Addressing Global Ruminant Agricultural Challenges Through Understanding the Rumen Microbiome: Past, Present, and Future

Abstract

The rumen is a complex ecosystem composed of anaerobic bacteria, protozoa, fungi, methanogenic archaea and phages. These microbes interact closely to breakdown plant material that cannot be digested by humans, whilst providing metabolic energy to the host and, in the case of archaea, producing methane. Consequently, ruminants produce meat and milk, which are rich in high-quality protein, vitamins and minerals, and therefore contribute to food security. As the world population is predicted to reach approximately 9.7 billion by 2050, an increase in ruminant production to satisfy global protein demand is necessary, despite limited land availability, and whilst ensuring environmental impact is minimized. Although challenging, these goals can be met, but depend on our understanding of the rumen microbiome. Attempts to manipulate the rumen microbiome to benefit global agricultural challenges have been ongoing for decades with limited success, mostly due to the lack of a detailed understanding of this microbiome and our limited ability to culture most of these microbes outside the rumen. The potential to manipulate the rumen microbiome and meet global livestock challenges through animal breeding and introduction of dietary interventions during early life have recently emerged as promising new technologies. Our inability to phenotype ruminants in a high-throughput manner has also hampered progress, although the recent increase in "omic" data may allow further development of mathematical models and rumen microbial gene biomarkers as proxies. Advances in computational tools, high-throughput sequencing technologies and cultivation-independent "omics" approaches continue to revolutionize our understanding of the rumen microbiome. This will ultimately provide the knowledge framework needed to solve current and future ruminant livestock challenges.

Keywords: diet; host; methane; microbiome; omics; production; rumen.

Figure 1

The hydrogenotrophic methane production pathway including enzyme classifications (EC) for enzyme involved in the process. Reproduced from Shi et al. (2014).

Figure 2

Light microscopy image of rumen contents taken from a ruminant possessing B-type protozoal diversity and showing close interactions of Epidinium spp. with fresh perennial ryegrass. Scale bar: 200 μM.

Figure 3

Biofilm community on the adaxial surface of fresh perennial following in vitro incubation in the presence of rumen fluid as outlined in Huws et al. (2014). Scale bar: 10 μM.

Figure 4

Membrane vesicles isolated from Prevotella ruminocola incubated in vitro in Hungate tubes. Scale bar: 200 nM.