Bovine Rumen Microbiome: Impact of DNA Extraction Methods and Comparison of Non-Invasive Sampling Sites

Abstract

With increasing global demand for animal protein, it is very important to investigate the impact of the bovine rumen microbiome on its functional traits. In order to acquire accurate and reproducible data for this type of study, it is important to understand what factors can affect the results of microbial community analysis, and where biases can occur. This study shows the impact of different DNA extraction methods on microbial community composition. Five DNA extraction methods were used on a ruminal sample. These experiments expose a high level of variability between extraction methods in relation to the microbial communities observed. As direct access to the rumen is required, we also investigated possible alternative sampling sites that could be utilised as non-invasive indicators of the bovine rumen microbiome. Therefore, oral swabs and faecal samples were taken in addition to ruminal samples, and DNA was extracted using a single method, reducing bias, and analysed. This is a small pilot study intending to reinforce the need for a universally used methodology for rumen microbiome analysis. Although alternative sampling points can indicate some of the communities present in the rumen, this must be approached cautiously, as there are limits to the depth of community analysis possible without direct rumen sampling.