Multiplex Microbial DNA Profiling for Rapid Species Identification
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Solution Overview
Problem
Existing methods for characterizing microbial populations, particularly the gut microbiota, are limited by time-consuming culturing processes and provide insufficiently comprehensive and accurate information due to variations in growth conditions and amplicon targeting in nucleic acid analysis, necessitating more sensitive and comprehensive methods for microbial detection and identification.
Innovation Solution
The use of nucleic acid compositions and methods involving specific nucleic acid sequences, including multiplex amplification of microbial populations using primers and probes that target unique and homologous nucleic acid sequences, enabling sensitive and accurate detection and identification of microbial species and levels, and multiplex amplification of microbial populations in a single reaction mixture.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If microbial culture processes are used to identify microbes, then microbial growth can be observed, but the process is time-consuming and provides limited information due to varying growth conditions
Solution Approach 1:
The patent replaces traditional mechanical microbial culture processes with nucleic acid-based molecular detection methods. Specifically, it uses nucleic acid extraction followed by amplification (PCR) and sequencing to directly detect microbial genetic material without requiring microbial growth, thereby eliminating the time-consuming culture step while maintaining or improving identification accuracy
Solution Approach 2:
The patent uses nucleic acid amplification techniques to create multiple copies of target microbial DNA sequences. By amplifying specific genomic regions (such as 16S rRNA genes), the method generates sufficient material for detailed analysis rapidly, avoiding the need to wait for microbial cultures to grow to detectable levels
2Productivity
If nucleic acid amplification methods are used to analyze microbial populations, then time and labor are reduced, but the comprehensiveness, accuracy, quality and depth of information obtained can vary and be limited by amplicons targeted and primers used
Solution Approach 1:
The patent segments the microbial genome into multiple distinct genomic regions for simultaneous analysis. Rather than targeting a single amplicon, the method analyzes multiple genomic loci (such as different regions of the 16S rRNA gene combined with other housekeeping genes), providing a more comprehensive and accurate characterization of microbial species while maintaining rapid throughput
Solution Approach 2:
The patent employs universal primers that can amplify conserved genomic regions across diverse microbial taxa, combined with variable regions for species-specific identification. This multi-functional approach allows a single methodology to characterize entire microbial communities comprehensively, from phylum-level to species-level taxonomy, without requiring multiple separate assays
3Loss of time
If traditional nucleic acid analysis methods are used, then culturing time is eliminated, but the information obtained is limited by the specific amplicons and primers targeted
Solution Approach 1:
The patent adds dimensional depth to microbial characterization by analyzing multiple independent genomic dimensions simultaneously. Instead of relying on a single amplicon, the method sequences multiple genomic regions (different gene loci, varying lengths, different functional categories), creating a multi-dimensional profile of each microbe that captures更全面 information about microbial identity, diversity, and functional potential
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 highly sensitive, specific, and accurate detection and identification of microbial species and levels, facilitating rapid and high-throughput assessment of microbial populations, particularly in the gut microbiota, for diagnosing and treating microbial imbalances and associated disorders.
Implementation Method 1
The primers and/or probes are capable of binding to, hybridizing to, amplifying and/or detecting target nucleic acids of microorganisms
Implementation Method 2
nucleic acid amplification (e.g., PCR) and/or sequencing
Data Source
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AI summary
The present disclosure provides compositions and methods, as well as combinations, kits, and systems that include the compositions and methods, for amplification, detection, characterization, assessment, profiling and/or measurement of nucleic acids in samples, particularly biological samples. Compositions and methods provided herein include combinations of microbial species target-specific nucleic acid primers for selective amplification and/or combinations of primers for amplification of nucleic acids from a large group of taxonomically related microorganisms. In one aspect, amplified nucleic acids obtained using the compositions and methods can be used in various processes including nucleic acid sequencing and used to detect the presence of microbial species and assess microbial populations in a variety of samples. In accordance with the teachings and principles, new methods, systems and non-transitory machine-readable storage medium are provided to compress reference sequence databases used in mapping sequence reads for analysis and profiling of microbial populations.