Microbial diversity for ruminants

The gut plays a critical role in health and wellbeing and accommodates a vastly complex community of micro-organisms.

Inoculation occurs immediately after birth, with diversity and complexity increasing until it has reached a relatively steady state. This diversity is crucial to the gut’s function as a protective barrier and provides resistance to colonisation of pathogenic organisms while having beneficial effects on the immune function.

The ruminant has a digestive strategy that relies on an intimate relationship with various micro-organisms and, as such, can utilise feedstuffs that other animals cannot. Mammals have little-to-no ability to degrade fibrous plant material. But, bacteria, protozoa and fungi produce cellulases, a group of enzymes that can breakdown cellulose and other related polysaccharides found in plant cell wall material. The ruminant foregut houses an ecosystem of these anaerobic microbes that allows ruminants to obtain nutrients from not only fibrous plant-based material but also the microbes themselves. This strategy allows ruminant agriculture to produce human-edible product from human-inedible feed (i.e., forage).

General gut physiologogy : The gastrointestinal (GI) tract is the primary site of nutrient absorption and digestion. It is also the largest endocrine organ of the body. However, the epithelial lining is only a single layer of cells that, together, absorb nutrients, provide a barrier protecting internal tissues and produce protective mucin and antimicrobial compounds. 
The rumen ecosystem : The rumen essentially acts as a large fermentation vessel where bacteria, protozoa and fungi digest and degrade fibrous and non-fibrous plant material, as well as protein and non-protein nitrogen sources. There is also digestion and modification of lipids by bacterial lipases and biohydrogenation. The rumen ecosystem consists of 4 groups of microbes: bacteria, protozoa, fungi and archaea.
The role of the gut microbiota : The gut microbiota can vary greatly between individuals, depending on genotype, age, environmental factors, diet and the use of antimicrobials. However, despite this variation, ~90% of the contributing organisms are of the phyla Bacteriodetes and Firmicutes. The gut microbiota can profoundly influence the health of the host and it has been implicated in many disease states, including insulin resistance, pancreatic disease and cardiovascular disease, to name but a few conditions. Animals are born with no effective gut microbiota and inoculation and colonisation begins to occur immediately after birth. Colonisation both educates the immune system and moderates its reaction to antigens, while providing nutrients, such as some vitamins and amino acids, as well as short-chain fatty acids. It is well established that the gut microbiota can have a significant role in food-component digestion and absorption and can have a positive effect on energy release from the diet.

The rumen microbiota is a diverse and complex ecosystem that dictates rumen health and function. Rumen bacteria are probably the microbial group that has been studied most. However, it is only in the last few years that we are starting to get a picture of the extent of the diversity and nature of rumen bacterial strains. The gut microbiota has a significant influence on host health, immunity and physiology and can play a role in helping to reduce reliance on antimicrobials. However, a diverse and complex microbiota is required in order to maximise resistance to colonisation by pathogenic species and reduce the susceptibility to disease.

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