Metagenomics — Who is there and what are they doing?
By: Vijini Mallawaarachchi
Tags: Biology, Data Science, Science, Bioinformatics, Genomics

Metagenomics — Who is there and what are they doing?

Gaining insights into data from microbial communities

Did you know that your body houses about 100 trillion bacteria? Estimates show that a human has approximately a pound or two of bacteria living in his/her gut (stomach) [1] (Now don’t go and drink all the antibiotics you know, to kill those bacteria. In fact, these bacteria play an important role in our metabolism and immune system). The same goes for the backyard of your house. There can be many species of bacteria living in the soil and they help to enrich the soil (e.g.: nitrifying bacteria produce nitrates which are essential for plants). These microscopic communities have very diverse ecosystems and studying their composition and behaviour can provide us with valuable insights. In this article, I will provide a basic introduction to metagenomics, which is the study of genetic material obtained from microbial communities.

Image by Arek Socha from Pixabay

What is Metagenomics?

Metagenomics is the application of modern genomic techniques to the study of communities of microbial organisms directly in their natural environments, bypassing the need for isolation and lab cultivation of individual species [2].

Different communities of microorganisms can be found in soil, sea, mud, forests, space and even in the human body. Microorganisms that can be found in these environments can include bacteria, viruses/phages, microbial eukaryotes (e.g.: yeast) and worms (e.g.: helminths and nematodes).

Why Metagenomics?

Now you must be wondering how can we study these tiny organisms which we cannot even see. The old school way to study them would be to obtain samples, plate them in Petri dishes, see if anything grows, isolate the culture, and sequence. However, the majority of the bacterial species cannot be cultured using this traditional way. So in metagenomics, what we do is we obtain samples from the microbial communities directly and sequence them [3].

Metagenomics helps in the discovery of novel natural products, antibiotics and enzymes with new functions in many areas such as medicine, agriculture, energy, food and nutrition, etc.

Two Main Questions in Metagenomics

Every metagenomics study comes across two main questions [4];

Who is there? What are they doing?

When we consider the question “who is there”, we want to identify what species of micro-organisms are present in the sample. The question “what are they doing” implies that we have to determine their functions and behaviours.

Shotgun vs. Targeted Metagenomics

Once you have obtained samples from the environment, you have to prepare libraries so that it becomes easy to analyse. The two current methods of creating your libraries for analysis are

Targeted metagenomics: targeting a specific region of a genome (e.g.: 16S rRNA and 18S rRNA) that is shared across multiple organisms and samples. It provides more precise data with more depth but it may result in unequal amplification for certain targeted regions. Shotgun metagenomics: can sequence everything in your sample. It is perfect for all organisms. It provides greater resolution to genetic content (especially DNA) but will result in very complex datasets.

Shotgun Metagenomics Analysis

There are three main approaches when dealing with metagenomic datasets [4] as shown in Figure 1.