Elucidating the role of the rumen microbiome in cattle feed efficiency and its potential as a reservoir for novel enzyme discovery

• Author / Creator

  Neves, Andre Luis Alves

• The rapid advances in omics technologies have led to a tremendous progress in our understanding of the rumen microbiome and its influence on cattle feed efficiency. However, significant gaps remain in the literature concerning the driving forces that influence the relationship between the rumen microbiota and host individual variation, and how their interactive effects on animal productivity contribute to the identification of cattle with improved feed efficiency. Furthermore, little is known about the impact of mRNA-based metatranscriptomics on the analysis of rumen taxonomic profiles, and a strategy for the discovery of lignocellulolytic enzymes through the targeted functional profiling of carbohydrate-active enzymes (CAZymes) remains to be developed. Study 1 investigated the dynamics of rumen microorganisms in cattle raised under different feeding regimens (forage vs. grain) and studied the relationship among the abundance of these microorganisms, host individuality and the diet. To examine host individual variation in the rumen microbial abundance following dietary switches, hosts were grouped based on the magnitude of microbial population shift using log2-fold change (log2-fc) in the copy numbers of bacteria, archaea, protozoa and fungi. Three groups of log2-fc in the bacterial and fungal abundance (Low, log2-fc < -1; Stable, -1 < log2-fc < 1; and High, log2-fc > 1) were identified from the magnitude of change in baseline rumen microbial populations. By monitoring the microbial population shift within the same animal in response to the diet, significant ecological features of rumen microorganisms were identified and shed new light on their dynamic roles in animal feed utilization and individual variation. Study 2 compared the outcomes of two methods, Kraken (mRNA based) and a pipeline developed in-house based on Mothur (16S rRNA based), concerning the taxonomic profiles (bacteria and archaea) of rumen microbial communities using total RNA sequencing of rumen fluid collected from cattle with different feed conversion ratios (FCR). Both approaches revealed a similar phyla distribution of the most abundant taxa, with Bacteroidetes, Firmicutes, and Proteobacteria accounting for approximately 80% of total bacterial abundance. For bacterial taxa, although 69 genera were commonly detected by both methods, an additional 159 genera were exclusively identified by Kraken. Kraken detected 423 species, while Mothur was not able to assign bacterial sequences to the species level. For archaea, both methods generated similar results only for the abundance of Methanomassiliicoccaceae and Methanobrevibacter ruminantium. Although Kraken enhanced the microbial classification at the species level, identification of bacteria or archaea in the rumen was limited due to a lack of reference genomes for the rumen microbiome. Study 3 investigated the effect of cattle breeds on specific ruminal taxonomic microbial groups and functions associated with FCR, using two genetically related Angus breeds as a model. Total RNA was extracted from rumen content samples collected from purebred Black and Red Angus bulls fed the same forage diet and then subjected to metatranscriptomic analysis. Multivariate discriminant analysis (sPLS-DA) and analysis of composition of microbiomes (ANCOM) were conducted to identify microbial signatures characterizing Black and Red Angus cattle. Although Black and Red Angus are genetically similar, sPLS-DA detected 25 bacterial species and ten functions that differentiated the rumen microbial signatures between those two breeds. ANCOM revealed an association between FCR and breed with Chitinophaga pinensis and Clostridium stercorarium, suggesting that these bacterial species may play a key role in the feed conversion efficiency of forage-fed bulls. Study 4 combined selective pressure to enrich the rumen for lignocellulolytic microbes with bioinformatic tools to guide the discovery of unknown CAZymes in the microbiome. It was demonstrated that the rumen microbiome increased the abundance of lignocellulolytic bacteria, such as Fibrobacter succinogens, and a diverse set of CAZymes over time, including 18 uncharacterized members of the family GH11 (xylanases) and three of the family GH45 (endoglucanases). Further experiments confirmed the lignocellulolytic activity of xylanase using such approach. In summary, the data presented in this thesis provide fundamental knowledge on the role of the rumen microbiome in cattle feed efficiency and offers opportunities to further explore the potential of the rumen as a source for novel enzyme discovery.

• Subjects / Keywords

  • feed efficiency
  • rumen
  • metatranscriptomics
  • glycoside hydrolyses

• Graduation date

  Fall 2019

• Type of Item

  Thesis

• Degree

  Doctor of Philosophy

• DOI

  https://doi.org/10.7939/r3-9mn5-fm71

• License

  Permission is hereby granted to the University of Alberta Libraries to reproduce single copies of this thesis and to lend or sell such copies for private, scholarly or scientific research purposes only. Where the thesis is converted to, or otherwise made available in digital form, the University of Alberta will advise potential users of the thesis of these terms. The author reserves all other publication and other rights in association with the copyright in the thesis and, except as herein before provided, neither the thesis nor any substantial portion thereof may be printed or otherwise reproduced in any material form whatsoever without the author's prior written permission.