Metagenomics: A New Approach to Explore Microbiome

Microbes influence almost every process of life in one or the other way. We have been employing various techniques to study microbial communities and their interactions with the environment. With advances in molecular biology, we are now able to study microbes which were unculturable a few decades ago. The study of microbial communities by sequencing DNA samples from various ecological niches is called metagenomics. Parallel advancements in Next Generation Sequencing (NGS) technologies have made it possible to explore complex biological samples cost-effectively. Generation of billions of reads in a single NGS run poses a significant challenge to store, manage and analyze this vast data. Development of novel bioinformatics applications, specifically for metagenomics data, is therefore vital to assign biological significance to metagenomics data. Science of meta-genomics makes it possible to investigate resource for the development of novel genes, enzymes and chemical compounds for use in biotechnology. Microbes, as communities, are key players in maintaining environmental stability. Introduction Microorganisms constitute two third of the Earth’s biological diversity. Importance of microbes in the ecosystem can be estimated form that fact that these unseen microbes influence every part of almost all life on this mother Earth in one way or the other. The number of ways in which microbes influence daily life is countless. Almost every process this living world is touched by the seemingly endless capacity of microbes. All plants and animals have microbial communities as their inherent partners which help them with the availability of essential nutrients, metals, and vitamins. The microbial communities hosted by plants or living around them play a key role in maintaining their health and productivity. Soil is a house to most complexes of these communities most of which have developed synergistic relationship with it. A typical example is nitrogen fixing bacteria which converts the nitrogen from unusable form to the form readily usable by plants. Many specialized soil microbes operate on decaying plants and animals to recycle nutrients while others convert elements, such as iron and manganese, to forms suitable for plant nutrition. Microbes are known to create foods or add values to them through a number of natural processes including fermentation making them useful for human consumption. Additionally, microbes have been useful to remediate toxins in the environment, both natural as well as produced by human activities including oil and chemical spills. They have been evolved to be a part of diverse strata of this biosphere including soil, water and air, apart from being coevolving within their living hosts including gut of higher organisms. © 2019 JETIR July 2019, Volume 6, Issue 7 www.jetir. org (ISSN-2349-5162) JETIR1912142 Journal of Emerging Technologies and Innovative Research (JETIR) www.jetir. org 1050 The microbes present in the human intestine and mouth helps to extract energy from food that we could not digest apart for providing us protection against a variety of disease-causing pathogens (National Research Council (US), 2007). Recent surge in antibiotic resistance of infectious pathogens makes it more important for us to understand role of microbial communities in disease protection. The detailed understanding of mechanisms by which microbial communities can aid our protection from infectious agents may enable us to exploit specific genes or mechanisms to develop future medicines. Additionally, microbes have been the source of numerous innovations and technologies that have playing key role in improving the human life (Pharmacopeia). Marine microbes play a very significant role in maintaining the global biogeochemical cycles through a number of chemical transformations. The combine activities of marine microbial communities have global effects on fluxes of energy and matter in the sea, on the composition of Earth’s atmosphere, and on global climate. Therefore, the role played by microbial communities in maintaining the chemistry of the oceans if critical in maintaining the habitability of the entire planet (Falkowski et al., 1998). It is surprising to observe that on the one hand, microbial organisms important players in preserving environmental stability and the health of individuals, while on the other hand, they can cope with extremities of temperature, pressure and pH levels to survive, where no other organism can thrive. This ability of microbes to survive under extreme environment has developed due to their smart strategies for survival. Their genomes have gone through countless biochemical transformations, to make their countless generations of their communities to adapt to enormous environmental changes for the billions of years (Sleator et al., 2008). This diversity presents a bountiful of genetic and biological pool that may be exploited to discover novel products including novel genes, metabolic pathways and their products (Cowan et al., 2005). However, majority of this genetic and functional diversity is still unexploited. Around 4×10 6×10 estimated prokaryotic cells are yet to be characterize which represent the largest proportion of individual organisms, comprising 10 to 10 separate genospecies (Turnbaugh and Gordon. 2008; Sleator et al., 2008). The study of microorganisms that pervade every nook and corner of this planet has faced many challenges over time, such as discovering unknown organisms and recognizing how they interact with their environment (Escobar-Zepeda et al., 2015). Moreover, in the present scenario marked by unprecedented and dramatic global change, understanding the dynamic role of microbial communities has become more challenging. In the past, microbes were hard to study in their own environments; microbiologists studied individual species in the laboratory one by one. Historically, study of microbes in the laboratories has been limited to single species. This approach has limited our knowledge about different aspects microbial communities as compared to our understanding about microbes as individuals. However, with the advancement in science and technology, we have developed strategies to study microbes in the complex communities in their natural environments thus making us more capable understand more about their capabilities and specific roles. No doubt, traditional approaches to study microbes have established their importance in the ecosystem, the novel approach of metagenomics will further extend our ability to discover much more and novel about microbial © 2019 JETIR July 2019, Volume 6, Issue 7 www.jetir. org (ISSN-2349-5162) JETIR1912142 Journal of Emerging Technologies and Innovative Research (JETIR) www.jetir. org 1051 capabilities. The knowledge thus gained, will definitely be applied to better human life, and life as a whole in the current challenges and dynamics of the biosphere (National Research Council (US), 2007). Microbial community study: A historical perspective Microbial communities can be defined as the set of organisms (in this case, microorganisms) coexisting in the same space and time (Begon et al., 1986). The roots of microbiology are firmly associated with the microscope with the first record of a human being’s seeing a bacterial cell in 1663. Using a homemade microscope, Antonie van Leeuwenhoek watched bacteria recovered from his own teeth. Since the first report of microbes made by Leeuwenhoek and their oral organisms in 1676 (Schierbeek, 1959), our understanding about microbes and their communities has gone far ahead using the current molecular techniques. However, this journey was not straight forward but, in fact, has been marked by some great contributions from some pioneers. Isolation and cultivation of these “invisible” organisms by Robert Koch later on helped to understand microorganisms’ physiologies (Blevins and Bronze, 2010). Resolution of microscopy was significantly enhanced by development of practical staining techniques such as Gram, Ziehl– Neelsen, and Schaeffer and Fulton (Beveridge, 2001; Blevins and Bronze, 2010). Winogradsky achieved a break through by establishing formulations of the culture media which were similar to the natural growth conditions of microbes (McFall-Ngai, 2008). This helped a lot to bridge the gap between the number of observed microorganisms in a microscope and the number of microorganism obtained in culture plates (Staley and Konopka, 1985). Winogradsky’s ideas and his contribution to ecology revolutionized microbiology and gave birth to a new concept named “microbial ecology,” which refers to the study of microorganisms and their environmental roles (Ackert, 2012). The study of microorganisms has been based on morphology, characteristics, growth, and selection of some biochemical profiles for almost 300 years (Roszak et al., 1984; Oliver et al., 1991; Colwell et al., 1996). These techniques provided insight into the microbial world but in the present scenario, they extract limited information, to be used for other applications. Our understanding of life at molecular level gave us new opportunities to explore the microbial world using advanced molecular biological techniques. In the late 1970s, Carl Woese gave an idea of using ribosomal RNA genes as molecular markers to classify life (Woese and Fox, 1977). Fortunately, the introduction of Sanger automated sequencing (Sanger et al., 1977), at the same time, made it possible to sequence ribosomal RNA genes from several species. Both these developments revolutionized the study and classification of microorganisms. Due to established evidence that many microbes resist being cultured; the use of molecular markers provided a successful alternative identifying and enumerating microbes without culturing them in laboratories (Pace, N. R. 1997). Later on, further advances in molecular biological techniques such as polymerase chain reaction (PCR), rRNA genes cloning