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seasons of the year. Recently, Hovda etal. (2011) used a molecular approach to examine the gut
microbiota of farmed Atlantic salmon during an annual cycle. These authors reported that LAB
were among the predominant bacterial groups as Lactococcus , Weissella and Lactobacillus
were observed in all molecular profiles derived from samples collected during a year-long
study. In contrast, Gram-negative bacteria such as Vibrio and Photobacterium and also an
uncultivable spirochete were observed only at some time points.
In another case, Romero and Navarrete (2006) followed the microbiota composition of indi-
vidual juvenile coho salmon from the same cohort collected during a 3 month period. During
this period the ish were reared under controlled conditions and fed the same diet. The collected
specimens started at 2 g (body weight) and finished at 15 g. The examination was focused on
individually collected samples from intestinal contents. Using a culture-independent method,
all individuals tested showed almost identical molecular profiles with dominant bacteria cor-
responding to Pseudomonas and Aeromonas . These data suggest that these bacteria may be
part of the GI microbiota of coho salmon and seem to be stable during the stages analysed
(2-15 g). It is important to notice that in several investigations it has been consistently reported
that there is a predominance of a limited number of bacterial groups in salmonid guts within
Chilean farms (Romero and Navarrete 2006; Navarrete etal. 2009; 2010a), in accordance with
the observation by Holben et al. (2002).
One study evaluated the short term (weeks) stability of the rainbow trout gut microbiota
when investigating a feed additive (Navarrete et al. 2010b). The diet assessment was focused
on determining the effect of the dietary inclusion of Thymus vulgaris essential oil (TVEO)
on microbiota composition, compared with a control diet without TVEO. Rainbow trout
were reared under similar conditions and the gut microbiota was investigated over 5 weeks,
sampling intestinal contents by stripping. Comparison of the molecular microbiota profiles
was performed by using the Dice index (Cs) calculated using TTGE/RISA profiles derived
from samples collected at the same time. This analysis showed relatively high similarities
(
71%) between the TVEO-treated and untreated trout. No statistical differences were
observed between the TVEO-treated and untreated fish. Thus, for these concentrations,
TVEO induced negligible changes in the gut microbiota profiles. When the molecular profiles
within the same groups (treated or untreated) were compared throughout the collection
period, common bacterial components were mostly observed. These microbes were persistent
throughout the trial, producing constant molecular profiles, indicative of the stability of
the microbiota composition in both TVEO-treated and untreated fish. The stability of the
TTGE pattern over time was revealed by the Dice index (Cs), which exhibited average values
>
>
65% for both TVEO-treated and untreated trout (Figure 4.6). The molecular identification
showed that the intestinal microbiota of trout was composed of three phyla: Proteobacteria,
Firmicutes, and Actinobacteria. These taxa have been reported previously in salmonids, and
they represent the abundant bacterial populations present in the gut of these fish (Huber et al.
2004; Holben et al. 2002; Navarrete et al. 2009).
In order to further understand the relationship of the gut microbiota of fish to biotic and
abiotic factors, Sullam et al. (2012) performed a meta-analysis based on 25 bacterial 16S
rRNA gene sequence libraries obtained from the intestines of different fish species, including
from different trophic levels and habitats (such as salmon, trout and zebrafish). They observed
an increased representation of operational taxonomic units (OTUs) from the bacterial order
Aeromonadales in freshwater fishes and Vibrionales in saltwater fishes. However, additional
research is needed to determine whether the differences could be attributed to the availability
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