A robust metatranscriptomic technology for population-scale studies of diet, gut microbiome, and human health

The gut microbiome plays a major role in many chronic diseases. It is the only “organ” in our body whose function can easily be manipulated by our diet and lifestyle. Using personalized nutrition should enable precise control of the gut microbiome’s functions that support human health and prevent chronic diseases. Without a functional readout of the gut microbiome, however, personalized nutrition cannot be realized.Stool metatranscriptomic analysis offers a comprehensive functional view of the gut microbiome. Despite its usefulness, metatranscriptomics has seen very limited use in clinical studies due to its complexity, cost, and bioinformatic challenges associated with both microbial taxonomy and functions. This method has also received some criticism due to potential intra-sample variability, rapid changes, and RNA degradation.Here, we describe a robust and automated stool metatranscriptomic method, Viomega. This method was specifically developed for population-scale studies on the effects of gut microbiome on human health and disease, with the goal to develop personalized nutrition algorithms. Viomega includes sample collection, ambient temperature sample preservation, total RNA extraction, physical removal of ribosomal RNAs (rRNAs), preparation of directional Illumina libraries, Illumina sequencing, taxonomic classification based on a database of >110,000 microbial genomes, and quantitative microbial gene expression analysis using a database of ~100 million microbial genes.In this report, we demonstrate the robustness of Viomega technology. We also applied the method to 10,000 human stool samples and report the taxonomic and functional data. Finally, we performed several small clinical studies to demonstrate the connections between diet and the gut metatranscriptome.