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FISH techniques, using rRNA target probes, have been developed for
the in situ identifi cation of single microbial cells (Amann et al., 1990). This
method is based on the hybridization of synthetic oligonucleotide probes
to specifi c regions within the bacterial ribosome and does not require
cultivation. Due to its speed and sensitivity, this technique is considered a
powerful tool for phylogenetic, ecological, diagnostic and environmental
studies in microbiology (Bottari et al., 2006). In aquaculture, this technique
has been used to determine bacterial composition in a Pacifi c white shrimp
( Litopenaeus vannamei ) hatchery (GarcĂ­a and Olmos, 2007) and in red sea
bream ( Pagrus major ) and marble goby ( Oxyeleotris marmoratus ) larvae
(Nakase et al., 2007). Recently, a probiotic photosynthetic bacteria mixture
used in aquaculture, was characterized by FISH, applying a group of
species-specifi c probes (Qi et al., 2009).
In studies of host-microorganisms interactions, gene profi ling can be
carried out by microarray technology, which allows quantifi cation of the
transcriptional status of thousands of genes simultaneously (Douglas,
2006) and can help to elucidate global patterns of gene expression
(Arcand et al., 2004). For the construction of a cDNA microarray, cDNA
fragments or EST (Expressed Sequenced Tags) sequences for the fi sh
species of interest must be prepared from cDNA library or PCR-amplifi ed
products. Transcriptome sequences of many fi sh species are now available
in the National Centre for Biotechnology Information (NCBI) GenBank
database, and these collected EST sequences can be used to synthesize
oligonucleotides and can be spotted onto array chips to produce cDNA
microarrays. Microarray analyses have been used to search for immune-
related genes that are expressed following DNA vaccination of infection
by fi sh pathogens (Byon et al., 2005; Kurobe et al., 2005) and to study
environmental infl uences on gene expression of fi sh larvae (Williams et
al., 2003), fry (Koskinen et al., 2004) and adults (Lam et al., 2006). Hossain
et al. (2006) found, by using microarray technology, that the differences
between virulence determinant functions of different pathogens can
be refl ected by specifi c host gene expression patterns, suggesting their
adaptive survival strategies inside the host.
The intensive rearing of marine fi sh larvae is highly susceptible to
bacterial infections. Environmental and health concerns have resulted
in a progressive reduction of the use of chemotherapeutics and to the
search for alternatives, which should be based on considering bacteria as
an active part of the rearing ecosystems. The selection of the appropriate
strategy for microbial control would rely on a deep understanding of the
microbial ecology in fi sh larvae, live food and rearing systems, of the origin
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