A Short Look Into How To Conduct A Microbiome Study

Lines of evidence and range of conditions with host-microbiome interactions continue to rise. Therefore, many researchers from various fields are interested to see whether gut microbiota or its related metabolites are associated with pathologies and whether targeting specific microbes or microbial metabolites can show novel therapeutic properties. So, it is critical to understand different aspects of microbiome studies for “first” microbiome projects. In general, microbiome data are majorly obtained by three approaches: Metagenomics (which bacteria are present), Metatranscriptomics (which bacteria have active gene expression) and Metabolomics (which bacterial metabolites are present) (Figure).

metagenomics, metaranscriptomics, and metabolodics diagram

Major approaches for obtaining microbiome data: Different approaches aim to investigate different outcomes yet, a combination of various methods would result in a better understanding of microbiome with respect to different disease phenotype.

Sequencing of metagenome allows portraying of functional potentials and is based on the direct sequencing of total DNA. This approach allows the investigation of gut microbiota composition and usually involves next generation sequencing after extracting sample DNAs. A widely used and popular economical method is 16s rRNA gene surveys, which can be scaled to larger projects. 16s rRNA gene is a housekeeping genetic marker that is highly conserved between different species of bacteria. Also, these 16s rRNAs contain hypervariable regions that are bacterium specific; hence, it will allow identifying and quantifying different bacterial taxa within the gut microbiome samples.

Based on the specificity of different types of enzymatic machinery, the gut microbial composition and activity may be characterized by the profile of small metabolites that are produced in the gut.  The advent of omics-based system biology has provided novel opportunities for deciphering the gut ecosystem and its interplay with body metabolism and the role of nutrients in health as well as the cross talk of distinct factors in disease development. In other words, gut metabolites comprise a plethora of derivatives of the intermediate metabolism that can be explored by metabolomics approaches in a more exhaustive fashion to discriminate between healthy and unhealthy subjects.

Regardless of the approach taken to study gut microbiome, many of the fundamentals are shared between different methods. The challenge would be to interpret the human body as a single system rather than single parts, therefore, a range of approaches should be used to analyze the metabolic interaction of host and gut microbiota. Hence, combining different approaches backed up by rigorous statistical assessments may generate a holistic view of the metabolic interactions between gut microbiota and whole body.

Shayan Mohammad Moradi Headshot

Shayan is a caffeine-dependent Ph.D. Candidate at the Saha Cardiovascular Research Center, University of Kentucky. His research area is focused on vascular biology and lipid metabolism. He tweets @MoradiShayan, blogs at shayanmoradi.com and he is the Winner of World’s Best Husband Award (Category: nagging).