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Background <p>The associations between the gut microbiome and growth performance in calves have been investigated; however, most existing studies have primarily focused on rumen microbiomes. Whether fecal microbiomes in terms of composition and function are altered among calves with different growth rates remains unclear. Therefore, the objective of this study was to investigate how fecal microbiomes influence calf growth rates. A total of 16 beef calves under the same management were recruited and classified into two groups based on their growth rates (average daily gain: ADG; 4-month-old, <i>n</i> = 8 per group x 2 growth rate groups). At 4 months of age, fecal samples were collected from the rectum for the quantification of volatile fatty acids (VFAs) and characterization of microbial communities via metagenomic sequencing.</p> Results <p>The VFA profiles did not differ between the two groups. Calves with higher growth rates exhibited lower bacterial and archaeal Shannon diversity, and the overall microbial community structure showed a clear separation between the two groups. Moreover, fecal bacterial and archaeal species associated with improved growth performance were identified, characterized by the enrichment of <i>Alistipes shahii</i>, <i>Alistipes onderdonkii</i>, <i>Bifidobacterium thermophilum</i>, <i>Akkermansia glycaniphila</i>, and <i>Methanobrevibacter sp. AbM4</i> in calves with higher growth rates. In addition, the metabolic pathways involved in lipid and amino acid metabolism and CAZyme genes linked to carbohydrate degradation were enriched in the calves with better growth performance. The viral community composition and diversity differed between the two groups, with lower diversity observed in calves exhibiting higher growth rates. Additionally, viruses predicted to infect bacterial hosts such as <i>Prevotella</i> and <i>Succinivibrio</i>, which are involved in carbohydrate degradation, were positively associated with ADG. Interestingly, a virus associated with <i>Methanobrevibacter sp017652345</i> exhibited a positive correlation with ADG. The relationships between fecal microbes and host phenotypic traits were divergent between the two groups.</p> Conclusions <p>These findings suggest that fecal microbiomes are associated with calf growth rates through potential multi-kingdom interactions, particularly those between viruses and their prokaryotic hosts, indicating possible avenues to improve animal performance via microbiome modulation.</p>

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Multi-kingdom fecal microbiome and virus–host interactions associated with growth performance of indigenous beef calves in Guizhou

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年1月24日

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  • Wei Guo,
  • Jiangkun Yu,
  • Weiwei Wang,
  • Jian Wang,
  • Mengmeng Ni,
  • Mi Zhou,
  • Xiang Chen

摘要

Background

The associations between the gut microbiome and growth performance in calves have been investigated; however, most existing studies have primarily focused on rumen microbiomes. Whether fecal microbiomes in terms of composition and function are altered among calves with different growth rates remains unclear. Therefore, the objective of this study was to investigate how fecal microbiomes influence calf growth rates. A total of 16 beef calves under the same management were recruited and classified into two groups based on their growth rates (average daily gain: ADG; 4-month-old, n = 8 per group x 2 growth rate groups). At 4 months of age, fecal samples were collected from the rectum for the quantification of volatile fatty acids (VFAs) and characterization of microbial communities via metagenomic sequencing.

Results

The VFA profiles did not differ between the two groups. Calves with higher growth rates exhibited lower bacterial and archaeal Shannon diversity, and the overall microbial community structure showed a clear separation between the two groups. Moreover, fecal bacterial and archaeal species associated with improved growth performance were identified, characterized by the enrichment of Alistipes shahii, Alistipes onderdonkii, Bifidobacterium thermophilum, Akkermansia glycaniphila, and Methanobrevibacter sp. AbM4 in calves with higher growth rates. In addition, the metabolic pathways involved in lipid and amino acid metabolism and CAZyme genes linked to carbohydrate degradation were enriched in the calves with better growth performance. The viral community composition and diversity differed between the two groups, with lower diversity observed in calves exhibiting higher growth rates. Additionally, viruses predicted to infect bacterial hosts such as Prevotella and Succinivibrio, which are involved in carbohydrate degradation, were positively associated with ADG. Interestingly, a virus associated with Methanobrevibacter sp017652345 exhibited a positive correlation with ADG. The relationships between fecal microbes and host phenotypic traits were divergent between the two groups.

Conclusions

These findings suggest that fecal microbiomes are associated with calf growth rates through potential multi-kingdom interactions, particularly those between viruses and their prokaryotic hosts, indicating possible avenues to improve animal performance via microbiome modulation.