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Animals : an open access journal from MDPI2025; 15(20); 2938; doi: 10.3390/ani15202938

Metagenomic Applications to Herbivore Gut Microbiomes: A Comprehensive Review of Microbial Diversity and Host Interactions.

Abstract: Herbivorous animals rely on complex gastrointestinal systems and microbial communities to efficiently digest plant-based diets, extract nutrients, and maintain health. Recent advances in metagenomic technologies have enabled high-resolution, culture-independent analysis of gut microbiota composition, functional potential, and host-microbe interactions, providing insights into microbial diversity across the herbivore digestive tract. This review summarizes key findings on the gastrointestinal microbiota of herbivores, focusing on ruminant foregut and non-ruminant hindgut fermentation. Ruminants like cattle, sheep, and goats host microbiota enriched with fibrolytic and methanogenic microbes that facilitate fiber degradation and volatile fatty acid production, contributing significantly to energy balance. In contrast, non-ruminants such as horses and rabbits rely on hindgut fermentation, with distinct microbial taxa contributing to carbohydrate and protein breakdown. The review further explores how specific microbial taxa, including , , and , correlate with improved feed efficiency and growth performance, particularly in ruminants. Additionally, the roles of probiotics, prebiotics, and symbiotics in modulating gut microbial composition and enhancing productivity are discussed. Despite significant advances, challenges remain in microbial sampling, functional annotation, and understanding the integration of microbiota with host physiology. The review emphasizes the potential of metagenomic insights in optimizing herbivore gut microbiota to improve feed efficiency, health, and sustainable livestock production.
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Publication Date: 2025-10-10 PubMed ID: 41153865PubMed Central: PMC12560936DOI: 10.3390/ani15202938Google Scholar: Lookup
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Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

Overview

  • This research article reviews the application of metagenomic techniques to studying the gut microbiomes of herbivorous animals.
  • It summarizes current knowledge on microbial diversity and host-microbe interactions in different herbivore digestive systems and discusses implications for improving animal health and productivity.

Introduction to Herbivore Gut Microbiomes

  • Herbivores depend on complex gastrointestinal systems and associated microbial communities to break down plant materials.
  • Microbes in the gut help digest fibers, extract nutrients, and maintain overall health of the host animal.
  • Traditional culture-based methods limited understanding due to inability to grow many gut microbes.
  • Advances in metagenomics allow culture-independent, detailed analysis of microbial composition and functions in the herbivore gut.

Metagenomic Technologies and Their Significance

  • Metagenomics involves sequencing DNA directly from gut samples to identify microbial taxa and their genetic capabilities.
  • This enables high-resolution studies of microbial diversity without needing to culture organisms.
  • Functional potential of microbial communities can be inferred, allowing insight into metabolic pathways and host interactions.
  • Understanding these relationships facilitates optimization of diet and health management in herbivores.

Microbial Diversity in Herbivore Digestive Systems

  • There are two main types of herbivore fermentation systems:
    • Ruminant Foregut Fermentation: Found in animals like cattle, sheep, and goats.
      • Microbial communities are rich in fibrolytic (fiber-degrading) and methanogenic microbes.
      • These microbes degrade complex plant fibers into volatile fatty acids (VFAs) that supply energy to the host.
      • Methanogens participate in methane production, impacting energy loss and environmental output.
    • Non-Ruminant Hindgut Fermentation: Present in animals such as horses and rabbits.
      • Fermentation primarily occurs in the hindgut (cecum and colon).
      • Distinct microbial populations help break down carbohydrates and proteins.
      • Microbes here enable nutrient extraction despite less specialized digestive anatomy compared to ruminants.

Key Microbial Taxa and Their Host Impact

  • The review identifies specific microbial taxa linked to better feed efficiency and growth, especially in ruminants.
  • Microbes contributing to fiber degradation, nutrient synthesis, and metabolic functions are critical.
  • Examples of important taxa may include (although not fully spelled out in abstract):
    • Fibrobacter and Ruminococcus – fiber degradation specialists.
    • Methanobrevibacter – methanogenic archaea involved in methane production.
    • Other beneficial microbes that promote feed conversion and animal performance.

Modulation of Gut Microbiota

  • Probiotics, prebiotics, and symbiotics are explored as strategies to alter gut microbial composition positively.
  • These interventions can enhance productivity, animal health, and nutrient utilization.
  • Probiotics involve adding beneficial live microbes; prebiotics provide substrates to stimulate helpful microbes; symbiotics combine both approaches.
  • Optimizing microbial communities could reduce methane emissions and improve sustainability.

Challenges and Future Directions

  • Challenges remain in:
    • Sampling gut microbiota accurately without contamination or bias.
    • Functionally annotating genes and understanding microbial roles beyond taxonomic identification.
    • Integrating microbiome data with host physiological systems for holistic understanding.
  • Future research aims to leverage metagenomic insights to:
    • Improve feed efficiency and animal growth sustainably.
    • Reduce environmental impacts of livestock through microbiome management.
    • Develop precision feeding and microbiome-based therapeutics.

Conclusions

  • Metagenomics provides powerful tools to explore the diverse and functionally important microbial communities in herbivore guts.
  • Microbial populations vary by digestive system type but are essential for fiber breakdown and nutrient acquisition.
  • Host-microbe interactions influence animal health, feeding efficiency, and productivity.
  • Modulating gut microbiota represents a promising avenue for sustainable livestock improvement.

Cite This Article

APA
Wei J, Wei L, Ullah A, Geng M, Zhang X, Wang C, Khan MZ, Wang C, Zhang Z. (2025). Metagenomic Applications to Herbivore Gut Microbiomes: A Comprehensive Review of Microbial Diversity and Host Interactions. Animals (Basel), 15(20), 2938. https://doi.org/10.3390/ani15202938

Publication

Animals : an open access journal from MDPI
ISSN: 2076-2615
NlmUniqueID: 101635614
Country: Switzerland
Language: English
Volume: 15
Issue: 20
PII: 2938

Researcher Affiliations

Wei, Jinjin
  • College of Agriculture and Biology, Liaocheng University, Liaocheng 252000, China.
Wei, Lin
  • College of Agriculture and Biology, Liaocheng University, Liaocheng 252000, China.
Ullah, Abd
  • College of Agriculture and Biology, Liaocheng University, Liaocheng 252000, China.
Geng, Mingyang
  • College of Agriculture and Biology, Liaocheng University, Liaocheng 252000, China.
Zhang, Xuemin
  • Yili Kazak Autonomous Prefecture Livestock General Station, Yili 835000, China.
Wang, Changfa
  • College of Agriculture and Biology, Liaocheng University, Liaocheng 252000, China.
Khan, Muhammad Zahoor
  • College of Agriculture and Biology, Liaocheng University, Liaocheng 252000, China.
Wang, Chunming
  • College of Agriculture and Biology, Liaocheng University, Liaocheng 252000, China.
Zhang, Zhenwei
  • College of Agriculture and Biology, Liaocheng University, Liaocheng 252000, China.

Grant Funding

  • 2022YFD1600103; 2023YFD1302004 / the National Key R&D Program of China

Conflict of Interest Statement

The authors declare no conflicts of interest.

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