Monday, 31 March 2014

Characterising the gut microbiota of economically important fish

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.


  1. It surprises me that microbiota diversity typically increases from carnivore to omnivore to herbivore, I would have thought that omnivores, as generalists, would have a more diverse gut community. Why do you think herbivores communities are more diverse?
    When they say that studies have failed to demonstrate any benefits from terrestrial lactic acid bacteria probiotics, it doesn't entirely contradict the paper I reviewed, as in that study they used only LAB isolated from the marine environment, and found that they did indeed have benefits.

    1. I was wondering this too; I think it is because a plant diet has a much wider range of different molecules available for gut microbes, especially carbohydrates, so larger diversity is nutritionally supported.
      So although lactic acid bacteria make good probiotics, better strains must be selected for marine organisms, because apparently terrestrial ones are the most commonly used in fish feeds today.

  2. Find it really interesting how in this paper the main ID'ed bacterium phylum was that of Fusobacterium, followed by Proteobacteria - when in the paper I reviewed (Sullam et al., 2012) documented that Proteobacteria are the dominating phylum, usually followed by Firmicutes. My paper did mention that omnivores are usually enriched with Fusobacterium although overall Fusobacterium do not dominate gut microbe communities. I wonder if these different results are due to sampling/experiemtnal differences between the papers; or if gut communities are just wildly different between habitats (which seems more likely considering all three of your species were from the same area and showed similar microbe communities).
    [Just for clarification, I am right in thinking that all three species originated from the same habitat?]

    1. Yes, all three species were raised in the same area. It is not clear which is a more important determinant of gut microbiota; these 3 species could have similar gut microbes because they were exposed to the same local populations. Or it could be that they all have similar gut selection pressures which would shape similar communities. Host colonisation can require as little as a few individual microbes, which would then be amplified in the gut, where most environmental competitors are excluded by the extreme conditions there.