A Brief History of Microbial Study and Techniques for Exploring the Gastrointestinal Microbiome

Over the past 20 years, the study of microbial communities has benefited from simultaneous advancements across several fields resulting in a high-resolution view of human consortia. Although the first bacterium was described in the mid-1600s, the interest in community membership and function has not been a focus or feasible until recent decades. With strategies such as shotgun sequencing, microbes can be taxonomically profiled without culturing and their unique variants defined and compared across phenotypes. Approaches such as metatranscriptomics, metaproteomics, and metabolomics can define the current functional state of a population through the identification of bioactive compounds and significant pathways. Prior to sample collection in microbiome-based studies it is critical to evaluate the requirements of downstream analyses to ensure accurate processing and storage for generation of high data quality. A common pipeline for the analysis of human samples includes approval of collection protocols and method finalization, patient sample collection, sample processing, data analysis, and visualization. Human-based microbiome studies are inherently challenging but with the application of complementary multi-omic strategies there is an unbounded potential for discovery.

Automated summary

In the past 20 years, advancements in multiple fields have enabled a detailed understanding of microbial communities in humans. New strategies such as shotgun sequencing allow for taxonomic profiling and comparison of microbial variants without culturing. Approaches like metatranscriptomics, metaproteomics, and metabolomics can define the functional state of populations through the identification of bioactive compounds and pathways.