Your new experience awaits. Try the new design now and help us make it even better

ORIGINAL RESEARCH article

Front. Microbiol.

Sec. Microorganisms in Vertebrate Digestive Systems

Volume 16 - 2025 | doi: 10.3389/fmicb.2025.1657402

This article is part of the Research TopicNew Horizons in Gut Microbiome Research for Enhancing Livestock ProductivityView all 19 articles

Feeding Regimens Reshape Rumen Microbiota and Metabolome in Shorthorn cattle: A Multi-Omic Insight into Microbial Diversity and Metabolic Pathway Dynamics

Provisionally accepted
  • Yunnan Agricultural University, Kunming, China

The final, formatted version of the article will be published soon.

The rumen microbiome plays a central role in ruminant nutrition and health. To investigate the effects of different feeding regimens on it, this study employed multi-omics analysis to reveal how natural grazing versus intensive feeding alters the rumen microbiota and metabolites in Shorthorn cattle. A total of 18 male shorthorn cattle of about 17 months of age and similar body weight were selected and randomly divided into 3 groups: natural grazing bull group (DJCF), intensive feeding bull group (DJCY) and intensive feeding steer group (DJC). The experiment period was 361 days. After the fattening trial, rumen fluid was collected at slaughter. Microbiota and metabolites were analyzed by 16S rRNA sequencing and LC-MS, and correlations were assessed. The results indicate that different feeding regimens were strongly associated with shifts in rumen microbial diversity and community composition. The ACE and Shannon indices of DJCF group were significantly higher than those of DJCY and DJC group (P < 0.05). Bacteroidetes and Firmicutes were the dominant phyla, with relative abundances of 57.62% (DJCF), 54.11% (DJCY), 48.84% (DJC) and 34.07%, 38.31%, 43.08%, respectively, showing no significant differences (P > 0.05). At the genus level, Prevotella and Rikenellaceae_RC9_gut_group were dominant. The abundance of Prevotella was highest in DJCY (22.52%), significantly differing from DJC (12.43%; P < 0.05), while Rikenellaceae_RC9_gut_group abundances were 12.56% (DJCF), 9.92% (DJCY), and 11.89% (DJC). In the fungal community, Neocallimastigomycota and Ascomycota were the dominant phyla, and there were no significant differences among the three groups. At the genus level, Caecomyces, the highest in the DJC group, with a significant difference from the DJCF group (P < 0.05). Orpinomyces, the highest in the DJCF group, with significant differences from the DJCY and DJC groups (P < 0.05). There were significant differences in rumen metabolites between different groups, and a variety of different metabolites were identified, involving sucrose and starch metabolism, purine metabolism and other pathways (P < 0.05). In addition, there was a significant correlation between rumen microbes and metabolites (P < 0.05). Thus, an intensive feeding system altered the rumen microbiome, resulting in improvements of Shorthorn cattle growth.

Keywords: Shorthorn cattle, Rumen, microbial community, Metabolomics, different feeding methods

Received: 01 Jul 2025; Accepted: 06 Oct 2025.

Copyright: © 2025 DAI, HE, ZHAO, LI, MAO and WU. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: FAN SI DAI, 15987179618@163.com

Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.