Development of a high-throughput qPCR platform for precise taxonomic characterization of the human gut microbiome. a high-throughput qPCR platform for precise taxonomic characterization of the human gut microbiome

Over the past decades, next-generation sequencing (NGS) has been a major tool for investigating the human gut microbiome, leading to key discoveries about the role of gut flora in health and disease. However, challenges related to turnaround time, reproducibility, and cost, among others, make the use of NGS technologies in the clinical setting limited. Here, we present Precision Microbiome Profiling (PMP™), a microbiome profiling method based on high throughput quantitative PCR (qPCR) that allows the analysis of prokaryotic species and strains without the need for bioinformatics for data processing. In this study, 103 microbial species known to be prevalent in the human gut and/or associated with disease were analyzed by PMP™ in 74 stool samples. These samples were also profiled by 16S rRNA gene sequencing (16S) and shotgun metagenomics (SMS). PMP™ generated comparable results to SMS in terms of species relative abundances and microbial community compositions, and both methods were significantly correlated. On the other hand, 16S showed a much lower correlation to PMP™ and SMS, which may be explained by its lower species-level resolution. PMP™ platform can form the basis for accurate, quick, precise, and cost-efficient large-scale microbiome profiling.