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<p>Animal gut microbiomes—comprising bacteria, archaea, fungi, viruses, and protozoa—are fundamental to host evolution, physiology, and ecosystem resilience. This review synthesizes 21st-century advances in their diversity, spatiotemporal dynamics, and functional roles across the animal kingdom. Although high-throughput metagenomics has transformed the field, major biases remain: most studies still focus on domesticated vertebrates and fecal samples, leaving substantial “microbial dark matter” in wild hosts, invertebrates, and non-bacterial domains unexplored. We highlight how gut microbiomes mediate adaptation to environmental extremes, including hypoxia, temperature stress, and toxins, and how industrialization disrupts these communities, contributing to biodiversity loss and disease risk. We further integrate eco-evolutionary theory, multi-omics, and spatial modeling to clarify cross-kingdom interactions and functional networks. Finally, we discuss translational applications—including probiotics, fecal microbiota transplantation (FMT), phage therapy, and synthetic consortia—and emphasize the need for global collaborative initiatives, artificial intelligence (AI)-driven discovery, and standardized databases to unlock the full potential of animal gut microbiomes for biodiversity conservation, climate resilience, and planetary health in the coming decades.</p>

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Animal gut microbes and microbiomes in the 21st century and beyond

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2026年5月12日

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  • Zhigang Zhang,
  • Feng Jiang,
  • Zhipeng Li,
  • Limei Lin,
  • Bin Qi,
  • Dandan Han,
  • Chao Ran,
  • Shengyong Mao,
  • Junjun Wang,
  • Zhigang Zhou,
  • Min Wang,
  • Jilian Li,
  • Guanhong Wang,
  • Shuaishuai Kang,
  • Tongzuo Zhang

摘要

Animal gut microbiomes—comprising bacteria, archaea, fungi, viruses, and protozoa—are fundamental to host evolution, physiology, and ecosystem resilience. This review synthesizes 21st-century advances in their diversity, spatiotemporal dynamics, and functional roles across the animal kingdom. Although high-throughput metagenomics has transformed the field, major biases remain: most studies still focus on domesticated vertebrates and fecal samples, leaving substantial “microbial dark matter” in wild hosts, invertebrates, and non-bacterial domains unexplored. We highlight how gut microbiomes mediate adaptation to environmental extremes, including hypoxia, temperature stress, and toxins, and how industrialization disrupts these communities, contributing to biodiversity loss and disease risk. We further integrate eco-evolutionary theory, multi-omics, and spatial modeling to clarify cross-kingdom interactions and functional networks. Finally, we discuss translational applications—including probiotics, fecal microbiota transplantation (FMT), phage therapy, and synthetic consortia—and emphasize the need for global collaborative initiatives, artificial intelligence (AI)-driven discovery, and standardized databases to unlock the full potential of animal gut microbiomes for biodiversity conservation, climate resilience, and planetary health in the coming decades.