Chapter 21, Problem 1RQ

Summary Introduction

To review:

The method to analyse the metagenome of a microbial community and the advantages and disadvantages of metagenomics as compared to culturing microbes.

Introduction:

To identify and study microorganisms, the microbes need to be cultured on nutrient media. Most of the microbes are difficult to culture and hence, cannot be characterized completely. Norman Pace was the first one to identify the microbe, by sequencing its Deoxyribonucleic acid (DNA). Metagenomics deals with the sequencing of the entire DNA extracted from the microbial community.

Explanation of Solution

The sequencing and analysis of the metagenome require a series of steps. The DNA samples are collected from the target community after separating the targeted microbes from their natural environment. The DNA is then isolated and purified from the microbes of interest. The small-subunit ribosomal RNA (SSU rRNA) amplification is done to study the species diversity.

The extracted and purified DNA can be cloned and sequenced. The assembling of sequenced DNA into genome can also reveal the diversity of species. One such technique is Illumina, which generates a large amount of data and require computational analysis. The sequenced DNA fragments are assembled using mathematical tools. The ecological functions of the microbes can be studied by functional annotations.

The limitations of the metagenomics are: it is difficult to assign the correct DNA sequence to the shared genomes. Different computational pipelines may predict different partial genomes. It is difficult to discover genomes of close relatives using pipelines based on reference genomes.

The metagenomics is an important toll that may reveal the characteristics and species diversity of an organism that cannot be cultured. It can also play a vital role in determining the species of microbes that are related closely. The evolutionary line of a microbe can also be revealed by the metagenomics.