Metagenomics and its applications
Last decades have seen a total jump into different aspects of science and research. The methods for identifying an organism genome, transcriptome, Exome, etc. has always been on the forefront. But the question lies what to use when group of organisms co-existing together in an environment. With an experience of dealing with such sequencing, Eurofins provides “Metagenomics” services which has various different applications, such as amplicon based method and shotgun method which is reliable and fast. This service can be applied in various way such as Food testing, vaccine validation, disease identification, agriculture, soil testing and so on.
Introduction
Microorganisms has always been the centre of study for any form of diseases. Their constant interaction with the surrounding environment answers a lot of questions to their behaviour. A major challenge lies in identifying novel organisms and further understanding their interaction with the environment. This has led to the emergence of new methods and hence a new area of science “Metagenomics”. Metagenomics is such an approach where the structure and function of all the microorganism from the sample of study can be analysed together.
Broadly, Metagenomics falls into two main approaches:
- Taxonomic
- Functional
Already sequenced and known microorganisms are stored in specific databases to be accessed by the scientific community. Whenever a sequenced gene needs to be identified, it’s phylogenetic relationship with these stored genes in the database is studied. The other approach deals with studying the functional aspects of the sequenced gene. Mostly, in case of novel genes identified from a population of organisms, the functional studies are a crucial thing to consider.
Tools and techniques in Metagenomics
For every metagenomics research a well defined experimental design is always required. The basic workflow of the approach consists of:
- Sampling: The process of collection of samples from different sources such as plants, soil, water etc. is known as sampling.
- DNA extraction: The process of sampling is followed through the extraction of DNA from the cells.
- DNA sequencing: Sequencing strategies are followed to identify the sequence of the microorganism present in the sample. Mostly two strategies are considered: Amplicon and Shotgun Metagenomics sequencing.
- Analysis: depending on the approach the analysis pipeline is considered.
Bioinformatics Analysis
NGS workflows employ simultaneous and parallel techniques to amplify and sequence large amounts of genetic material, with potential microbes being identified via result comparison to databases by bioinformatic analysis. Shotgun metagenomic sequence as much DNA and/or RNA as possible in a sample, whereas amplicon NGS enrich specific genetic targets for sequencing. These sequencing reads require considerable pre-processing, including trimming, merging, assembly, scaffolding, gene prediction, taxonomic assignment and functional analysis. In amplicon analysis, data is denoised followed by taxonomic annotation of ASVs and sample normalization. Data analysis involves the construction of a phylogenetic tree, alpha and beta diversity analysis. Diversity analysis often includes visualization through pie charts/ bar plots, heat maps, Krona charts and may include predictive functional analysis through PICRUSt2/Taxa4Fun2.
Metagenomics and its applications
Applications of metagenomics lies in varied areas such as Agriculture, Biotechnology, Medicine, etc. Since ages, microorganisms were always considered to be an important factor in industry. Identifying biomolecules acting as industrial enzymes is one of the important application of this field of study. Such example of industrial enzymes includes cellulases, etc. Another widely applied area is the “healthcare” industry. Most of the infectious and the emerging diseases are caused by microorganisms which are mostly antibiotic resistant. Hence understanding antibiotic resistance mechanism has proved to be beneficial in developing effective medicines and antibiotics. And with the availability of Metagenomics approaches, it is therefore becoming a crucial way for searching bioactive compounds against such infections. Also, metagenomics stands as a way to provide information about microorganisms those are essential in the degradation of natural pollutants.