**3. Microbiota of cultivated species in Chile**

#### **3.1 Microbiota**

Multicellular eukaryotes (plants and animals) have traditionally been classified as highly complex organisms independent of the community of commensal

#### *Application of Metagenomics to Chilean Aquaculture DOI: http://dx.doi.org/10.5772/intechopen.86302*

microorganisms that colonize them [29, 30]. This community of microorganisms is known as microbiota and represents between 50 and 90% of an individual's cells in pluricellular forms of life [31]. Our initial failure to appreciate its importance is derived from biases arising from analyzing only cultivable microorganisms, which represent less than 1% of the diversity in a determined environment [32]. The development of non-culturing methods for microbial identification like PCR amplification of rRNA genes (16S or 18S) [33] and subsequent DGGE/TGGE analysis [34] and the development of massive sequencing techniques [35] allowed to broaden our knowledge, making possible to assess the complex community of microorganisms colonizing animals and plants such as bacteria, archaea, yeasts, and fungi. In humans, the gut microbiota is now considered as a complex endocrine organ that has coevolved with us through time, including cultural evolution [36–38], secreting several molecules that modulate human physiology [39]. The intimate and indissoluble relationship between microbiota and its host led to redefining the term organism and the emergence of the concept holobiont, which is used to define a community composed of host and hosted microbiota [40].

A healthy host has a stable microbiota which is altered when the metabolism or behavior of the host changes. In turn, changes in the microbiota composition caused by imbalances in the microorganisms that compose it (dysbiosis) can also produce metabolic changes in the host [41]. To date, there is abundant evidence showing that microbiota from mammalian participates directly in four processes: (a) protection against pathogens [42], (b) behavior [43], (c) energy balance [44], and (d) stimulation and maturation of the immune system [45, 46].

Much less is known about the characteristics and role of microorganisms that normally colonize the Atlantic salmon or rainbow trout and other teleost fishes [47]. Despite this, there is evidence showing a functional similarity between the roles of commensal microorganisms of salmonids and mammals [48]. In both cases, a complex community is established at the mucosal level that changes according to diet [49–56], temperature [57], season [57, 58], geographical location [59], culture condition [60–63], genetic [64], and stage of growth [58, 59, 65–67]. Microbiota composition also varies depending on the mucosal surface and epithelial location [68, 69]. High-resolution maps using next-generation sequencing (NGS) have identified around 950 operational taxonomic units (OTUs) in Atlantic salmon, with a slightly higher number in the skin [65, 68]. In the gastrointestinal tract (GT), these OTUs belong mainly to the phyla *Proteobacteria*, *Firmicutes*, and *Tenericutes* [55], while in the skin the main phylum is *Proteobacteria* [65]. As expected, the exposure to antibiotics such as oxytetracycline produces profound changes in culturable [70] and non-cultivable microbiota (Tello unpublished).
