The Gut Microbiota of Fish - Aquaculture Nutrition: Gut Health, Probiotics and Prebiotics - page 88

4.4 FACTORS THAT INFLUENCE MICROBIOTA
COMPOSITION
4.4.1 Host factors
The relationship between marine or aquatic eukaryotes and specific microbial populations has
been reported in several examples using molecular approaches: sponges, shrimps, molluscs
and finfish (Griffiths et al. 2001; Hentschel et al. 2002; Lau et al. 2002; Holben et al. 2002;
Rawls et al. 2004; Mansfield et al. 2010). Furthermore, subsets of the marine microbiota seem
to be associated with specific organisms, suggesting particular functions or roles for this inter-
action. For example, Gammaproteobacteria are well known to colonize particles and animals in
the sea; however, not Gamma- but rather Alphaproteobacteria were described on diatoms and
algae (Schäfer et al. 2002; Jensen et al. 2004). This could be extrapolated to the aquatic ani-
mals used in aquaculture systems, with particular considerations. Some of these animals have
been domesticated and their reproduction and rearing are processes performed in enclosed
facilities; therefore, they have no contact with their respective natural habitat, the place where
their wild ancestors were formerly collected. The microbial colonization in these animals and
its consequences for the health status of the host will be strongly dependent on the manage-
ment of environmental and sanitary conditions. Nevertheless, some recent investigations have
revealed that host factors are very important in the definition of the fish gut microbiota, and
some evidence for the existence of a core microbiota in fish has been presented (Roeselers
et al. 2011).
Roeselers et al. (2011) addressed the influence of the host in the selection of the micro-
bial community that inhabits the gut. These authors argued two possibilities: gut microbial
communities are shaped by the composition of the microbial community present in the local
environment; or gut microbial community composition is shaped by selective pressures that
occur within the host gut habitat. In the first case, temporal and spatial separation of reared
animals from their natural habitat could result in major differences in gut microbiota compo-
sition compared with wild hosts. In the second option, wild hosts and those reared in different
facilities could have similar gut microbial communities. Roeselers et al. (2011) observed vari-
ation between wild (recently caught) and domesticated zebrafish; however, the scale of these
variations was no larger than that observed between or within different zebrafish lab facilities.
In addition, the bacterial taxa identified as dominant in the gut of wild zebrafish were largely
the same as those dominating the domesticated zebrafish gut. Altogether, these results indicate
that wild zebrafish in their natural habitat and domesticated zebrafish maintained in aquacul-
ture facilities acquire a common gut bacterial community. This suggests that features of the
intestinal habitat in these fish select for specific bacterial taxa, revealing that a set of bacterial
genera (a core gut microbiota) is present in domesticated and wild zebrafish despite differ-
ences in their local environments. The influence of the microbiota on the host may not only
be derived from the composition of the microbial community or from the activities expressed
by these microbes, because other factors could be involved as specific adaptations of the host,
and on the modulation of microbe and host effects by environmental factors (Rawls et al.
2006). Little information is available about the interaction between microbial communities,
host factors, and the physical environment (Spor et al. 2011). Recently, a study by Navarrete
et al. (2012) assessed the relative contributions of host genetics and diet in shaping the gut
microbiota of rainbow trout. Fish from different full-sib non-related families were fed diets