The Gut Microbiota of Fish - Aquaculture Nutrition: Gut Health, Probiotics and Prebiotics - page 76

Fig. 4.1 Scanning electron micrograph of the anterior intestinal mucosa of rainbow trout; a pair of
autochthonous bacterial rods is present in close association with the mucosal brush border. Scale bar =
2 μ m. (Source: Merrifield et al . 2009. Reproduced with permission of John Wiley & Sons.)

or digesta (the allochthonous microbiota), whereas the other group is potentially resident and
intimately associated with host tissues (the autochthonous microbiota; Figure 4.1) (Ringø and
Birkbeck 1999). The normal microbiota has also been defined as the community of microbes
present in most individuals of a population or a species that, despite continual contact with
different tissues, cause no harm to the host (Berg 1996).
In previous investigations to study the microbiota of the GI tract of fishes, the general
approach has been the use of conventional culture based methods (Cahill 1990; Ringø and
Birkbeck 1999). However, it has been reported that these methods present several disadvan-
tages since the number and species of bacteria detected are affected mainly by the culture
conditions and the culture media used, particularly certain fastidious and obligate anaerobes
(Spanggaard et al . 2000). These conventional methods are time consuming and lack accuracy
in isolate identification. Early in the 1990s, Cahill (1990) reviewed the current knowledge
concerning the bacterial communities in fishes, at that time mostly based on culture-dependent
observations. The description provided in that review was mainly based on biochemical identi-
fication of the microorganisms, which has restricted discrimination power and may lack proper
definitions of relationships between aquatic-environmental microorganisms and fish micro-
biota. The lack of cultivability of the majority of the indigenous bacteria in many aquatic
environments, including the GI tract of aquatic animals, is becoming increasingly apparent
(Amann et al. 1995; as discussed in Chapter 5 ). For example, in Atlantic salmon ( Salmo
salar L.), coho salmon ( Oncorhynchus kisutch ) or yellowtail ( Seriola lalandi ), cultivable bac-
teria (using tryptic soy agar (TSA) incubated at 10 days at 17 ∘ C) represent

1% of the
total bacteria (Romero and Navarrete 2006; Navarrete et al. 2009; Aguilera et al. 2013). To

≤