What is one major challenge associated with Whole-Genome Shotgun Metagenomic Sequencing in a business context?

One major challenge is the very high cost of sequencing and data analysis, which can make it difficult for a company to justify the investment. Whole‑genome shotgun sequencing generates huge volumes of raw DNA reads that must be assembled, annotated, and interpreted, requiring powerful computers and specialized bioinformatics expertise. Because the data are noisy and contain many short fragments from many organisms, errors in assembly can lead to incorrect conclusions about which microbes are present and how they affect a product. For example, a startup developing a new probiotic might spend millions on sequencing but still need to hire a bioinformatics team to clean and interpret the data before it can decide which strains to include. This combination of expensive hardware, software, and skilled labor creates a significant barrier for businesses that need quick, reliable results.