MaP-seq Spatial Metagenomics Preserves Microbial Co-localization
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Solution Overview
Problem
Current microbiome profiling methods, such as metagenomic sequencing, require homogenization of samples, leading to the destruction of spatial information, and imaging techniques suffer from low taxonomic resolution and are challenging to scale for complex natural microbiomes, limiting the understanding of the gut microbiome's role in health and disease.
Innovation Solution
A multiplexed sequencing technique, Metagenomic Plot-sampling by sequencing (MaP-seq), which preserves spatial organization by immobilizing samples in a gel matrix, fracturing them into clusters, and using microfluidic encapsulation with barcoded beads for deep sequencing to determine microbial co-localization at a micron-scale.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If metagenomic sequencing is used to profile microbiome, then taxonomic resolution is improved, but spatial information is lost due to sample homogenization
Solution Approach 1:
The sample is segmented into multiple discrete plots or spatial compartments that are processed separately through the sequencing workflow. Each plot maintains its spatial identity and is assigned a unique barcode, allowing spatial information to be preserved while still enabling high-throughput sequencing analysis of multiple locations simultaneously.
Solution Approach 2:
A spatial barcode or index is introduced as an intermediary element that links the physical spatial location of each plot to its sequencing data. This barcode is incorporated into the DNA library preparation process, serving as a mediator that allows computational reconstruction of spatial relationships from the sequencing output without requiring physical preservation of the original spatial arrangement.
2Loss of information
If imaging techniques are used to reveal spatial information, then spatial organization is detected, but taxonomic resolution is limited and extensive empirical optimization is required
Solution Approach 1:
The mechanical and optical imaging system is replaced with a molecular-based sequencing system. Instead of using fluorescent probes and microscopy to detect spatial organization, the method uses DNA barcodes and high-throughput sequencing, which provide superior taxonomic resolution while maintaining spatial information through the barcode assignment to each plot.
Solution Approach 2:
The detection parameter is changed from optical fluorescence intensity (used in imaging) to DNA sequence variation (used in sequencing). This parameter change enables much higher taxonomic resolution because sequencing can distinguish between closely related species based on genetic differences, whereas imaging relies on spectral properties of fluorescent probes that have limited diversity.
3Measurement precision
If imaging techniques are optimized for complex natural microbiomes, then analysis accuracy is improved, but device complexity and scaling difficulty increase
Solution Approach 1:
The sequencing-based platform is designed to be universal and scalable across different microbiome samples and experimental conditions. The same basic workflow of plot assignment, barcode incorporation, and sequencing can be applied to any microbial community without requiring sample-specific optimization, making the system both simple to scale and highly accurate for complex natural microbiomes.
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 high-taxonomic resolution and unbiased analysis of microbial spatial organization, revealing specific associations between taxa and providing insights into the gut microbiome's ecological interactions and community stability.
Implementation Method 1
immobilizing the biological sample in a matrix
Implementation Method 2
fracturing them into clusters
Data Source
AI summary
The present disclosure provides for a method of determining microbial identities and/or abundances in a biological sample. The method may comprise: (a) immobilizing the biological sample in a matrix; (b) fracturing/breaking the matrix (that comprises the biological sample) into clusters; and (c) determining identities and/or abundances of microbes in the clusters.