A Microbial Sampling and Community Reconstruction Activity for Introducing Students to the Burgeoning Field of Metagenomics

摘要

The identification and characterization of microbial communities within diverse biomes is important in many areas of science, ranging from healthcare to agriculture. Traditional methods of bacterial community analysis would often begin by attempting to culture sample populations on agar; however, we now know that these methods fall short since only a tiny proportion of bacteria in a sample are culturable on standard agar plates ( – ). Metagenomics is a cutting-edge, culture-independent technique that involves the sequencing of all DNA extracted from a given sample, referred to as whole genome sequencing ( ). This approach has allowed for the rapid identification and cataloguing of microorganisms in any environment or biome, telling us “who” is there and allowing for an estimation of the relative abundance of known, novel, and unculturable species within a sample ( ). The term “metagenomics” is sometimes used to describe community profiling, whereby the members present in a given community are determined by sequencing a specific often universal region of DNA (or “barcode”) from an extracted sample, such as the 16S ribosomal RNA ( ). These sequences are then compared with a database to determine the identity of the microbes ( ). Metagenomics has now become mainstream across many disciplines, including medicine, biotechnology, agriculture, and ecology, with applications ranging from identifying and improving microbial communities in agricultural soils to characterizing bacteria in the human gut that may contribute to various diseases and disorders ( ). With the advent of next-generation sequencing and the reduction in sequencing costs, this mainstream scientific approach has broadened our understanding of the role of microbes in our environment and in our everyday life ( ).