**1. Introduction**

The ability to decipher the molecular composition of nucleic acids of living organisms is of prime importance in biological sciences. Although the traditional approaches of single gene expression analyses using polymerase chain reaction (PCR) tests [1, 2], quantitative real

© 2016 The Author(s). Licensee InTech. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. © 2017 The Author(s). Licensee InTech. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

time PCRs (qRT‐PCRs) [3, 4], competitive PCRs [5] or nested PCRs [6] have been and are still widely used in biological sciences, they inherently lack the ability to provide a global overview of genomic transcripts found in living organisms. However, the recent advent of omics technologies such as metagenomics, nutrigenomics and epigenetics based on high throughput sequencing (HTS) is rapidly enhancing our ability to understand complex sys‐ tems underlying different biological functions. These omics technologies have not only accel‐ erated whole genome sequencing projects of different aquatic organisms [7, 8], but they also have the capacity to unravel the sequences of entire genomes without prior knowledge of the genes to be sequenced thereby enhancing the discovery and annotation of novel genes in non‐model species. And as shown from recent studies, their applications in aquaculture have accelerated our ability to identify emerging pathogens [9], monitor the microbiomes of different aquatic environments [10], develop nutritional diets with less side effects [11, 12] and understand the cellular networks that regulate different biological processes in aquatic organisms [13–15]. It is evident from studies carried out this far that an integrated use of dif‐ ferent omics technologies is bound to improve our production systems in aquaculture [10, 12, 16–18]. Hence, this chapter provides an overview of different omics technologies currently used in aquaculture mainly focusing on their overall contribution to transforming genomics studies into functional applications.

causing disease outbreaks reaching epidemic proportions [21]. Using metagenomics, several novel pathogens have been identified at a much faster rate than traditional approaches in which the duration from first observation of clinical signs to identification of the pathogens is long [10]. For example, infectious pancreatic necrosis (IPN) was first reported as an acute infectious enteritis [22] in salmonids in the 1940s while the etiological was later characterized as IPN virus after 20 years in 1960 [23]. Similarly, viral haemorrhagic septicaemia (VHS) was first reported in the early 1950s in salmonids while the causative agent was characterized later after 10 years in 1962 [24]. This trend was observed for several other diseases such as infec‐ tious hematopoietic necrosis virus (IHNV), nervous necrosis virus (NNV), heart and skeletal muscle inflammation (HSMI) and cardiac myopathy syndrome (CMS) in which identification of the etiological agents took long after clinical signs were first reported [25–33]. However, the upcoming of metagenomics has accelerated our discovery of novel pathogens in which the duration from observation of first clinical signs to identification of the etiological agent has been reduced. In fish, viruses discovered using metagenomics include circoviruses from com‐ mon bream [34] and European eel [35], posavirus [36] and seadornavirus [37] from freshwater carp and totivirus from golden shiner. As shown in our recent study [9], more than 20 novel fish pathogenic viruses have been identified using metagenomics in the last 4 years, which is more than the number identified using traditional diagnostic tools in the last 5 decades, clearly showing the rapid rate at which metagenomics has accelerated our ability to identify novel

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In crustaceans, mortalities due to white spot syndrome virus (WSSV) in shrimps were first reported in 1992 while the causative agent was identified in 2001 [38–40]. Mortalities due to taura syndrome virus (TSV) in shrimps were first reported in Ecuador in 1991 [41] and the virus was characterized in 1994 [42]. A similar trend was observed for Yellow heard disease virus (YTV) [43, 44], infectious hypodermal and hematopoietic necrosis virus (IHHNV) [45–47], shrimp infectious myonecrosis virus (SIMV) [48] and *Penaues vannamei* nodavirus (PvNV) [49, 50] in which the duration between the first report of the disease and identification of the etiological agent was long. Shrimps viruses discovered using metagenomics analyses include *Frafantepenaeus duorarum* nodavirus (FdNV) and shrimp hepatopancreas‐associated circular

A good understanding of microbial communities found in freshwater and marine environ‐ ment used for aquaculture is a prerequisite to designing effective disease control strategies tailored for each ecosystem. Metagenomics analyses provide a unique opportunity to study infectious agents in water samples outside their susceptible hosts [10]. Its ability to sequence all nucleic acids present in a sample at once enables it to profile microbial communities found in different ecosystems. For example, Angly et al. [52] showed that microbial composition varies with latitude gradient with highest diversity being in warm climates around the equa‐ tor and less diversity in the poles. After analysis of viromes from 32 different marine sites, Dinsdale et al. [53] noted that viral richness decreased from deep sea to surface waters and with distance from shore in surface waters and increased from winter to summer. Given that

pathogens compared with traditional diagnostic methods.

nodavirus (ShrimpCDV) [51].

**2.2. Monitoring of environmental microbiomes**
