Thursday, 3 April 2014

Role of GI microbiota in fish (Review of a review - reviewception)

Role of gastrointestinal microbiota in fish (REVIEW ARTICLE)
Sorry about the length of this post, this is a review of a review so I just tried to put in the main points. I would DEFINITELY recommend giving this paper a read as it is a brilliant overview of the current (pre-2010) research done on fish GI microbiota, and I found it really helpful.

Development, establishment and composition of GI microbiota of fish

The microbial colonization, establishment, composition and diversity in the GI tract of fish is believed to be linked to the microbial composition of the rearing water, diet and environment. Critical factors such as the developmental stage of the fish, gut structure, the surrounding environment (e.g. external temperature), rearing/farming conditions and stress (e.g. pollution) may affect initial colonisation and subsequent establishment process. Generally the total bacterial load of fish at the larval stage is low before active feeding, and the initial load is mostly derived from the water by larvae to maintain osmotic balance.

In fish two distinct groups of bacteria are usually found in the GI tract: allochthonous (transient) and autochthonous (adherent). Autochthonous bacteria are able to tolerate low pHs and may therefore colonise epithelial surfaces of the stomach, small and large intestines; however allochthonous bacteria are only present transiently in the GI tract due to no, or a easily out-competeable ability to colonise epithelial surfaces.

The microbial composition and density vary in different regions of the GI tract depending on the physio-chemical conditions of the gut. Another generally reported rule in fish is that there is a progressive increase in culturable bacterial levels when progressing from the stomach to the posterior intestine. However, this trend may be refuted once more data is gained via the use of modern non-culturable techniques. Interesting some fish species have been documented to show seasonal and day-to-day fluctuations in the GI bacteria.

Many early studies done on fish GI microbial communities have been derived from the homogenates of intestinal content and/or faecal matter using culture-based techniques (using selective or non-selective isolation media), followed by a phenotypic characterization using a series of conventional morphological and biochemical assays. These culture-based studies do not show us the full picture, and therefore a lot of the past work loses value. As of 2010 we have several novel molecular technologies currently available, which are sure to dramatically increase our current understanding of the GI microbiotia (e.g. Denatured gradient gel electrophoresis aka DGGE is a genetic fingerprint method of molecular detection, based on PCR amplification of 16S rDNA which has been used to successfully study and characterize the microbes in the GI tracts of many animals including fish.)

Usually the GI microbiota of fish consists mainly of aerobic, facultative anaerobic and obligate anaerobic microorganisms (e.g. Bacteroides and Fusabacterium). As seen in many of the papers currently on the blog, bacterial composition varies from FW to marine fish e.g. Aeromonads are commonly associated with FW fish.

General effects of the GI microbiota

Epithelial differentiation:

·        Microbes have been shown to up-regulate genes involved in DNA replication and cell division for epithelial proliferation
·        The GI microbiota is key in the metabolism and trafficking of cholesterol
·        Microbial regulation of glycoprotein production in the GI tract has been previously reported
·        Germ-free fish often do not show a differential of the gut epithelium
·        Several studies show germ-free fish  display a decreased level of alkaline phosphatase activity (a marker of epithelial maturation/differentiation) mucous-secreting goblet cells and hormone-secreting enteroendocrine cells

Fish immunity

·        The gut immune system (aka GALT, the gut-associated lymphoid tissue) provides defence against infectious agents and regulates immunity in the GI tract. GI microbes play a critical role in development and maturation of this GALT, which in turn, will mediate a variety of host immune functions.
·        In fish GALT consists principally of lymphocytes, eosinophil granular cells, and several types of granulocytes and plasma cells
·        Microbiota have been found to up-regulate the genes involved in innate immunity parameters
·        The early exposure of the intestine to live bacteria and subsequent colonization is very important for the development of the gut barrier
·        The GI microorganisms of fish have been previously reported to synthesise vitamins, animo acids, metabolites and digestive enzymes (e.g. the presence of a high concentration of Aeromonas in the GI tract can play an important role in digestion as Aeromonas species secrete several proteases types).
·        Recent studies indicate that anaerobic bacteria might play a role in the digestion and absorption of nutrients, alongside contributing to fish nutrition by supplying the host with volatile fatty acids.
·        GI bacteria have been well documented in their ability to produce the vitamin B12 (the production of which varies with species, but is generally correlated with the abundance or anaerobes as opposed to aerobes)

Disease outbreak/health management

In a healthy organism some microbiota are established whereas others are merely transient in the intestine. There is a delicate balance between these microbes and if this balance is disturbed pathogens (present in a transient state) may establish lethal infections.
The gut microbiota can protect the host by depriving invading pathogens of nutrients and/or secreting a range of antimicrobial substances. Many fish species harbour a wide range of intestinal bacteria that have the ability to inhibit pathogens. Some are specific, whereas others show a broad-spectrum inhibitory activity (e.g. Carnobacterium spp., a species often isolated from the GI tracts of salmonids, has been shown to inhibit several pathogens)

We may maniple the GI microbial community via the addition of probiotics, prebiotics or synbiotics (nutritional supplements containing both probiotics and prebiotics).

Usually, supplying probiotics through feed (rather than water additives) results in a more successful establishment and colonisation in adult fish, whereas larvae often response better to water additives. Probiotics may increase survival, production, growth, immunity, protection from pathogens. Growth may be increased due to probiotics enhancing feed conversion efficiency. Protection from harmful bacteria may result from competitive exclusion, production of organic acids, antibiotics, bacterioncins or lysozymes (or by triggering the immune system)


Prebiotics are usually non-digestible oligosaccharides used as food ingredients to enhance the composition of certain endogenous health-promoting bacteria in the GI tract of the host. They may help by generating specific microbiota, and have been shown to stimulate the growth of specific intestinal bacteria in fish. Past studies have shown they may lead to improved growth, immunity and disease resistance. However, there are some concerns when using prebiotics as several pathogens (as well as opportunistic bacteria) may metabolise the prebiotics, leading to their widespread proliferation – causing health issues for the host.

Nayak, S. K. (2010). Role of gastrointestinal microbiota in fish. Aquaculture Research41(11), 1553-1573.

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