Agriculture Reference
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containing vegetable proteins or vegetable oils for two months in comparison to a control diet
consisting of only fish protein and fish oil. These authors focused on transcriptionally active
bacterial populations, which were examined based on RNA analysis using RT-PCR, TTGE
profiles and TTGE band sequencing. Results showed that some bacterial groups were signifi-
cantly ( P
0.05) associated with specific trout families, indicating that the host may influence
microbiota composition. In addition, the effect of diet on microbiota composition was depen-
dent on the trout family. The host factors, such as the genetic background, that select specific
bacterial groups are unknown and could be the subject of future analysis.
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4.4.2 Diet
Numerous studies have investigated the impact of dietary changes on the GI microbiota of
aquatic animals (Table 4.2). Generally speaking this research has focused on: dietary form,
the effect of replacing fishmeal with alternative proteins, dietary lipids and feed additives
(e.g. phytobiotics, immunostimulants, probiotics and prebiotics). As some of these topics have
been comprehensively reviewed elsewhere recently (Merrifield etal. 2010; 2011b; Ringø etal.
2010; 2012; Dimitroglou et al. 2011) the effects of dietary components on the gut microbiota
will not be discussed in detail within this chapter.
Antimicrobial treatments are effective at reducing or preventing mortalities caused by the
primary pathogen but, as many antibiotics are broad spectrum, they may impact upon the gut
microbiota. This topic is often overlooked but several studies have reported that the indigenous
gut microbiota may be altered in terms of total viable numbers and/or diversity of populations
after antibiotic exposure (Austin and Al-Zahrani 1988; Lesel et al. 1989; Moffitt and Mobin
2006; Bakke-McKellep et al. 2007; Navarrete et al. 2008; Romero et al. 2012). Any reduction
of microbial levels or diversity could lead to a reduction of the effective barrier provided by the
commensal microbiota. Antibiotic treatment can eradicate susceptible microorganisms from
the microbiota and facilitate the proliferation of resistant opportunistic pathogens by minimiz-
ing competition and promote opportunists that may occupy previously unavailable ecologi-
cal niches. Additionally, it has been suggested that genetic material conferring antimicrobial
resistance may be transferred from the remaining indigenous populations to opportunistic or
potentially pathogenic visitors to the GI tract (Navarrete et al. 2008). In fish, this is a more
dangerous situation than is the case for terrestrial animals as the rearing water readily supports
and spreads bacterial pathogens. Future studies should further address this topic. In addition
the use of feed additives to promote a healthy microbial balance after antibiotic treatments
should be further explored.
4.4.3 Environmental factors
The early view (1970s-1980s) was that the existence of a stable microbiota in aquatic animals
was controversial (Cahill 1990; Spanggaard et al. 2000), but over the past few decades signif-
icant numbers of studies have been carried out to characterize the microbiota in a wide range
of fish species (Nayak 2010). One important attribute of GI microbiota is that bacterial com-
ponents must be present in the majority of healthy individuals and represent populations that
are readily stable over time (Berg 1996; Ringø and Birkbeck 1999). There are limited studies
available that address the microbiota stability issue. Some of them are focused on the changes
in a short time scale (weeks, months), but others compare microbiota composition between
different seasons (or years).
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