simultaneously contain universal primer sequence regions of two or more different microorganisms, also contains an artificially recognizable specific sequence, and is used for type and abundance comparison among different species of microorganisms.