The rumen ecosystem The rumen essentially acts as a large fermentation vessel where bacteria, protozoa and fungi digest and degrade fi- brous 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 biohydrogena- tion. End-products of rumen fermentation are either ab- sorbed directly through the rumen wall − for example, vola- tile fatty acids (VFA) − or in the small intestine (SI) − for example, small peptides/amino acids and lipids. Dead mi- crobes are also washed through the forestomach and can be digested and absorbed in the SI, thus making a significant contribution to the host’s nitrogen requirement. The rumen ecosystem consists of four groups of microbes: bacteria, pro- tozoa, fungi and archaea. There are also bacteriophages, my- coplasmas and archaeophages. In terms of numbers, bacteria are by far the most abundant at 1010 -1011 cells/ml, followed by archaea (106 -108 cells/ml), protozoa (105 cells/ml) and fungi (103 -105 cells/ml). Bacteria make up around two-thirds of the rumen microbial biomass, with protozoa making up to 50%, due mainly to their size.

Rumen bacteria Bacteria are a diverse, plastic group with a core community that appears relatively consistent across diets. While much re- search has historically focused on individual strains, recent re- search has started to look at the whole bacterial community in response to changes in the rumen environment, namely di- etary changes. Studies of rumen bacteria have shown three major phyla that comprise the core community, irrespective of diet: Bacteriodetes, Firmicutes and Proteobacteria. A large- scale study examining microbial communities across a range of ruminant and camelid species, diets and geographical re- gions found that seven bacterial groups accounted for over 60% of the bacterial samples they sequenced. The authors hypothesised that, even though we can identify the ‘core’ spe- cies, more research is required in order to understand them and their role in the microbial community. Similarly, an earlier meta-analysis revealed that 19 bacterial phyla were present in the rumen microbiome. According to this meta-analysis (the Ribosomal Database Project), 71% of the bacterial spe- cies have been covered, meaning that around 30% remain unknown. A core microbiome notwithstanding, diet appears to have a major effect on bacterial diversity.

Rumen protozoa Protozoa are comparatively large microbes that are present in the rumen at a concentration of ~105 cells/ml. They play a cru- cial role in providing nutrients for hosts, as well as the genera- tion of methane. Protozoa produce a great deal of butyrate and acetate, which yields hydrogen molecules that are subse- quently taken up and converted into methane by methano- genic archaea. It is well-established that defaunation results in

a reduction in methane output and this has also been shown to improve the efficiency of nutrient use. It is also known that protozoa predate bacteria within the rumen microbial com- munity. This negatively impacts microbial protein synthesis and, subsequently, nitrogen use efficiency in the cow. Protozoa have also been implicated in the generation of conjugated lin- oleic acid (CLA) isomers. Although many studies have exam- ined protozoal effects, far less is known about rumen protozoal communities and diversity compared with bacteria.

Rumen fungi Fungi are the largest of the rumen microbes, with the longest generation time. There are six genera: the monocentric Neo- callimastix, Piromyces, and Caecomyceas and the polycentric Oprinomyces, Anaeromyces, and Cyllamyces. They are per- haps best known for their ability to degrade fibre by burrow- ing into cell-wall material, rendering it more accessible to bacterial enzymes and, ultimately, increasing ruminal fibre degradation. Fungi have also been shown to partially bio- hydrogenate linoleic acid to t11 C18:1. Like rumen bacteria, fungal diversity is affected by diet.

Archaea Many archaea are methanogens and these are responsible for generating methane from substrates such as hydrogen and carbon dioxide. Compared with bacteria, rumen archaea appear to be much less diverse. However, an increase in methanogen numbers does not necessarily translate into greater methane production, as rumen conditions may affect the expression of genes in methane production. There are known associations between both rumen cellulolytic bacteria and archaea, as well as protozoa and archaea. The link is hy- drogen, which archaea use to reduce CO2

to methane. Proto-

zoa are known hydrogen producers and archaea associate with protozoa to make use of the available hydrogen. Meth- ane production is thus used as a hydrogen sink to try to avoid significant drops in rumen pH.

The role of the gut microbiota The gut microbiota can vary greatly between individuals,

▶ ALL ABOUT FEED | Volume 28, No. 8, 2020 15

The gut microbi- ota has a signifi- cant influence on host health, immunity and physiology and can play a role in helping to re- duce reliance on antimicrobials.


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