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that colonize the digestive tract (Rawls et al. 2004; 2007). Hence, it is relevant to know the
composition of this microbiota in fish.
Using germ-free zebrafish, Rawls et al. (2007) investigated microbiota-zebrafish interac-
tions. Pseudomonas , as a common bacterial genus described in fish microbiota, were inves-
tigated in comparison with defective Pseudomonas mutants. Pseudomonas lacking flagella
were unable to interact with host, and non-motile mutants expressing flagella showed very
limited interaction. Hence, Pseudomonas spp. also require motility to stimulate inflammatory
signals in zebrafish. These authors suggested that flagella-dependent swimming motility pro-
motes physical interaction between Pseudomonas and the host epithelium, where the presence
of surface-attached antigens (including the flagellum itself) and other bacterial products can
be detected and monitored by the host.
Other studies using germ-free zebrafish reveal the importance of gut microbes on host
digestive tract development and function. Bates and colleagues (2006) observed that the dif-
ferentiation of the GI tract was arrested in the absence of the microbiota, as was illustrated
by a lack of brush border intestinal alkaline phosphatase activity (an enzyme associated with
mucosal tolerance with respect to detoxifying bacterial lipopolysaccharide endotoxins), imma-
ture patterns of glycan expression, and a reduction of goblet cells (mucus producing) and
enteroendocrine cells which ultimately leads to the failure to uptake protein macromolecules
in the distal intestine. Interestingly, however, the reintroduction of microbiota can reverse these
phenotypic changes in the GI tract.
Beyond the developmental stages, the microbiota continues to be involved in nutritional
functions. Smriga et al. (2010) suggested that members of Proteobacteria, Bacteroidetes, Fir-
micutes and Fusobacteria phyla may contribute to the digestive process by providing a variety
of enzymes in fish such as parrotfish, snapper or surgeons. Members of the phylum Fusobac-
teria, which are known to colonize the gut of zebrafish (Roeselers et al. 2011), can excrete
butyrate (Kapatral et al. 2003) or synthesize vitamins (Roeselers et al. 2011) which may exert
a positive effect on fish health. The phylum Actinobacteria represents one of the largest tax-
onomic units among the 18 major lineages currently recognized within the domain Bacteria.
Members of this phylum exhibit diverse physiological and metabolic properties, such as the
production of extracellular enzymes and the formation of a wide variety of secondary metabo-
lites (Ventura et al. 2007).
A particularly interesting case is that of Cetobacterium somerae (previously named
Bacteroides type A), a microaerotolerant bacterium detected in many different fish species:
long-jawed mudsucker (Bano et al. 2007), rainbow trout (Kim et al. 2007), common carp
( Cyprinus carpio ) (Omar et al. 2012), tilapia ( Oreochromis niloticus ) (Tsuchiya et al. 2008),
zebrafish (Roeselers et al. 2011) and goldfish (Silva et al. 2011). As Cetobacterium somerae
produces large quantities of vitamin B 12 (cobalamin) and is present in high numbers, it has
been suggested that this species provides a source of vitamin B 12 for some freshwater fish
species (Sugita et al. 1991; Tsuchiya et al. 2008; NRC 2011). Indeed, it is interesting to note
that some fish species such as tilapia and carp, where C. somerae has often been reported to be
a constituent of the GI microbiota, have no dietary vitamin B 12 requirements, whereas other
species such as channel catfish ( Ictalurus punctatus ) and Japanese eel ( Anguilla japonica ),
where Cetobacterium somerae is not a common component of the GI microbiota, have a
requirement for dietary vitamin B 12 (NRC 2011). However, it is important to consider that
since the application of molecular methods has allowed the identification and classification of
Cetobacterium as a separate genus from Bacteroides it may be the case that some of the earlier
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