Thursday, 20 March 2014

Fish gut microbiology: a brief overview (on herbivorous fish)

Despite representing the greatest ecological and taxonomic diversity of vertebrates, the literature lacks a consensus of marine fish herbivory and of the functional role of fish gut microbiota. To date most the work on fish herbivory has primarily had an ecosystem-based focus: feeding behaviour, algal removal rates etc. though there has been an upsurge in interest in postingestive aspects of herbivory, principally related to the gut microbiota. I’ll be presenting the key points from a paper that reviewed our knowledge of microbiota-host relationships, current sampling limitations and the role of microbiota in digestive processes of herbivorous fish.

Microbiota-host relationships
Fish harbour specialised complex communities of indigenous microbiota within their intestinal tract, which don’t reflect allochthonous microorganisms. Whilst diet has a profound influence, there are many other interacting environmental, ecological and host physiological factors which have been demonstrated to influence microbial composition within the gut:

-host taxonomy
-host trophic level
-host physiology and gut anatomy

Limitations in samplingDue to the nature of the sampling, most fish are caught and kept captive throughout though this is not without imposing limitations to the usefulness of results as microbiota of captive and wild fish differ substantially…

…as microbial communities can differ in composition and function temporally samples must be taken in a timely manner to be truly representative. The stress induced from capture and confinement could confound microbial analyses by inducing a shift in community structure. As previously mentioned diet heavily influences microbiota: a change in diet upon introduction to captivity changes gut microbial composition. The overall change in environment has marked effects with wild fish reported to lose aspects of their microbiota within days of captivity.

Physiological differences between fish and disparities in sampling technique can also limit data accuracy. The intestinal morphologies are disparate between fish and it is evidenced that distinct microbial populations with distinct metabolic functions occur in different regions of the intestinal tract. Consequently caution should be applied when comparing samples from different fish, and attempting to infer and compare physiological function in the gut from samples which may be generalised and misrepresentative e.g. comparing a sample taken from a localised region in the gut to a sample in which microbes from the whole gut are analysed.

Role of microbes in digestion
There is a functional relationship between diet and intestinal communities. It was previously thought that herbivory in mammals and fish was ultimately linked by the process of gut fermentation in both. However, fermentation is a disparate phenomenon in fish compared to mammals.

Many herbivorous marine fish require gut microbes to convert unassimilable algal constituents into smaller metabolically useful short-chain fatty acids (SCFA) and possess metabolic specialisation to conduct hindgut fermentation. It is suggested that the level of fermentation within herbivorous fish is closely associated to diet and feeding behaviour on a continuum: nutrient rich filamentous algal feeders have a rapid gut throughput time and limited fermentation whereas kelp grazers have a slower throughput time and high levels of fermentation in the hindgut.

Whilst the functionality of microorganisms in plant material digestion within the fish intestinal tract is evidenced in marine fish, no freshwater fish have been documented to rely on fermentation to the same extent (Figure 1.), with accounts of soluble sugars and proteins being released from plant material via the action of pharangeal teeth as opposed to a fermentative process.

Figure 1. Concentration of short chain fatty acids (SCFA) compared to gut transit time. High levels of fermentation occurs mainly in marine herbivorous fish (9,11,12,13) with freshwater fish (4,5,6,7) and fish with different diets having relatively lower SCFA concentrations and a quicker gut transit time (species names given in original paper if required).

Most of our current knowledge is derived from culture-based approaches; though useful in inferring function does little to enhance our understanding of in vivo microbial processes. Culture-independent approaches are becoming increasingly common and allow access to the underlying genetic make-up of microbial communities increasing the ease of generating functionality profiles. There is a lot that is still unknown about fish gut microbiology, and whilst current methods have enhanced our understanding, improved methodology can provide more insight into the functional roles and the extent to which fish rely on the microbes living within their gut.

Clements K., Angert E., Montgomery W. and Choat J. (2014) Intestinal microbiota in fishes: what’s known and what’s not. Molecular Ecology

Available online prior to being published in an issue therefor no issue number or page numbers


  1. This has peaked my curiosity with regards to the relationship between gut microbiotia between mammals and herbivorous fish. I think one possible future idea would be to build up a phylogenetic tree of relatedness (with regards to gut microbiotia) comparing herbivorous fish species with perhaps a model mammalian species. We could then use this tree to see if relatedness was linked to variables such as teeth type (e.g. pharangeal teeth) or concentration of short chain fatty acids in the organism. I think this relationship is very interesting and if we could further understand the link between mammals and herbivorous fish, we open the door to the possibility of extrapolating data from mammalian studies to herbivorous fish! Always a good thing when we have so few papers on fish gut microbe communities.

  2. I think you are right, it is always beneficial to gather information from a better studies species (as are many terrestrial mammals) and extrapolate it to a less understood/studies species. It's an understatement to say my knowledge of terrestrial mammal gut microbiota is somewhat limited, but there dependence on gut microbiota may also be heavily influenced by the plant matter itself as is the case with herbivorous fish and as you suggest there may be similarities in microbial communities between fish and mammals based on diet.