Influence of Sire Breed on the Interplay among Rumen Microbial Populations Inhabiting the Rumen Liquid of the Progeny in Beef Cattle Emma Hernandez-Sanabria 1 , Laksiri A. Goonewardene 1 , Zhiquan Wang 1 , Mi Zhou 1 , Stephen S. Moore 1,2 , Le Luo Guan 1 * 1 Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada, 2 The University of Queensland Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, St. Lucia, Queensland, Australia Abstract This study aimed to evaluate whether the host genetic background impact the ruminal microbial communities of the progeny of sires from three different breeds under different diets. Eighty five bacterial and twenty eight methanogen phylotypes from 49 individuals of diverging sire breed (Angus, ANG; Charolais, CHA; and Hybrid, HYB), fed high energy density (HE) and low energy density (LE) diets were determined and correlated with breed, rumen fermentation and phenotypic variables, using multivariate statistical approaches. When bacterial phylotypes were compared between diets, ANG offspring showed the lowest number of diet-associated phylotypes, whereas CHA and HYB progenies had seventeen and twenty-three diet-associated phylotypes, respectively. For the methanogen phylotypes, there were no sire breed- associated phylotypes; however, seven phylotypes were significantly different among breeds on either diet (P,0.05). Sire breed did not influence the metabolic variables measured when high energy diet was fed. A correlation matrix of all pairwise comparisons among frequencies of bacterial and methanogen phylotypes uncovered their relationships with sire breed. A cluster containing methanogen phylotypes M16 (Methanobrevibacter gottschalkii) and M20 (Methanobrevibacter smithii), and bacterial phylotype B62 (Robinsoniella sp.) in Angus offspring fed low energy diet reflected the metabolic interactions among microbial consortia. The clustering of the phylotype frequencies from the three breeds indicated that phylotypes detected in CHA and HYB progenies are more similar among them, compared to ANG animals. Our results revealed that the frequency of particular microbial phylotypes in the progeny of cattle may be influenced by the sire breed when different diets are fed and ultimately further impact host metabolic functions, such as feed efficiency. Citation: Hernandez-Sanabria E, Goonewardene LA, Wang Z, Zhou M, Moore SS, et al. (2013) Influence of Sire Breed on the Interplay among Rumen Microbial Populations Inhabiting the Rumen Liquid of the Progeny in Beef Cattle. PLoS ONE 8(3): e58461. doi:10.1371/journal.pone.0058461 Editor: Zhi Zhou, National University of Singapore, Singapore Received August 12, 2012; Accepted February 4, 2013; Published March 8, 2013 Copyright: ß 2013 Hernandez-Sanabria et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This study was supported by the Alberta Livestock Industry Development Fund, Alberta Livestock Meat Agency, Alberta Agricultural Research Institute (ALIDF/ALMA/AARI 2007F041R and ALMA2010R086R), and by a CONACyT Scholarship. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: lguan@ualberta.ca Introduction The rumen ecosystem has been found to be a complex system of vital importance for the productivity of ruminant livestock. Although the composition of rumen microbiota across individuals has been demonstrated to include a stable core [1,2], the animal- to-animal differences in the abundance of particular genera [3,4] indicate that rumen microbiota can be influenced by a number of environmental factors [5,6,7]. The development of molecular tools have revealed the extraordinary richness of bacterial species in the rumen [8] and metagenomic analysis have provided additional knowledge of the bacterial community and their potential functions impacting host performance [9,10]. While activities and interactions among bacterial communities in the rumen appear to be formerly examined [11], little is known about the fluctuations in microbial populations influenced by the host genotype. Previous studies have demonstrated that the composi- tion of the human gut bacterial community is host-specific [12,13], and that the presence of particular microbial groups in the gastrointestinal tract may be determined by the host influence [14]. Thus, the host effects on the gut microbial ecosystem cannot be neglected [15]. The effect of host genetics on the gut microbiota has been reported in studies conducted in related individuals [16]. Research in humans revealed associations between similarity of bacterial profiles and genetic relatedness of the subjects [17,18]. Further studies in mice showed high similarity of the gut microbiota composition within mouse lines [19]. Moreover, variations at a given host locus have been associated with variations in the abundance of particular microbial taxa [20]. Hence, host genetics can have an effect on the composition of its associated gut microbiota [21]. Nevertheless, the particular host mechanisms responsible for the variations in the microbial populations and their interactions in the rumen have not been explored and defined. In the present study, we hypothesised that sire breed may impact ruminal microbial groups and bacterial-methanogen interactions of the progeny. The relevance of revealing the relationships with sire breed is enlarged, because selection strategies are mainly geared towards improving the efficiency of PLOS ONE | www.plosone.org 1 March 2013 | Volume 8 | Issue 3 | e58461