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Rumen Microbiome Associated with Feed Efficiency and Host Genetics in Beef Cattle Open Access


Other title
Rumen microbiome
Beef cattle
Feed efficiency
Genome wide association study
Host genetics
Type of item
Degree grantor
University of Alberta
Author or creator
Li, Fuyong
Supervisor and department
Leluo Guan (Department of Agricultural, Food and Nutritional Science)
Examining committee member and department
Ben Willing (Department of Agricultural, Food and Nutritional Science)
Roderick Mackie (Division of Nutritional Sciences, University of Illinois at Urbana-Champaign)
Changxi Li (Department of Agricultural, Food and Nutritional Science)
Paul Stothard (Department of Agricultural, Food and Nutritional Science)
Masahito Oba (Department of Agricultural, Food and Nutritional Science)
Department of Agricultural, Food, and Nutritional Science
Animal Science
Date accepted
Graduation date
2017-11:Fall 2017
Doctor of Philosophy
Degree level
In ruminants, evidence is accumulating regarding the associations between rumen microbial taxonomic features and feed efficiency. However, to date, how rumen microbial functional features contribute to the variations in feed efficiency of beef cattle has not been well understood. Moreover, whether the rumen microbiota could be selected and regulated by host genetics still needs to be answered. To fill the knowledge gap, four studies (Chapters 2 - 5) were designed and performed in this thesis. Chapter 2 aimed to develop a pipeline to identify and quantify the active rumen microbiota using total-RNA-based sequencing (metatranscriptomics), and to compare its outcomes with widely used 16S rRNA/rDNA amplicon sequencing. Taxonomic assessments of metatranscriptomics, 16S rRNA and 16S rDNA amplicon sequencing datasets were performed using a pipeline developed in house. Compared to 16S rRNA/rDNA amplicon sequencing, metatranscriptomics can identify more bacterial and archaeal taxa, and detect more interactions among microbial taxa. These findings validated the feasibility to conduct the taxonomic analysis for the active rumen microbiota using metatranscriptomics. In Chapter 3, metatranscriptomics was applied to characterize active rumen microbiomes of beef cattle with different feed efficiency (efficient: low residual feed intake [L-RFI]; inefficient: high residual feed intake [H-RFI]). Lachnospiraceae, Lactobacillaceae, and Veillonellaceae were more abundant in H-RFI cattle, and Methanomassiliicoccale were more abundant in L-RFI ones (P < 0.10). Meanwhile, 32 microbial metabolic pathways and 12 carbohydrate-active enzymes were differentially abundant (P < 0.05) between two groups, where most of them were more abundant in H-RFI cattle. These results suggest that rumen microbiomes of inefficient cattle may have higher and more diverse activities than those of efficient cattle. Chapter 4 was conducted to investigate the associations between the rumen microbiome and feed efficiency (RFI) in various beef cattle breeds. Rumen microbiomes from three breeds (Angus, Charolais, and Kinsella composite hybrid) were profiled using metagenomics and metatranscriptomics. There were distinguishable rumen microbiota and functional potentials among three breeds, but differences of functional activities caused by the breed effect were less apparent. Differential microbial taxonomic and functional features at both DNA and RNA levels were detected between H- and L-RFI cattle; nevertheless, most of them only showed differences between H- and L-RFI animals within a breed, suggesting that there are host genetics and rumen microbiome interactions contributing to the variations in feed efficiency. In Chapter 5, rumen microbiota from a cohort of 712 beef cattle were assessed using 16S rDNA amplicon sequencing, and results showed that breed, sex, and diet could influence rumen microbiota. Heritability estimation was conducted for microbial taxonomic features using the animal model based on the genomic relationship matrix. It revealed that host genetics affected the alpha- and beta-diversities of rumen microbiota, and the abundance of ~30% of rumen microbial taxa (heritability estimate ≥ 0.15). In addition, 19 SNPs located on 12 bovine chromosomes were found to be associated with 14 rumen microbial taxa. Our study revealed the host genetic effect on the rumen microbial colonization in cattle, highlighting the potential to manipulate the rumen microbiota through genetic selection and breeding. Overall, findings in this thesis enhanced our understanding on the associations between rumen microbial functional features (at both DNA and RNA levels) and feed efficiency in various beef cattle breeds. Moreover, it provides the evidence that the rumen microbiota is partially shaped by host genetics, which built a theoretical foundation for further manipulating the rumen microbiota using genetic approaches to improve feed efficiency in beef cattle.
This thesis is made available by the University of Alberta Libraries with permission of the copyright owner solely for the purpose of private, scholarly or scientific research. This thesis, or any portion thereof, may not otherwise be copied or reproduced without the written consent of the copyright owner, except to the extent permitted by Canadian copyright law.
Citation for previous publication
Li, F., Henderson, G., Sun, X., Cox, F., Janssen, P. H., & Guan L. L. (2016). “Taxonomic Assessment of Rumen Microbiota Using Total RNA and Targeted Amplicon Sequencing Approaches”. Front Microbiol, 7, 987. doi:10.3389/fmicb.2016.00987.Li, F., & Guan, L. L. (2017). “Metatranscriptomic Profiling Reveals Linkages between the Active Rumen Microbiome and Feed Efficiency in Beef Cattle”. Appl Environ Microbiol, 83(9). doi:10.1128/aem.00061-17.

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