Applications of Metagenomics in Biotechnology and Health Care

Microbes are present almost everywhere. They play a vital role in cycling carbon, release important compounds, and may be associated with infectious diseases. Metagenomics is the culture-independent genomic research of microbial communities. Metagenomics presents a powerful tool to study prokaryotes and viruses in the environment via the analysis of their DNA obtained directly from environmental samples. This technology considers the DNA of microbes in a population as a whole. It can not only identify the microbial species present but also provide insight into the functional roles and metabolic activities of the microorganisms. The coupling of this method with function-based activity is a powerful technique for the discovery of new functional genes in uncultured microbes.

Biotechnological applications

Currently, there is a global political drive to promote biotechnology as a key feature of modern industrialized society. Metagenomics has the potential to substantially impact industrial production.

Bioactive compounds: Unique bioactive compounds have been identified through metagenomics studies, including terragines, violacein, and indirubin. Drugs originating from marine microorganisms, such as cytarabine (anti-cancer), cephalosporins (anti-microbial), and vidarabine (anti-virus), have been established on the pharmaceutical market.

Antibiotics: Novel antibiotics and enzymes are among the early discoveries from metagenomics. The discovery of streptomycin, turbomycin, and other antibiotics sprang from basic studies of the soil microbiome. Functional metagenomics serves to find novel antibiotics or novel antibiotic resistance genes, and descriptive metagenomics serves to analyze changes in the composition of the microbiome and to track the presence and abundance of known antibiotic resistance genes in different environments.

Enzymes: New genetic information on industrial enzymes, such as lipases, proteases, lyases, amylases, nitrilases, has been produced by metagenomics approaches. Enzymes have a wide range of applications, including the production of highly active pharmaceuticals and active ingredients (such as high-performance laundry detergents). The versatility of industrial enzymes allows their use in processes to degrade natural polymers such as cellulose, proteins and starch, as well as for the synthesis of asymmetric chemicals.

Health care

Infections disease. Metagenomics has now been applied to identify an unknown pathogen in outbreaks of disease. Shotgun metagenomics can also be used in the discovery and detection of pathogens in clinical samples. For RNA viruses, RNA isolated from a sample usually needs to be converted to cDNA first. In addition to bacterial pathogens and viruses, metagenomics has so far seen little use in the detection of parasitic infections. For example, Plasmodium and Toxoplasma sequences were found in the metagenome of Egyptian mummies (Khairat et al. 2013). Potential applications of metagenomics in parasitology include recovery of genomic-epidemiological data and determination of the influence of parasites on the microbial ecology in the gut.

Gut health. 16S/18S/ITS amplicon sequencing is a powerful and affordable tool for clinical microbiota analysis. It can be used to determine gut microbial species and their abundance, and allow monitoring of human health and well-being. Metagenomics sheds light on the development of probiotics. Monitoring of human-associated bacterial communities allows to establish ways to modulate them, so as to optimize human health. Personalized metagenomics has been on the market and is available for purchase. It is always better to prevent than to treat. And personal metagenomics, in conjunction with personal genomics and epigenomics, may be the foundation of the health care of tomorrow.

Wildlife conservation

Microbial ecology and next-generation sequencing offer valuable perspectives and tools for investigating and monitoring wildlife health. The microbial communities inhabiting animals and plants profoundly affect host health, nutrition, physiology, and immune systems. DNA sequencing technologies allow us to identify microbes among and within hosts. Microbial communities are sensitive to changes in the external environment, and microbial diversity correlates with habitat quality. Therefore, incorporating microbial host and biogeographic variation holds great potential for forest corridor assessments and reintroduction efforts. Additionally, microbial pathogens pose a great threat to wildlife health.