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Title:Influence of nutrition on the muscle transcriptome and ruminal microbiome in cattle
Author(s):McCann, Joshua C
Director of Research:Loor, Juan J; Shike, Daniel W
Doctoral Committee Chair(s):Loor, Juan J; Shike, Daniel W
Doctoral Committee Member(s):Pan, Yuan-Xiang; Khafipour, Ehsan
Department / Program:Animal Sciences
Discipline:Animal Sciences
Degree Granting Institution:University of Illinois at Urbana-Champaign
Degree:Ph.D.
Genre:Dissertation
Subject(s):Cattle
Rumen microbiome
Muscle transcriptome
Rumen epithelium
Abstract:Beef cattle nutrition research has historically focused on formulating diets to address nutrient requirements of cattle for given level of animal performance. While predictive models account for many factors that may affect nutrient requirements, additional physiological effects can alter the animal's ability to utilize dietary nutrients. Several of these factors include the ruminal microbiome composition and epithelial tissue function, and nutrient provision in utero. The objective of this dissertation was to evaluate the effects of nutrition on these physiological effects to determine their potential to influence nutrient utilization. Supplemental sources of fat, such as condensed distillers solubles (CDS), are often added to the diets of growing cattle to increase the energy density of the diet, but these products may negatively impact rumen bacteria at high inclusion levels. Five ruminally-fistulated steers were used in a 5 × 5 Latin square design to determine the effects of increasing dietary fat and sulfur from (CDS) on the ruminal microbiome. Alpha-diversity and species richness decreased (linear; P < 0.05) in the liquid fraction for steers fed greater CDS. At the phyla level, relative abundance of Bacteroidetes decreased in steers fed increasing dietary inclusion of CDS as Firmicutes increased to 82% of sequences for the 27% CDS treatment. The most abundant family of sulfate-reducing bacteria, Desulfovibrionaceae, increased (P < 0.03) in the solid and liquid fraction in steers fed additional dietary CDS and sulfur. There were no effects (P > 0.10) of feeding increasing dietary fat from CDS on fibroylytic phyla Fibrobacteres in either fraction. Rapid consumption of a highly digestible diet causes rapid fermentation and may lead to the onset of subacute ruminal acidosis (SARA), a condition that negatively impacts the dairy industry by decreasing dry matter intake, milk production, and profitability. Six ruminallyfistulated, lactating Holstein cows were used in a replicated incomplete Latin square design to determine the effects of SARA induction on the ruminal microbiome and epithelium using a SARA induction model. Ruminal contents and epithelial biopsies were collected on d 1 and 6 of each period prior to feeding. Principal coordinate analysis of beta-diversity indicated samples within the liquid fraction separated by day and coincided with an increased relative abundance of genera Prevotella, Ruminococcus, Streptococcus, and Lactobacillus on d 6 (P < 0.06). Phylum Bacteroidetes increased on d 6 (P < 0.01) for SARA cows driven by greater genera Prevotella and YRC22 (P < 0.01). Streptococcus bovis and Succinivibrio dextrinosolvens populations tended to increase on d 6 but were not affected by the severity of acidotic bout. In ruminal epithelium, CLDN1 and CLDN4 expression increased on d 6 (P < 0.03) 24 h after SARA induction, but overall effects on ruminal epithelium were modest. Maternal nutrition provided during mid-gestation may influence skeletal muscle development and long-term metabolism. Three planes of nutrition were provided to cows to address 70% (70%REQ), 100% (REQ), and 130% NRC energy and protein requirements (130%REQ) during mid-gestation. All calf progeny were managed as a single contemporary group and longissimus muscles biopsies were taken on 99, 197, and 392 d of age. The skeletal muscle transcriptome analysis at d 392 indicated over 2,000 co-expressed genes were downregulated in progeny born to 130%REQ-fed compared with REQ-fed dams. These genes were annotated to many lipid-associated pathways including steroid and steroid hormone biosynthesis, sulfur metabolism, retinol metabolism, ketone synthesis and degradation, fat digestion and absorption, and PPAR signaling pathways. Another set of genes (342) was activated in progeny born to 130%REQ-fed compared with 70%REQ-fed dams and correlated negatively with marbling score. These genes were annotated to pathways centered on glycolysis/gluconeogenesis, energy metabolism, and calcium signaling to support increased glycolytic muscle fibers (type 2x) in progeny born to 130%REQ-fed dams. Skeletal muscle miRNA were tightly regulated over time suggesting various roles in postnatal hypertrophy. Maternal plane of nutrition effects (P < 0.1) were observed for miR-376d and miR-381. Results indicate that maternal plane of nutrition has a long-term impact on the skeletal muscle transcriptome and may be linked to effects on meat quality.
Issue Date:2016-06-20
Type:Thesis
URI:http://hdl.handle.net/2142/92899
Rights Information:Copyright 2016 Joshua McCann
Date Available in IDEALS:2016-11-10
Date Deposited:2016-08


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