Microbial Ecology Shift Assay for Reproducible Microbiome Analysis
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Solution Overview
Problem
Current methods lack reliable and reproducible ways to assess the impact of agents on microbial communities, particularly in diagnosing and treating conditions related to microbiota imbalances, such as Clostridium difficile infection and inflammatory bowel disease, due to intrinsic variations across host species and time, and safety regulations complicate the evaluation of unapproved agents.
Innovation Solution
The development of in vitro assay methods that involve obtaining a sample from a subject, contacting it with an agent in a reaction mixture, and enumerating the abundance of microbial taxa or taxon-identifying chemical species to determine the agent's effects, which can be used for counseling on the use or discontinuation of the agent and for treating various conditions.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If current methods are used to assess agent impact on microbial communities, then evaluation can be performed, but reliability and reproducibility are poor due to intrinsic variations across host species and time
Solution Approach 1:
The patent creates in vitro copies of the in vivo microbial community environment by culturing microbiota from host subjects under controlled laboratory conditions. These cultured models replicate the complexity and composition of natural microbial communities while eliminating host-specific biological variations, enabling reliable and reproducible assessment of agent effects across different hosts.
Solution Approach 2:
The patent extracts microbial communities from their native host environments and isolates them for in vitro cultivation. By separating the microbiota from the host organism, the method removes the confounding factor of host species and temporal variations, allowing consistent assessment of agent impacts on microbial communities independent of host variability.
2Object-affected harmful factors
If safety regulations are applied to evaluate unapproved agents, then subject safety is protected, but the evaluation process becomes complicated and time-consuming
Solution Approach 1:
The patent performs preliminary safety and efficacy assessments of unapproved agents using in vitro microbial community models before human or animal testing. This preliminary evaluation screens out potentially harmful agents and identifies promising candidates, reducing the number of agents requiring full regulatory evaluation and simplifying the overall assessment process while maintaining safety standards.
Solution Approach 2:
The patent introduces an intermediary in vitro assessment system between agent development and full regulatory evaluation. This intermediate step provides preliminary safety and efficacy data that informs regulatory decision-making, streamlining the evaluation process by filtering out unsafe or ineffective agents before they undergo complex and time-consuming full-scale regulatory assessments.
3Manufacturing precision
If in vitro assay methods are developed to standardize assessment, then reproducibility improves, but method complexity increases
Solution Approach 1:
The patent segments the complex task of agent evaluation into standardized in vitro assay components: sample collection from hosts, controlled microbial cultivation, agent exposure protocols, and systematic data collection. By breaking down the assessment process into discrete, standardized steps, the method achieves reproducibility while managing complexity through modular, protocol-driven procedures.
Data Source
AI summary
The disclosure provides assay methods for characterizing the effects of an agent on a microbiome of a subject. Moreover, the disclosure provides methods for practical applications of assay results. The biological sample is extracted and the microbial population is enumerated by using signals or markers specific to the microbial species. The enumerated population is subjected to the action of one or many therapeutic agents and the efficiency is assessed by deriving a score based on the effects in the individual samples and in the population of samples.