Metaomic Approaches to Study the Rumen Microbiome: Challenges and Innovation

The rumen ecosystem is diverse and complex, with the microbiome consisting of symbiotic bacteria, archaea, protozoa, fungi and phage. The function of the rumen microbiome governs production efficiency, ruminant product quality and the environmental impact of ruminant agriculture. The use of metaomic-based techniques to study complex symbiotic ecosystems, such as the rumen, has grown exponentially since the onset of next generation sequencing (NGS). This has resulted in the generation of vast quantities of sequencing data, with a particular focus of on rRNA genes to understand microbial diversity. However, our ability to understand the complexity of the rumen microbiome is often hindered by a lack of standardized pre- and post sequencing approaches, resulting in a mass of data being produced, which is often not comparable across studies. For example variation in DNA extraction methods, PCR protocols, sequencing platforms, normalisation techniques coupled with the use of different software to analyse data causes a lack of firm conclusions to be drawn and hinders our ability to really understand the rumen microbiome. Therefore there is an urgent need to both consolidate the current data and to provide methodological recommendations for future studies. Because of the current focus on rRNA-gene analysis, there is also a gap between our knowledge of what microorganisms are present and our understanding of what roles they actually play in the rumen and with respect to animal health. In order to increase functional based understanding of the rumen microbiome, techniques such as metatranscriptomics and metaproteomics are also currently under development. Moreover, there is a need to understand the function of the microbiome alongside our understanding the ruminant as a whole. 

In light of metaomic developments and challenges, this special edition will focus on the issues with rRNA-gene based sequencing techniques with the aim to ultimately deliver methodological recommendations.

This Research Topic will also discuss advances in the field for increasing the understanding of the function of the rumen microbiome. Whilst this Research Topic will have methodological focus, original papers detailing use of these methodologies to address key agricultural challenges, such as production and mitigation of greenhouse gas will be a key component.