Comparative metagenomics reveal the effect of diet on the fecal virome and the associations with production traits of beef cattle

Authors: ZHANG, YUJIE - Oak Ridge Institute For Science And Education (ORISE); Liao, Yen-Te; LIU, FANG - Ocean University Of China; Li, Robert; Wu, Vivian

Submitted to: Microbiome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/10/2025
Publication Date: N/A
Citation: N/A

Interpretive Summary: The United States has the world’s largest cattle-feeding industry and beef producer, providing high-quality products for domestic and export needs. In general, grass-fed and grain-fed cattle are the two most common feeding types in the beef industry. Different dietary conditions could cause diverse metabolic pathways of the rumen gastrointestinal microbiota and subsequently affect the animal’s production traits. Viruses are important members of the animal gut microbiome and can co-exist and co-evolve with other microorganisms in the gut environment. In this study, the objectives were to investigate the effects of feeding types on the fecal viral population and the subsequent association with animal production traits. The post-weaning weight of grain-fed cattle was higher than that of grass-fed cattle after day 56. Furthermore, the sequencing results showed that bacteriophages predominated the viral population in both groups of cattle feces. However, the types and abundance of these viruses were different between grain-fed and grass-fed cattle feces. The finding from this study suggests that fecal viruses affected by different dietary conditions may correlate with cattle physiological traits.

Technical Abstract: Beef is one of the primary protein sources in the human diet. In the United States, grain-fed and grass-fed methods are the most common types of cattle feeding in the beef industry. Different cattle feeding methods were found to affect the compositions of gut microbiota, particularly the bacterial population, and subsequently change microbial adaptation and cattle metabolism. However, there is less information regarding the association between cattle gastrointestinal virome and its physiological traits. The objectives of this study were to examine the composition of fecal virome from grain-fed and grass-fed beef cattle and to identify unique virome features to understand the relationship between different feeding types and cattle physiological traits. Six grain-fed and six grass-fed Angus beef cattle were weighted, and their fecal samples were collected for further viral metagenomic sequencing, respectively. The difference in animal growth revealed a significantly higher post-weaning weight of grain-fed cattle compared to the grass-fed cattle after day 56. Furthermore, the analysis of the fecal viral population showed that approximately 795 and 1,266 predicted viral sequences were obtained in the grain-fed and grass-fed samples, respectively. Among those, 54.3% of the grain-fed and 26.3% of the grass-fed viral sequences were identified as known viruses. The taxonomic classification showed that viruses belonging to the order Caudovirales, mostly bacteriophages, dominated the cattle virome in both sample groups, followed by the orders Cremeviriles and Petitvirales. At the family level, there were 13 viral families detected in the grain-fed group and 16 viral families found in the grass-fed group. The comparison of virome features from two groups indicated that the viral population from the kingdom Bamfordvirae had a significantly higher abundance in the grain-fed group than in the grass-fed cattle virome, whereas the kingdom Heunggongvirae had a significantly higher abundance in the grass-fed group than in the grain-fed cattle virome. Moreover, random forest analysis showed that the viruses belonging to the order Caudovirales and the family Podoviridae had significantly higher abundances in the grass-fed virome than in the grain-fed virome. The findings indicate the influence of animal feeds on the changes in gastrointestinal viral compositions and their potential association with cattle weight gain. The current outcome could contribute to further understanding of phage-bacterial interactions and their underlying mechanisms in the regulation of the animal host’s metabolism and feed efficiency.