Effect of phenotypic residual feed intake and dietary forage content on the rumen microbial community of beef cattle

Abstract

Feed-efficient animals have lower production costs and reduced environmental impact. Given that rumen microbial fermentation plays a pivotal role in host nutrition, the premise that rumen microbiota may contribute to host feed efficiency is gaining momentum. Since diet is a major factor in determining rumen community structure and fermentation patterns, we investigated the effect of divergence in phenotypic residual feed intake (RFI) on ruminal community structure of beef cattle across two contrasting diets. PCR-denaturing gradient gel electrophoresis (DGGE) and quantitative PCR (qPCR) were performed to profile the rumen bacterial population and to quantify the ruminal populations of Entodinium spp., protozoa, Fibrobacter succinogenes, Ruminococcus flavefaciens, Ruminococcus albus, Prevotella brevis, the genus Prevotella, and fungi in 14 low (efficient)- and 14 high (inefficient)-RFI animals offered a low-energy, high-forage diet, followed by a high-energy, low-forage diet. Canonical correspondence and Spearman correlation analyses were used to investigate associations between physiological variables and rumen microbial structure and specific microbial populations, respectively. The effect of RFI on bacterial profiles was influenced by diet, with the association between RFI group and PCR-DGGE profiles stronger for the higher forage diet. qPCR showed that Prevotella abundance was higher (P < 0.0001) in inefficient animals. A higher (P < 0.0001) abundance of Entodinium and Prevotella spp. and a lower (P < 0.0001) abundance of Fibrobacter succinogenes were observed when animals were offered the low-forage diet. Thus, differences in the ruminal microflora may contribute to host feed efficiency, although this effect may also be modulated by the diet offered.

Fig 1

MDS plot of the PCR-DGGE profiles shown in Fig. S2 in the supplemental material. HF diet profiles are shown in green, and LF diet profiles are shown in red.

Fig 2

Canonical correspondence analysis (CCA) biplot of bacterial community diversity patterns generated by 16S rRNA gene DGGE banding patterns of 56 rumen fluid samples. Each symbol represents an individual DGGE profile (i.e., ○ = H-RFI HF diet, ● = L-RFI HF diet, □ = H-RFI LF diet, and ■ = L-RFI LF diet, respectively). On a CCA ordination plot (or biplot) the environmental variables are represented as arrows. In general, the direction of the arrows for individual environmental factors indicates an increasing concentration of that factor, while the angle between the arrows indicates the degree to which they are correlated. In addition, the magnitude of the arrows determines the importance of that variable on the bacterial profile. Environmental variables with long arrows are more strongly correlated with the ordination axes than short arrows and therefore have a greater influence on the pattern of variation.