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This minireview summarizes the present state of knowledge concerning the importance of yeasts in fish gut. Yeasts have been commonly isolated in the gastrointestinal tract, and high population densities were sometimes noted in healthy fish, but the data were quite variable in terms of colony counts and taxonomical diversity. Rhodotorula sp. seemed relatively frequent in both marine and freshwater fish, and Debaryomyces hansenii has been found to be dominant in rainbow trout. Some other dominant strains have been described, such as Metschnikowia zobelii, Trichosporon cutaneum, and Candida tropicalis in marine fish, and Candida sp., Saccharomyces cerevisiae, and Leucosporidium sp. in rainbow trout. The natural proliferation of yeasts in fish mucus may be generally considered as commensalism, in spite of a few cases of pathological infections mainly due to opportunistic strains. Several strains were documented to settle and grow in fish intestine after experimental introduction, particularly S. cerevisiae and D. hansenii in rainbow trout. There have been a few instances of competition among yeasts in fish intestine, while the effect of yeast on associated bacteria is still unclear. Yeasts can stimulate the immune response in fish. ß-glucans is likely the most important compound in this regard, but some other cell-wall components or soluble factors may also play a role. Both cellular and humoral responses have been educed by dietary yeast, depending on the experimental conditions. Other benefits may be expected for the host, especially the intestinal colonisation of early feeding fry with yeast, which may have some effect on development, e.g. by accelerating the maturation of the digestive system. In older fish, dietary yeast may stimulate metabolism and growth. Such beneficial effects need to be further investigated, either in cases of natural colonisation or after dietary introduction, while trying to elucidate the mode of action, and determine whether cellular viability is a prerequisite for efficacy.

Two fish protein hydrolysates (FPH) were incorporated into four diets prepared for start-feeding sea bass larvae, at two different levels (10% and 19% of total ingredients): a commercial FPH, CPSP, in which the molecular mass of the main fraction of soluble peptides (51%) was between 500-2500 Da, and an experimental FPH obtained by acidic silage of sardine offal, SH, with a main portion of soluble peptides (54%) ranging from 200 to 500 Da. The diet with 10% of the commercial FPH gave the best results in terms of growth, survival and intestinal development, as evaluated by the early activity of digestive enzymes in the brush border membrane (alkaline phosphatase and aminopeptidase N). This was related to the low level of Vibrio spp. counted in the larvae of group C10. The high dose of FPH, especially in the experimental preparation rich in short peptides, seemed to favour the dominance of Vibrio sp. TYH3, which behaved opportunistically. The effect of the experimental FPH was ambiguous, since early larvae challenged with Vibrio anguillarum were more resistant to the pathogen, especially at high FPH dose (group S19). This might be due either to direct antagonism between V. anguillarum and Vibrio sp. TYH3, or to the stimulation of the immune response in the larvae. These results indicate that different molecular weight fractions and concentrations of feed-soluble peptides may affect the growth performance and immunological status of sea bass larvae. Consequently, a low dose of commercial FPH seems advisable, both for larval development and for the bacterial environment, although further research is required to determine and characterize peptide fractions that may have a beneficial effect on growth and immune response, and to determine their optimal inclusion levels in diets for sea bass larvae.

Gut microbiota is increasingly regarded as an integral component of the host, due to important roles in the modulation of the immune system, the proliferation of the intestinal epithelium and the regulation of the dietary energy intake. Understanding the factors that influence the composition of these microbial communities is essential to health management, and the application to aquatic animals still requires basic investigation. In this study, we compared the bacterial communities harboured in the intestines and in the rearing water of grass carp (Ctenopharyngodon idellus), crucian carp (Carassius cuvieri), and bighead carp (Hypophthalmichthys nobilis), by using 454-pyrosequencing with barcoded primers targeting the V4 to V5 regions of the bacterial 16S rRNA gene. The specimens of the three species were cohabiting in the same pond. Between 6,218 and 10,220 effective sequences were read from each sample, resulting in a total of 110,398 sequences for 13 samples from gut microbiota and pond water. In general, the microbial communities of the three carps were dominated by Fusobacteria, Firmicutes, Proteobacteria and Bacteroidetes, but the abundance of each phylum was significantly different between species. At the genus level, the overwhelming group was Cetobacterium (97.29±0.46 %) in crucian carp, while its abundance averaged c. 40 and 60 % of the sequences read in the other two species. There was higher microbial diversity in the gut of filterfeeding bighead carp than the gut of the two other species, with grazing feeding habits. The composition of intestine microbiota of grass carp and crucian carp shared higher similarity when compared with bighead carp. The principal coordinates analysis (PCoA) with the weighted UniFrac distance and the heatmap analysis suggested that gut microbiota was not a simple reflection of the microbial community in the local habitat but resulted from species-specific selective pressures, possibly dependent on behavioural, immune and metabolic characteristics.

Many recent papers have deepened the state of knowledge about lactic acid bacteria (LAB) in fish gut. In spite of high variability in fish microbiota, LAB are sometimes abundant in the intestine, notably in freshwater fish. Several strains of Streptococcus are pathogenic to fish. Streptococcus iniae and Lactococcus garvieae are major fish pathogens, against which commercial vaccines are available. Fortunately, most LAB are harmless, and some strains have been reported for beneficial effects on fish health. A major step forward in recent years was the converging evidence that LAB can stimulate the immune system in fish. An open question is whether viability can affect immunostimulation. The issue is crucial to commercialize live probiotics rather than inactivated preparations or extracts. There has been a regain of interest in allochthonous strains used as probiotics for terrestrial animals or humans, due to economical and regulatory constraints, but the short survival in sea water may limit application to marine fish. If viability is required, alternative treatments may include the incorporation of prebiotics in feed, and other dietary manipulations that could promote intestinal LAB. Antagonism to pathogens is the other main feature of candidate probiotics, and there are many reports concerning mainly carnobacteria and Enterococcus. Some bacteriocins were characterized which may be of interest not only for aquaculture, but also for food preservation.

Preliminary experiments were undertaken to investigate the effect of dietary inulin (Raftiline ST), oligofructose (Raftilose P95) and lactosucrose on the growth and intestinal bacteria of the marine carnivorous turbot, Psetta maxima. Turbot larvae were weaned on compound diets containing 2% Rafiline ST, 2% Raftilose P95 or 2% lactosucrose; 2% cellulose was the carbon source in the control group. The final mean weight of the group weaned with Raftilose P95 was significantly higher than those observed with the other diets. The bacterial load was highly variable in weaning turbot, especially with respect to the putative Vibrio spp. growing on TCBS agar which, in general, seemed to be dominant. Of the total load of bacterial isolates from turbot weaned on oligofructose, 14% consisted of a strain of Bacillus spp. This strain could use Raftilose P95 as a single source of carbon, and it might play a role in the beneficial effect of oligofructose on turbot growth, since Bacillus spp. have been documented as probiotics in fish.

For most marine aquaculture species, one of the main bottlenecks is the stable production of high quality juveniles. The high and unpredictable mortality in the first weeks after hatching of marine fish larvae remains a challenging problem that needs to be solved. The severity of the problem differs between species, but cannot be considered adequately solved for any species. Both scientific evidence and experience in hatcheries for a variety of fish, shrimp and shellfish species are accumulating as support for the hypothesis that detrimental fish–microbe interactions are the cause of these problems. Host–microbe interactions in reared fish are still poorly understood, except for a few pathogens, and empirical data of the quality required to test this hypothesis, are lacking. This article provides an overview on the current knowledge of the microbial environment of fish larvae, including methodological aspects to characterize the microbial community (both using culture‐dependent and culture‐independent methods). Further, the current knowledge of the immunology of fish larvae is reviewed, including recent advances in the understanding of toll‐like receptors, inflammatory cytokines, mast cells and piscidins, and the ontogeny of the adaptive immune system. Finally, we provide an overview of the state of the art with respect to steering of microbial communities associated with fish larvae – both steering of community composition and of its activity (e.g. by quorum sensing interference).