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ARS Home » Midwest Area » Madison, Wisconsin » U.S. Dairy Forage Research Center » Cell Wall Biology and Utilization Research » Research » Publications at this Location » Publication #413676
Research Project: Developing Strategies to Improve Dairy Cow Performance and Nutrient Use Efficiency with Nutrition, Genetics, and Microbiology

Location: Cell Wall Biology and Utilization Research

Title: Defining the pre-harvest bovine gastrointestinal tract microbiome after lairage at a USDA processing facility

Author
item COSTELLO, MARGARET - University Of Wisconsin
item McClure, Jennifer
item BROWN, JESSICA - University Of Wisconsin
item MANTOVANI, HILARIO - University Of Wisconsin
item RICKE, STEVEN - University Of Wisconsin

Submitted to: Congress on Gastrointestinal Function
Publication Type: Abstract Only
Publication Acceptance Date: 3/14/2024
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: In the United States, cattle routinely undergo feed withdrawal between 8 and 24 hours before harvest, which can alter the gastrointestinal tract (GIT) microbiome. The objective of this study was to define the GIT microbiome prior to harvest, with the length of lairage ranging from 8 to 18 hours. Samples were collected in eight locations across the GIT - rumen solids and liquids, abomasum, duodenum, jejunum, ileum, cecum, and large intestines - from pre-slaughter cattle at the USDA Meat Plant at the University of Wisconsin-Madison. Samples were collected after evisceration, and the GIT locations were defined by visual histological identification. After harvest, DNA was extracted with the Qiagen DNeasy Blood & Tissue Kit and amplified at the V4 region of the 16S rRNA gene. Amplicons were then normalized, quantified, and pooled before being loaded onto an Illumina MiSeq. The paired-end sequences were exported from BaseSpace and analyzed with Qiime2-2023.9 and R Studio. There were significant differences in Kruskal-Wallis evenness (P < 0.05) between foregut (rumen solids and liquids) and hindgut (cecum and large intestines), with a higher richness in the hindgut locations. Beta diversity metrics were also significant across locations, represented by Bray-Curtis and Weighted Unifrac (P < 0.001). Predominant taxa in the foregut include Prevotella ruminicola and Methanobrevibacter spp., while in the hindgut Bacteriodes spp. and Clostrida spp. were relevant. Interestingly, archaeal populations across the GIT locations had a low relative abundance, with the most dominant genera in all locations being Methanobrevibacter. These results provide insight into the pre-harvest bovine GIT microbiome. However, further studies are needed to evaluate how the microbial communities shift after feed withdrawal and their influences on meat quality.