Probiotic Modulation of the Gut Microbiota of Fish - Aquaculture Nutrition: Gut Health, Probiotics and Prebiotics - page 214

population and/or via changes in the indigenous microbial populations, in order to be able to
apply probiotic applications with greater efficacy. We suggest that future studies assessing the
effects of probiotics on fish production and health must, as a golden rule, conduct investigations
of the gut microbiota. The very minimum that should be expected is the enumeration of the
probiotic and an overview of the impact on the indigenous microbes. However, it is hoped and
indeed expected that the application of next-generation sequencing approaches to quantify the
impact on indigenous populations and scanning confocal laser microscopy to observe potential
probiotic colonization on mucosal folds will become more common in future investigations.
The present literature is heavily focused on the bacterial microbiota and considerably less
information is available on indigenous yeast, bacteriophages, Archaea, microalgae and pro-
tozoans. In particular bacteriophage levels and their influence on indigenous and probiotic
bacteria must be the subject of future studies. The 'kill the winner' hypothesis could shape the
gastric microbiome (Mills et all . 2013) and may also have important implications for probi-
otics should the probiotic bacteria become dominant members of the microbiota. Surveys for
probiotic-specific bacteriophages should be undertaken in the fish environment, water and gut
contents in order to ascertain the potential danger to the probiont.
Furthermore, it is evident that the present studies have focused mainly on microbial abun-
dance, with functionality and activity all but unaddressed. Metagenomic and metabolomic
studies should be used to ascertain bacterial activities and proteomic studies should be used
to ascertain the host mucosal responses. These approaches will build on the foundation of
studies which have thus far only partly described the host mucosal response to probiotics, and
modulated microbial populations, using genomics, histochemistry and electron microscopy.
Indeed, it is this primary host benefit, the improvement of microbial balance and activity at
the host mucosal interface, which effectively drives the secondary host benefits in respect to
systemic health, disease resistance and growth performance. This point must not be forgotten
or overlooked.
8.7 ACKNOWLEDGEMENTS
The authors wish to thank Samuel Voller and Hugo Alexander Jaramillo Torres for their sup-
port with literature searches.
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