Metagenomics in microbiome research
Microbes and the microbiome?
When the existence of microbes was first unveiled by advances in microscopy in the 18th century, few could have imagined the full extent of their omnipresence upon this earth and beyond. Without hyperbole, it can easily be said that microbes run the world (1). They can be found just about everywhere, including the harshest and most inhospitable environments. Microbes are found to be involved in the regulation of both physical environments and organic biospheres. Unsurprisingly, microbes have formed a multitude of relationships – some beneficial, some deleterious – with single-celled and multicellular organisms alike, including humans. The importance of microbes to human health and disease has become abundantly apparent in the last several decades (1).
The complexity of these relationships is perhaps the largest obstacle to understanding microbes. Much of our knowledge in the field of microbiology comes from studies utilizing pure culture – isolating and growing a pure strain of a microbe within a controlled environment. However, not all microbes can be grown in cultures and artificial pure culture deprives microbes of the interactions with other species that have dictated their characteristics, behavior, and evolutionary path. This means that the genotypes and phenotypes of microbes within petri dishes are very likely different than those found in nature (1).
What is Metagenomics?
Broadly speaking, metagenomics, also known as community genomics, is the genetic analysis of microbial communities contained in natural living environments. From the perspective of microbiology, metagenomics studies microbes which cannot be cultured. This alternative to the genetic homogeneity of pure culture gives scientists the ability to better capture the extraordinary diversity present within microbial communities. Studying diverse microbial communities, in turn, presents the scientific community with a better understanding of both our own physiology and the systems of the world we live in (1).
Methods to study the microbiome
Shotgun sequencing offers the ability to simultaneously study non-bacterial microbes (e.g., fungi and viruses) alongside bacteria (2), but requires more sequencing labor. Alternatively, 16S sequencing can focus exclusively on one gene. In particular, 16S sequencing is useful for bacterial phylogeny and taxonomy investigations (2). Metatranscriptomics, as the investigation of metagenomic messenger RNA (mRNA), is extremely useful for studying how differences unveiled by metagenomic studies affect gene regulation and expression.