Universal Nucleic Acid Extraction from Diverse Microbial Populations
Find Innovative SolutionsGenerate Solutions
Solution Overview
Problem
Current methods face challenges in extracting nucleic acid molecules from diverse populations of microbes in biological samples without compromising the genetic material of different microbe types, making it difficult to accurately determine food consumption and nutritional breakdown for health improvement and disease prevention.
Innovation Solution
A method involving sequential lysis steps using detergent, lysozyme, and chaotropic agents, along with mechanical disruption, to effectively extract nucleic acids from a variety of microbes, including bacteria, fungi, and viruses, allowing for metagenomics analysis to determine food consumption and probiotic customization.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Adaptability or versatility
If a single lysis method is used, then the process is simple, but nucleic acid extraction from diverse microbial populations is incomplete
Solution Approach 1:
The lysis process is divided into multiple sequential steps, each targeting specific microbial types: mechanical disruption for initial cell breakage, enzymatic lysis for bacteria and fungi, and chemical lysis for spores and resistant structures. This segmentation allows each method to be optimized for specific microbial groups while maintaining overall process manageability.
Solution Approach 2:
The combined lysis protocol serves as a universal method that can extract nucleic acids from all major microbial types (bacteria, fungi, spores, viruses) using a single integrated procedure. The multi-step approach functions universally across diverse microbial populations that no single method could handle effectively alone.
2Quantity of substance
If mechanical disruption is used, then nucleic acid yield increases, but energy consumption and equipment complexity increase
Solution Approach 1:
Mechanical disruption is performed as a preliminary step before enzymatic and chemical lysis. This initial mechanical breakage of cell structures makes subsequent enzymatic digestion more efficient, reducing the total energy required for complete lysis compared to using mechanical methods alone or in combination with less effective sequencing.
3Reliability
If sequential lysis steps are used, then extraction completeness improves, but processing time increases
Solution Approach 1:
The lysis steps are designed to proceed sequentially without idle time between operations. Each step builds on the previous one, with reagents and conditions optimized to maintain continuous progress toward complete nucleic acid release. The protocol eliminates unnecessary waiting periods while ensuring each lysis mechanism has sufficient time to act on its target structures.
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 the successful extraction and analysis of nucleic acids from diverse microbial populations, facilitating the determination of food consumption and nutritional breakdown, and enabling probiotic customization for improved health and disease prevention.
Implementation Method 1
mixing the sample with a first lysis solution comprising a detergent, e.g., SDS
Implementation Method 2
mixing the sample with a first lysis solution comprising a detergent, e.g., SDS, and a chelator, e.g., EDTA
Implementation Method 3
adding a second lysis solution having a lysozyme to the mixture of step a())
Implementation Method 4
adding a third lysis solution comprising a chaotropic agent, e.g., urea, lithium acetate, guanidine hydrochloride
Data Source
AI summary
Disclosed herein are methods of extracting genetic material from a diverse population of one or more types of microbes in a sample. Microbes can be prokaryotes or eukaryotes and may include bacteria, archaea, fungi, protozoa, helminths, parasites, viruses, phages, and others. Extraction may be from a single sample and subsequent identification may be through a molecular method such as qPCR, PCR, RFLP, SSCP, allele specific PCR, targeted sequencing, pull down sequencing, whole shotgun sequencing, or other methods. Also provided are methods that include extracting nucleic acid molecules from a variety of organisms such as fungi (i.e., Saccharomyces spp.), animal cells (Bos taurus), plants (e.g., Hordeum vulgare) from the gut of a human subject, performing a metagenomics analysis therefrom, and determining a probiotic treatment or dietary guidance for the subject based on the metagenomics analysis.