Functions of the Microbiota

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Essential Functions

Though the microbiota is a dynamic and constantly changing ecosystem, it has a number of functions essential for normal metabolic, immunologic, neurologic and structural health[1]. An optimal or balanced microbiota can perform these functions more efficiently, ultimately having beneficial effects on the hosts nutritional health and immunological resistance[2].

Fermentation of Indigestible Fibres

One of the major, well-known functions of the microbiota is the fermentation of indigestible fibres to produce short chain fatty acids (SCFA)[3]. Propionate, acetate and butyrate are key SCFA produced from this fermentative process and have many host benefits such as providing vital nutrition for intestinal epithelial cells, modulating immune function, and increasing mucosal blood flow[2][4][5]. Specifically, acetate is utilised for lipid metabolism, propionate for gluconeogenesis and butyrate is utilised as a key energy source for enterocytes and colonocytes[6][7].

Additionally, lactic acid is a by-product of the fermentation process. It plays a vital role in the intestinal ecosystem such as turnover of epithelial cells, acting as a food source for other SCFA producing bacteria[2] and producing an unfavourable local environment for pathogenic bacteria such as Salmonella spp. and E. coli by altering pH[8].

Vitamin Synthesis

The gut microbiota is responsible for synthesising certain vitamins, notably vitamin K and B group vitamins. Not only are these vitamins important for bacterial metabolism, but studies in germ-free rats have revealed the metabolic and physiological significance of some of these pathways in mammals.[9]

Gut Structural Development

The microbiota plays an important function in normal gut structural development which is supported by studies that have shown structural gut disorders associated with germ-free mice.[10] This is further reinforced by studies investigating the effect of faecal microbiota transplantation (FMT) in mice with intestinal disorders such as ulcerative colitis. These demonstrate FMT to have a therapeutic effect through remodelling of the intestinal flora and immune modulation.[11] Such research has led us to believe that the microbiota is vital in regulating the development of the intestinal barrier and its functions.[10]

Regulation of Pathogens

Research has revealed direct and indirect mechanisms by which the microbiota can regulate colonisation and eliminate pathogens, thus potentially limiting enteric infections. Commensal bacteria produce bacteriocins which specifically inhibit potentially pathogenic members of the same or similar bacterial species. Furthermore, commensals are able to alter the pH of the environment to prevent growth of certain pathogenic bacteria and prevent pathogenic infections.[12] Finally, the microbiota can indirectly prevent pathogenic colonisation by competing with pathogens for nutrients and promoting epithelial barrier function and integrity. The latter is achieved through mucus production and improving host immunity to defend against enteric infections.

Oral Tolerance

One of the more significant roles of the microbiota is in the development of oral tolerance. That is, the suppression of the immune responses to harmless orally ingested antigens and commensal bacteria. Specialised dendritic cells located in the intestinal mucosa are responsible for collecting intestinal antigens and critical for inducing tolerance through detection of luminal contents.[13] Rodent experimental models have demonstrated the ability of oral tolerance to prevent autoimmune and inflammatory diseases. With the abundance of dietary intolerance seen in veterinary practices, understanding how to provide an optimal environment for oral tolerance to develop is crucial for veterinarians.


Many of these functions can only be achieved through a healthy, balanced and diversified microbiota. Ultimately this can have a large impact on the overall health of the host through preventing infections, autoimmune and inflammatory diseases. Thus, understanding the functions of the microbiota is fundamentally important when choosing therapeutics, such as antibiotics and probiotics, as they can have significant long term effects on the host.

In Partnership With Protexin Veterinary

Author: Benjamin Sofaer BVSc, Veterinary Territory Manager at Protexin Veterinary. Protexin Veterinary is a brand of ADM Protexin Ltd

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