Abstract
The current study employed both amplicon and shotgun sequencing to examine and compare the rumen microbiome in Angus bulls fed with either a backgrounding diet (BCK) or finishing diet (HG), to assess if both methods produce comparable results. Rumen digesta samples from 16 bulls were subjected for microbial profiling. Distinctive microbial profiles were revealed by the two methods, indicating that choice of sequencing approach may be a critical facet in studies of the rumen microbiome. Shotgun-sequencing identified the presence of 303 bacterial genera and 171 archaeal species, several of which exhibited differential abundance. Amplicon-sequencing identified 48 bacterial genera, 4 archaeal species, and 9 protozoal species. Among them, 20 bacterial genera and 5 protozoal species were differentially abundant between the two diets. Overall, amplicon-sequencing showed a more drastic diet-derived effect on the ruminal microbial profile compared to shotgun-sequencing. While both methods detected dietary differences at various taxonomic levels, few consistent patterns were evident. Opposite results were seen for the phyla Firmicutes and Bacteroidetes, and the genus Selenomonas. This study showcases the importance of sequencing platform choice and suggests a need for integrative methods that allow robust comparisons of microbial data drawn from various omic approaches, allowing for comprehensive comparisons across studies.
Highlights
The rumen microbiome plays an essential role in feed digestion, supplying volatile fatty acids (VFAs), protein, and other nutrients to the host for growth and development.The relationship between this microbiome and valuable production traits like feed efficiency [1,2,3] and milk quality [4] has resulted in many studies investigating rumen microbial diversity, with a view to potentially manipulating the rumen microbiome to improve host performance.Studies evaluating rumen microbial composition typically use one of two major sequencing approaches: (i) marker-based amplicon sequencing [5], or (ii) metagenomic shotgun sequencing [6,7]
Sixteen bulls raised at the Beef Research and Teaching Unit at the University of Saskatchewan were blocked by body weight (BW) and randomly assigned to one of two dietary treatments: medium-grain backgrounding (BCK, n = 8) or high grain (HG, n = 8)
The current study represents the first survey of rumen microbial composition and its response to diet in adult Angus bulls
Summary
The rumen microbiome plays an essential role in feed digestion, supplying volatile fatty acids (VFAs), protein, and other nutrients to the host for growth and development.The relationship between this microbiome and valuable production traits like feed efficiency [1,2,3] and milk quality [4] has resulted in many studies investigating rumen microbial diversity, with a view to potentially manipulating the rumen microbiome to improve host performance.Studies evaluating rumen microbial composition typically use one of two major sequencing approaches: (i) marker-based amplicon sequencing [5], or (ii) metagenomic shotgun sequencing [6,7]. The rumen microbiome plays an essential role in feed digestion, supplying volatile fatty acids (VFAs), protein, and other nutrients to the host for growth and development. The relationship between this microbiome and valuable production traits like feed efficiency [1,2,3] and milk quality [4] has resulted in many studies investigating rumen microbial diversity, with a view to potentially manipulating the rumen microbiome to improve host performance. Studies evaluating rumen microbial composition typically use one of two major sequencing approaches: (i) marker-based amplicon sequencing [5], or (ii) metagenomic shotgun sequencing [6,7]. Knowledge of the rumen microbiota in beef cattle is largely drawn from studies in steers, with only limited knowledge of rumen microbial composition in bulls [3] There is a well-defined relationship between host nutrition and fertility [16], but it is unknown if this is associated with microbial composition or function in the rumen
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