Bacterial standards for optimized metagenomics workflow

Diverse microbial communities in the human body play a vital role in health and disease. The gut microbiome has been studied intensively due to its high diversity and its role in many diseases such as inflammatory bowel diseases, obesity, diabetes and more. Significant advances in sequencing have facilitated metagenomic studies that presented a wealth of information on the human microbiome. Metagenomic studies often use the hypervariable region of the 16S rRNA gene for identification of microbial community composition via next generation sequencing (NGS).

This methodology suffers from bias that can be introduced at every stage of the workflow, from sample collection, DNA extraction, amplification, library preparation, sequencing, to data analysis. This bias can mask the true composition of a microbial community, leading to inaccurate analyses and conclusions.

Here, we present the development and use of bacterial reference standards comprising of genomic DNA or inactivated whole cell bacteria for a controlled metagenomics workflow. The standards enable the optimization of the 16S metagenomics workflow by selecting the best reagents and protocols while improving assay consistency. Also, the identification of bias assist in eliminating the analysis of low-quality data and increase the reliability of the results and conclusions.

There is no question that the human microbiome has significant effect on human health and can provide new therapeutic targets and treatment approaches in clinical practice. Using standards is critical for assessing the accuracy of NGS methods and for generating high quality data to drive new discoveries in this exciting field.