# Comparative study on the rumen microbial communities and functions between Wagyu and Holstein calves

## TL;DR

This study compares how the rumen microbes in Wagyu and Holstein calves develop over time, revealing breed-specific differences in microbial community structure and function.

## Contribution

The study provides new insights into breed-specific rumen microbial succession and functional maturation in calves.

## Key findings

- Wagyu calves showed a more pronounced decline in dominant microbial taxa with age compared to Holsteins.
- Wagyu calves had higher alpha diversity indices at 5 and 6 months than at 3 months and compared to Holsteins.
- Wagyu calves exhibited a shift in functional genes from metabolism-related to cellular processes and genetic information processing by 6 months.

## Abstract

Understanding the rumen microbiota’s development in calves is essential for optimizing breed-specific feeding strategies. This study aimed to comparatively investigate the dynamic changes in the rumen microbial community structure and function in Wagyu and Holstein calves.

Five 3-month-old Wagyu calves and five age-matched Holstein calves were selected. All animals received the same diet consisting of concentrate and hay, with free access to feed and water. Rumen fluid samples were collected monthly from 3 to 6 months of age. Metagenomic sequencing was performed to assess microbial composition (phylum and genus levels), alpha diversity (Shannon, Simpson, ACE, and Chao1 indices), and functional pathway (KEGG-based).

The cumulative relative abundance of dominant taxa at both phylum and genus levels declined with age in both breeds, more markedly in Wagyu calves than in Holsteins. From 3 to 6 months of age, the top five phyla combined dropped by 3.25% in Wagyu and 0.87% in Holstein calves, whereas the top ten genera combined decreased by 1.63% and 0.63%, respectively. Alpha diversity in Wagyu calves increased significantly with age. At 5 and 6 months, the Shannon, ACE, and Chao1 indices were significantly higher than those at 3 months (P < 0.05). Moreover, from 4 to 6 months, Wagyu calves consistently exhibited significantly higher diversity indices than Holsteins (P < 0.05). At 6 months, Wagyu calves showed a significant reduction in metabolism-related microbial genes and an increase in genes related to cellular processes and genetic information processing compared to earlier ages and Holstein calves (P < 0.05).

These findings suggest potential breed-specific differences in the succession and functional maturation of rumen microbiota. Holstein calves developed earlier and more stable metabolic functions, while Wagyu calves underwent a more dynamic microbial selection process.

Not applicable.

The online version contains supplementary material available at 10.1186/s12864-025-12392-1.