Microbiome

Metagenomics in microbiome research

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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).

Microbes run the world.

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.

Limitations of current methods

As promising as that may sound, metatranscriptomics can be limited by technical obstacles such as the short half-life of mRNA. As NGS technology has progressed, a variety of different techniques have been developed and subsequently adapted to metagenomic approaches. During the nascent stages of microbial metagenomics, many studies were conducted using medium-read techniques (~800 bp) such as pyrosequencing (using the Roche^® 454 platform, for example) (4). As time passed, shorter-read techniques (e.g., Illumina^® sequencing) offered a more cost-effective and higher-throughput alternative.

However, short-read sequencing has its own issues with certain biases and technical hurdles. More recently, technological advances have facilitated a move towards long-read sequencing, with techniques (e.g., SMRT sequencing and nanopore sequencing) now capable of generating reads which are tens of kilobases long. Although more error-prone, these longer reads have proven advantageous for assembling closed genomes if sequencing depth is high enough to allow error correction (5). However, owing to a paucity of generated genetic information compared to Illumina sequencing and the need for high amounts of raw DNA sample, these techniques are perhaps better suited for whole genome sequencing and similar applications at present (6).

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References:

National Research Council (US) Committee on Metagenomics: Challenges and Functional Applications. The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet. Washington (DC): National Academies Press (US); 2007.
Jovel, J. et al. (2016) Characterization of the gut microbiome using 16S or shotgun metagenomics. Front Microbiol. 7, 459.
Janda, J. M. and Abbott, S. L. (2007) 16s rRNA gene sequencing for bacterial identification in the diagnostic laboratory: pluses, perils, and pitfalls. Clin. Microbiol. 45(9), 2761–2764.
Bragg, L. and Tyson, G. W. (2014) Metagenomics using next-generation sequencing. Environ. Microbiol. 1096, 183–201.
Koren, S. and Phillippy, A. M. (2015) One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly. Curr. Opin. Microbiol. 23, 110–120.
Driscoll, C. B. et al. (2017) Towards long-read metagenomics: complete assembly of three novel genomes from bacteria dependent on a diazotrophic cyanobacterium in a freshwater lake co-culture. Stand. Genomic. Sci. 12, 9.