The gastrointestinal tract microbiome of Holstein × Angus cross cattle is negatively impacted by the pre-harvest process

Authors: COSTELLO, M - University Of Wisconsin; McClure, Jennifer; BROWN, J - University Of Wisconsin; MANTOVANI, H - University Of Wisconsin; RICKE, S - University Of Wisconsin

Submitted to: Applied and Environmental Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/17/2025
Publication Date: 4/11/2025
Citation: Costello, M.K., Mcclure, J.C., Brown, J.A., Mantovani, H.C., Ricke, S.C. 2025. The gastrointestinal tract microbiome of Holstein × Angus cross cattle is negatively impacted by the pre-harvest process. Applied and Environmental Microbiology. https://doi.org/10.1128/aem.02599-24.
DOI: https://doi.org/10.1128/aem.02599-24

Interpretive Summary: When beef cattle undergo pre-harvest, stress inflammation and acidosis can occur in the gastrointestinal tract (GIT) which may affect the GIT microbiome. The objective of this study was to characterize the status of the GIT microbiome at harvest in beef cattle entering a small USDA processing facility. Nine beef cattle were shipped from a single producer to the USDA processing facility at University of Wisconsin-Madison and were harvested across four dates. Digesta samples were collected from eight GIT locations: rumen solids, rumen liquids, abomasum, duodenum, jejunum, ileum, cecum, and large intestines. Harvest date, GIT location, and an interaction between these factors impacted microbial diversity and community composition. Taxonomic composition shifted throughout the GIT, though Prevotella and Treponema were core members in several different GIT locations. Potentially unfavorable microorganisms, such as Moryella in the rumen and Acinetobacter in the hindgut, were considered keystone species. These results suggest that the pre-harvest period may result in variability in the beef cattle GIT microbiome and modulating the GIT microbiome during the pre-harvest period may offer an opportunity to improve food safety.

Technical Abstract: Stress during the beef pre-harvest period can induce an inflammatory response and acidotic conditions in the gastrointestinal tract (GIT), which affects the gastrointestinal tract microbiome. The objective of this study was to characterize the status of the GIT microbiome at harvest in beef cattle entering a small USDA processing facility. Nine beef cattle were shipped from a producer in Columbia County, WI to the USDA processing facility at University of Wisconsin-Madison and were harvested across four dates. Digesta samples were collected from eight GIT locations: rumen solids, rumen liquids, abomasum, duodenum, jejunum, ileum, cecum, and large intestines. After DNA extraction with the DNeasy Blood & Tissue Kit, the V4 region of the 16S rRNA gene was amplified and sequenced on the Illumina MiSeq platform. Sequences were analyzed for alpha and beta diversity metrics (ANOVA and ADONOS), core microbiome, ANCOM, and co-occurrence network analyses. Harvest date and GIT location had a significant impact on microbial diversity and community composition (P<0.05), and there was an interaction between GIT location and harvest date (P<0.05). Taxonomic composition shifted throughout the GIT, though Prevotella and Treponema were core members in several different GIT locations. The co-occurrence analysis revealed microorganisms potentially associated with clinical infections, such as Moryella in the rumen and Acinetobacter in the hindgut, were considered keystone species. These results suggest that the pre-harvest period may negatively impact the beef cattle GIT microbiome. Modulating the GIT microbiome during the pre-harvest period may offer an opportunity to improve food safety.