Disease control is a major drag on aquaculture and one which antibiotics can only relieve in the short term, due to the rise of resistant strains. Probiotics are a promising alternative. They alter the host’s gut microbiota, improving health and fitness. Probiotic-enhanced gut communities can improve pathogen exclusion, normal gut development, nutrition and immune function.
At present, the favoured strategy is to use probiotics containing lactic acid and Bacillus bacteria, because we assume they are the best choice because they dominate terrestrial mammal guts. The extremely obvious problem with supplementing fish with these bacteria is reflected in the literature; the majority of studies have failed to demonstrate any fish health benefits from terrestrial lactic acid bacteria probiotics.
More modern research indicates that host species is a stronger determinant of gut community composition than the outside environment is. However, this body of information is very limited as nobody has bothered characterising the typical gut microbe communities of common aquaculture fish species.
Ictalurus punctatus (channel catfish), Micropterus salmoides (largemouth bass) and Leponis macrochirus (bluegill panfish) are the top aquaculture fish species in the USA, none of which have had their gut microbiota characterised. This study aimed to fill this information void, to provide a starting point for future probiotic design for these species.
After euthanization, all fish had the lower third of their intestines aseptically removed and the contents squeezed into a tube. These samples were then ran through pyrosequencing and 454 sequencing to determine community composition.
Most studies like this have used only 1 fish species. Multiple species comparison revealed a high specificity of association between host and microbial community, since all fish were from the same environment. M. salmoides is carnivorous, I. punctatus is carnivorous above a certain size and L. macrochirus is omnivorous. Though stomach contents were not analysed, gut community differences are likely due to diet.
Gut microbe diversity typically increases from carnivore to omnivore to herbivore, but this trend was not shown in these species. This may be because all species could have had similar diets, but without stomach content data this cannot be confirmed. The similarity between gut communities seems to suggest that diet should have been recorded.
The phylum Fusobacterium dominated the gut communities of all 3 species, with Proteobacteria in second place. Fusobacteria are anaerobic, gram-negative bacilli who produce butyrate by fermenting carbohydrates found in epithelial tissues. This short chain fatty acid can benefit the host by acting as the main energy source for gastrointestinal cells, aiding mucus production and immune functions. Butyrate is not expected to be prevalent in carnivore guts, given the low carbohydrate content of their diets. Butyrate has been shown to inhibit some freshwater pathogens and is used as a fish feed additive. However, as a supplement it has not been proven as beneficial to fish health. Perhaps Fusobacterium supplementation would be better, possibly by providing more appropriate doses or molecular forms of butyrate.
Over 70% of sequences were related to Cetobacterium somerae in all three species. C. somerae is an obscure, microaerotolerant fermentation bacteria found in many herbivorous fish. Though it can produce vitamin B12 and inhibit the growth of other strains, it has not been investigated as a potential probiotic microbe. The most abundant gut microbes found by this study seem like good candidates for improving fish health, providing a strong case for further characterisation of other commercially important species’ gut microbiotas.
Larsen, A. M., Mohammed, H. H., & Arias, C. R. (2014). Characterization of the gut microbiota of three commercially valuable warmwater fish species. Journal of applied microbiology.