Microbial Interaction Analysis via DNA Barcoding and Dilution
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Solution Overview
Problem
Current methods for evaluating microbial interactions are limited by the accuracy of gene annotations and metabolic models, and fail to capture cultivability information, leading to low throughput and incomplete assessment of multi-species processes.
Innovation Solution
A method involving serial dilution of microbial samples, followed by cultivation and sequencing to determine taxonomic information and interactions among microorganisms, using techniques such as gene amplicon sequencing of rRNA and ITS regions, to identify positive or negative interactions and co-occurrence probabilities.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If computational modeling is used to predict organism interactions, then the method can be performed, but it fails to capture cultivability information
Solution Approach 1:
The patent uses DNA barcodes as intermediaries to bridge computational modeling and experimental cultivation. Each microorganism is tagged with a unique DNA barcode that can be tracked through computational sequencing, while the actual cultivation occurs in experimental microcosms. This intermediary approach allows the system to maintain both high throughput (via computational analysis of barcode sequences) and reliability (via actual cultivation that captures cultivability information).
Solution Approach 2:
The patent replaces traditional mechanical observation methods with molecular-based detection. Instead of visually or mechanically tracking microorganism interactions in mixed cultures, the system uses DNA barcode sequencing to identify and quantify which organisms are present and interacting. This substitution enables high-throughput automated analysis while maintaining accurate cultivation-based reliability.
2Reliability
If classical co-incubation methods are used to evaluate microbial interactions, then cultivability information is captured, but the throughput is low
Solution Approach 1:
The patent segments the microbial community into individually barcoded members while maintaining their collective interaction dynamics. By assigning unique DNA barcodes to each microorganism or strain, the system can track and analyze interactions of individual members within the mixed culture. This segmentation enables high-throughput computational analysis of what would otherwise require low-throughput individual pairwise testing, while still capturing authentic cultivability information through actual mixed-culture incubation.
Solution Approach 2:
The DNA barcode system serves multiple functions simultaneously: it identifies individual microorganisms, tracks their proliferation and interactions, and enables computational analysis of community dynamics. This universal tagging approach allows a single experimental setup to evaluate interactions among many different taxa, replacing the need for numerous separate experiments and thereby increasing throughput while maintaining cultivation-based reliability.
3Productivity
If gene annotations and metabolic models are used to predict interactions, then the analysis can be performed, but the accuracy is limited
Solution Approach 1:
The patent performs preliminary action by experimentally determining actual interaction outcomes through controlled microcosm cultivations before using this empirical data to refine or validate computational models. The DNA barcode tracking in actual cultures provides ground-truth data on which organism interactions truly occur under specific conditions. This preliminary experimental data then improves the accuracy of subsequent predictive models, creating a feedback loop that enhances both speed and precision over time.
Data Source
AI summary
Disclosed herein are methods, compositions, and systems for determining specific microbial taxa, within a complex consortia of mixed taxa, which are interacting with each other in an environment of interest. In some embodiments, after diluting a sample comprising multiple different taxa of microorganisms, dilutions of the sample are cultivated for determining taxonomic information and interactions of multiple taxa of microorganisms in the sample.