The Possibility of Manipulating Rumen Microbiome to Reduce the Methane Emissions

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According to the Food Harvest 2020 report, there are ambitious targets set for the Irish dairy and beef industries, with increased output value of 50% and 40%, respectively, by the year 2020. The agricultural sector accounts for higher greenhouse gas emissions in Ireland in comparison to any other European Union country. Numerous research studies have established that the process of fermentation in the rumen of sheep and cows result in approximately 50% of the methane emissions (Waters, 2014). When carbohydrates are digested in the ruminant animals, carbon dioxide and methane are generated and are removed through eructation or via the rumen wall. The methane gas cannot be used as a source of energy while carbon dioxide is utilized to maintain the bicarbonate levels in the saliva through the intestinal microbes (Moran, 2005).

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In the Ruminant animals, the forestomachs have numerous eukaryotic micro-organisms such as fungi and protozoa and prokaryotic inclusive of virus, bacteria, and archaea, which together breakdown and are involved in the fermentation of the food ingested by the hosts. For the last 40 years, there have been efforts to establish the compounds that can transform the rumen fermentation towards proficient metabolic pathways. Based on the evidence derived from the past research studies, the feed-efficient ruminant animals have lower methane emissions. The microbes in the forestomach the rumen play a critical role in assisting the animals to digest the fibrous feeds such as forages in an efficient way through the process of fermentation. The unstable fatty acids derived from this process can supply approximately 60-70% of the energy needs of the animal.

The rumen microbiome refers to a dynamic, as well as complex ecosystem comprising of thousands of microbes. The study on the rumen microbiome can enhance the establishment of new strategies used in improving the nutrient utilization and manipulating the process of fermentation. At birth, the young ruminants have a reticulorumen, and until maturity they function as the monogastric fed on milk diets, which are digested in the abomasum but not in the rumen (Guan et al., 2010). The smooth transitions to ruminant from the monogastric animal needs the reticulorumen development, with least loss in growth, and it is related to the microbial population for the efficient use of forage and dry-based diets. If the rumen neither is nor adequately developed, it affects the digestion and absorption of nutrients, and consequently, leads to more methane emissions in the atmosphere.

Regardless of the ability of the cattle to digest the fiber-containing materials and forages, the fermentation by the rumen microbiome is associated with the production of the methane gas. This greenhouse gas is produced through the methanogenic archaea, which converts the hydrogen generated through the process of ruminal fermentation into methane. Even if this procedure assists in the maintenance of rumen pH by preventing the hydrogen ion accumulation in the rumen, also, it leads high emissions of methane.

The utilization of the molecular methods has shown the sophisticated microbial communities, which develop in the non-mature rumen. In a 14-days old calve, all the types of the rumen bacteria inclusive of the cellulolytic and the proteolytic species are found in the rumen microbial community. Also, other studies have shown that some rumen bacteria needed for the functionality of mature rumen can be identified as early as one day after their birth. The table below shows the age classification of the bacterial groups, which colonizes the rumen of the calves from birth to weaning.

Phyla Age (Days)

3 7 28 42

Bacteroidetes13.9, 42.6 56.3, 56.9 49.9, 56.3 56.3, 74

Actinobacteria0.05, 4.9 0.56, 5.0 0.26, 4.9 5.0

Firmicutes5.0, 13.9 13.9, 18.0 13.9, 35 10, 14.0

Fusobacteria4.7, 6.60 4.7, 5.6 0.23, 0.3 0.2, 0.4

(Yanez-Ruiz, Abecia, & Newbold, 2015)

Based on the findings of some of the research studies, there are methanogenic archaea in the rumen of the lambs before any solid substance arrives in their rumen between 2 to 4 days. Also, they reach the concentrations the same as that of the adult animals between one to two weeks after their birth (Guan et al., 2010). Protozoa are not required for the normal functionality of the rumen. However, the absence or presence of protozoa is related to the difference of methanogens communities, bacterial and rumen fermentation (Waters, 2014). For instance, the adult ruminants have distinctive protozoal populations with specific species like the Epidinium and Polyplastron indicatives of type B and A populations respectively. When the Polyplastron is introduced into the rumen having the type B protozoal communities it results to the alleviation of the type B protozoa.

Based on a study conducted by Belance et al. (2015), it was found that distinct patterns of the protozoa colonization in the artificially-reared animals different from those living in the dams (Yanez-Ruiz, Abecia, & Newbold, 2015). In the artificial method, it was established in the developing rumen there was lower pH in the kids, which stayed with their mothers that were beneficial for some of the microbial groups.

One of the best ways to manipulate the rumen microbiome to reduce the methane emissions by the ruminant animals is via the timely interventions in their early life. Given that there are numerous factors, which favor the development of specific micro-organisms, it is critical to identify the sensitive window for such action (Waters, 2014). It is established that, the first colonization takes place immediately after birth and takes a month of the bacterial community structure to stabilize implying that this duration is very critical. According to Guzman et al. (2015), the presence of fibrinolytic rumen bacteria and methanogenic archaea was reported at day 0 in the neonatal dairy calves suggesting that the intervention window begins from birth. The microbial equilibrium in the rumen can be attained by combining different mechanisms at the early life of the calves of the lambs through the supply of Immunoglobulins IgG and IgA via the saliva. Also, the peptidoglycan recognition proteins, genetically recognition receptors and the antimicrobial peptides defensins can be included in that strategy.

The key pathway for introducing the immunoglobulin into the ruminant animal is through saliva. Based on the recent studies on the levels of IgG and IgA in the rumen fluid, saliva and serum in the context of examining the possibility of vaccination against certain rumen microorganisms, it was established that this technique could minimize the methane emissions. Based on the findings of these studies, an increase of the Ig in the saliva can be attained, and its role is to shape the commensal microbial community (Waters, 2014). However, the process of this response has not yet been clarified. Also, transforming the diet of the ruminant animal can lead to a change in the number of the microbial groups found in the rumen. For instance, significant variation of the TLR4 gene in the epithelium of the rumen was found in animals having a diverse susceptibility to the acidosis. There are ten TLRs in the ruminants and the two main groups identified are TLRs3, 7-9 and the TLRs 1, 2, 4-6, 10. These elements are expressed in bacterial and the cell surface associated with the molecular patterns that differentiate the nucleic acids of the bacteria from that of the acids.

The expression of the TLRs is regulated in the gastrointestinal tract as the animal ages. Before the weaning of the calves, the restriction of expression PGLYRP1 and B-defensin show that there are significant developmental changes taking place in the cattles epithelial immune system (Yanez-Ruiz, Abecia, & Newbold, 2015). Also, colonization of certain microbial groups during the early stage of development may result in the manipulation of the rumen microbiome through the establishment of the 16SrRNA gene of the Lactobacillus and Bifidobacterium species. These genes are positively associated with the miR-196 and miR-29 expression levels.


It is critical to understand the rumen development at distinct levels inclusive of the microbial, functional and the anatomical stages because there are differences in their effects given their temporal sequences in the young and aged ruminant animals. Given the impacts of the methane gas in the atmosphere, the emissions can be reduced through the transformation of the microbial activities at the early stages of development. Some of the interventions, which can be used, include changing diet, gene expression, and prevention of colonization in the micro-organisms resulting to poor fermentation and utilization of nutrients.


Guan Y., Ranoa D. R., Jiang S., Mutha S. K., Li X., Baudry J., et al. (2010). Human TLRs 10 and 1 share common mechanisms of innate immune sensing but not signaling. J. Immunol. 184

Moran, J. (2005). How the Rumen Works. In J. Moran, Tropical Dairy Farming: Feeding Management for Small Scale Dairy Farmers in Humid Areas. Landlinks Press.

Waters, S. (2014). Understanding the Rumen Microfora to Enhance Nutrient Utilization and Reduce the Methane Emissions in Dairy and Beef Cattle.

Yanez-Ruiz, D. R., Abecia, L., & Newbold, C. J. (2015). Manipulating rumen microbiome and fermentation through interventions during early life: a review. Journal of Microbiology.

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