Phylogenetic Microarray for Fecal Source Identification

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Solution Overview

Problem

Current methods for monitoring fecal indicator bacteria (FIB) in recreational waters are inadequate as they often misinterpret sources due to the presence of FIB from wildlife and non-fecal sources, leading to insufficient health risk indication without additional source tracking data, and rely on single biomarkers which are not 100% specific.

Innovation Solution

A method using high-throughput DNA sequence analysis and phylogenetic microarray analysis to identify unique bacterial taxa specific to human, bird, and grazer feces, allowing for the detection of fecal contamination sources by determining the presence of specific taxa in environmental samples.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Ease of manufacture

If single biomarker methods are used for fecal source tracking, then the monitoring process is simple and cost-effective, but the specificity and accuracy of source identification is insufficient

Engineering Contradiction:

Improvemonitoring process simplicityVSAvoidsource identification accuracy

Core Design Contradiction:

Ease of manufactureVSMeasurement precision

Solution Approach 1:

The patent segments the microbial community into multiple operational taxonomic units (OTUs) and uses a combination of multiple biomarkers instead of a single biomarker. This segmentation approach allows simultaneous detection of multiple fecal sources (human, bird, grazer) by analyzing the presence and abundance of specific bacterial taxa, thereby improving source identification accuracy while maintaining a practical monitoring framework

Inventive Principle:

Principle #1Segmentation

Solution Approach 2:

The patent employs a composite approach by combining multiple bacterial taxa as biomarkers within a single qPCR assay system. Rather than relying on one biomarker, the method integrates detection of multiple OTUs that collectively provide more specific and accurate source tracking information, effectively creating a composite biomarker system that balances simplicity and precision

Inventive Principle:

Principle #40Composite materials

2Ease of operation

If FIB monitoring is performed without source tracking, then the monitoring process is straightforward, but the reliability of health risk indication is insufficient due to contamination from wildlife and non-fecal sources

Engineering Contradiction:

Improvemonitoring operation simplicityVSAvoidhealth risk indication reliability

Core Design Contradiction:

Ease of operationVSReliability

Solution Approach 1:

The patent introduces source tracking data as an intermediary layer between FIB detection and health risk assessment. By first identifying the fecal source (human, bird, or grazer) through specific bacterial taxa detection, the method provides contextual information that mediates the interpretation of FIB levels, thereby improving the reliability of health risk indications while maintaining operational simplicity through an integrated assay system

Inventive Principle:

Principle #24Intermediary (Mediator)

3Measurement precision

If multiple biomarkers are used for improved source tracking accuracy, then the identification precision is improved, but the device complexity and analysis requirements increase

Engineering Contradiction:

Improvesource identification accuracyVSAvoidassay system complexity

Core Design Contradiction:

Measurement precisionVSDevice complexity

Solution Approach 1:

The patent merges multiple biomarker detection targets into a single qPCR assay system. By designing primers and probes that simultaneously detect multiple operational taxonomic units (OTUs) associated with different fecal sources, the method achieves improved source identification accuracy without proportionally increasing device complexity. The integrated assay allows parallel detection of human-, bird-, and grazer-specific bacterial taxa in one experimental run

Inventive Principle:

Principle #5Merging (Combining)

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

This approach enables accurate identification of fecal contamination sources in recreational waters by distinguishing between human, bird, and grazer feces, improving the reliability of source tracking and reducing false positives from non-target sources.

Implementation Method 1

phylogenetic microarray analysis to identify unique bacterial taxa specific to human, bird, and grazer feces, allowing for the detection of fecal contamination sources by determining the presence of specific taxa in environmental samples

Methodology Applied

Scientific EffectDNA hybridization:

Data Source

PatentUS10961593B2Methods and compositions for identification of source of microbial contamination in a sample

Publication Date: 2021.03.30 RGT UNIV OF CALIFORNIA

AI summary

Herein are described 1058 different bacterial taxa that were unique to either human, grazing mammal, or bird fecal wastes. These identified taxa can serve as specific identifier taxa for these sources in environmental waters. Two field tests in marine waters demonstrate the capacity of phylogenetic microarray analysis to track multiple sources with one test.