CRISPR Microbiota Editing for Selective Bacterial Ratio Control

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Solution Overview

Problem

Existing technologies struggle to effectively inhibit bacterial population growth and alter the relative ratios of different bacterial species in mixed populations, particularly in environments such as human microbiota, without the need for prior genetic manipulation of host cells.

Innovation Solution

Utilizing a host modifying (HM) CRISPR/Cas system that harnesses wild-type endogenous Cas nuclease activity, comprising engineered CRISPR arrays and guide RNAs to selectively target and inhibit specific bacterial strains while sparing others, achieved through the use of vectors that introduce these components into host cells.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Reliability

If conventional methods are used to inhibit bacterial population growth, then some bacterial growth inhibition is achieved, but the ability to selectively target specific species while sparing others is insufficient

Engineering Contradiction:

Improveselectivity of bacterial inhibitionVSAvoidinability to distinguish between target and non-target bacteria

Core Design Contradiction:

ReliabilityVSObject-affected harmful factors

Solution Approach 1:

The patent applies local quality by designing CRISPR guide RNAs with species-specific sequences that target unique genomic regions of particular bacterial species. This allows the system to exert selective inhibitory action on target species while leaving non-target species unaffected, achieving reliable selective inhibition in mixed bacterial populations

Inventive Principle:

Principle #3Local quality

Solution Approach 2:

The invention segments the bacterial population into target and non-target groups by using multiple distinct guide RNAs, each specific to a different bacterial species. This segmentation enables differential control of bacterial subpopulations within the same ecosystem, resolving the contradiction between growth inhibition and selectivity

Inventive Principle:

Principle #1Segmentation

2Reliability

If CRISPR arrays are introduced into host cells to modify bacterial populations, then selective inhibition of specific strains is achieved, but the complexity of the system increases

Engineering Contradiction:

Improvespecificity of bacterial strain inhibitionVSAvoidcomplexity of CRISPR array introduction and maintenance

Core Design Contradiction:

ReliabilityVSDevice complexity

Solution Approach 1:

The patent employs a universal CRISPR-Cas system that can be programmed with different guide RNAs to target multiple bacterial species. The same Cas nuclease machinery serves multiple functions by recognizing different guide RNAs, each directing it to a specific bacterial target, thereby reducing overall system complexity while maintaining high specificity

Inventive Principle:

Principle #6Universality (Multi-functionality)

Solution Approach 2:

The guide RNA acts as an intermediary between the CRISPR-Cas system and the target bacterial DNA. This intermediary carries the species-specific recognition information, allowing the complex Cas nuclease to achieve high specificity without requiring complex structural modifications, thus resolving the contradiction between reliability and device complexity

Inventive Principle:

Principle #24Intermediary (Mediator)

3Manufacturing precision

If existing technologies attempt to alter bacterial ratios in mixed populations, then some population modification is achieved, but the precision and control over relative ratios are insufficient

Engineering Contradiction:

Improveprecision of bacterial ratio alterationVSAvoidability to control multiple bacterial species simultaneously

Core Design Contradiction:

Manufacturing precisionVSAdaptability or versatility

Solution Approach 1:

The patent implements dynamic control of bacterial populations by using inducible CRISPR systems where guide RNA expression can be activated or deactivated in response to environmental signals. This allows precise temporal and spatial control over which bacterial species are targeted, enabling accurate adjustment of bacterial ratios in mixed populations while maintaining adaptability to different ecological conditions

Inventive Principle:

Principle #15Dynamics

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

Achieves selective growth inhibition of specific bacterial species by at least 10-fold, allowing for the alteration of bacterial ratios in mixed populations, including human microbiota, and reducing the growth of antibiotic-resistant bacteria, while minimizing off-target effects.

Implementation Method 1

The HM-crRNA comprises a sequence that is capable of hybridising to a host cell target sequence

Methodology Applied

Scientific EffectHybridization:

Implementation Method 2

the HM-crRNA guides Cas to the target to modify the target sequence in the host cell

Methodology Applied

Scientific EffectNuclease activity:

Data Source

PatentUS12502401B2Altering microbial populations and modifying microbiota

Publication Date: 2025.12.23 SNIPR TECH

AI summary

The invention relates to methods, uses, systems, arrays, engineered nucleotide sequences and vectors for inhibiting bacterial population growth or for altering the relative ratio of sub-populations of first and second bacteria in a mixed population of bacteria. The invention is particularly useful, for example, for treatment of microbes such as for environmental, medical, food and beverage use. The invention relates inter alia to methods of controlling microbiologically influenced corrosion (MIC) or biofouling of a substrate or fluid in an industrial or domestic system.