Pan-Microbial Detection Using Axiom® Genotyping Solution from Affymetrix

Background

The dynamic interplay between microbial, plant, and animal populations is an active area of study. Agrigenomics-related microbiotas include species from archaeal, bacterial, viral, and eukaryotic origins and can span the spectrum from beneficial to pathogenic roles. With the expansion of sequenced microbial genomes, microarrays are well-positioned to capitalize on this information content. Here we present an overview of Axiom^® Genotyping Solution and a description of the design, development, and testing of an array for microbial detection.

Experimental design

Axiom^® Microbial Detection Array (Axiom^® MDA) contains approximately 1.3 million probe sequences targeted towards more than 12,000 microbial organisms. Probe sequence parameters including length, Tm, and mismatch tolerance were studied for optimal discrimination. The array design enables species/strain-level resolution from individual samples using a Composite Likelihood Maximization (CLiMax) algorithm developed at LLNL. Defined samples of increasing biological complexity were used to assess array sensitivity and specificity. Additionally, Axiom^® MDA was tested for the ability to identify microorganisms from bona fide biological samples, and results were compared to orthogonal approaches.

Conclusions

Axiom MDA offers a solution for the identification and enumeration of microbial entities comprising complex biological samples. The unbiased array content design is sample-type agnostic and thus has utility in the context of both plant and animal health and food safety. Furthermore, scalable sample throughput enabled by 24- and 96-array formats coupled with laboratory automation allows processing of thousands of samples per week with minimal manual intervention. This feature makes Axiom MDA a cost-effective means for detection and examination of microbiomes.