A team from the Institute for Animal Science and Technology at Universitat Politècnica de València conducted longitudinal 16S rRNA sequencing on 319 fecal samples from two maternal rabbit lines. Through alpha and beta diversity analyses and zero-inflated negative binomial mixed models, they identify age-driven declines in microbial diversity and taxa abundance, highlighting biomarkers tied to functional longevity.
Key points
Longitudinal 16S rRNA sequencing of 319 rabbit fecal samples across reproductive life reveals declines in observed richness, Shannon diversity, and evenness.
Aitchison-based PCA and PERMANOVA show age explains 6% of microbiome composition variance, indicating significant beta diversity changes.
Zero-inflated negative binomial mixed models identify over 20% of ASVs with age-dependent abundance shifts, mostly negative, across two maternal lines.
Why it matters:
Identifying age-associated microbiome shifts offers biomarkers to enhance rabbit longevity selection and welfare.
Q&A
What is alpha diversity?
How does Aitchison distance work?
What is a zero-inflated negative binomial mixed model (ZINBMM)?
Why compare two maternal rabbit lines?
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Academy
Gut Microbiome
The gut microbiome is the community of microorganisms—including bacteria, fungi, and viruses—residing in the digestive tract. These microbes participate in nutrient breakdown, immune system modulation, and barrier protection against pathogens. In mammals, trillions of gut microbes form a dynamic ecosystem that coevolves with its host, influencing digestion efficiency, metabolic health, and disease resistance. Balanced microbial communities produce beneficial compounds such as short-chain fatty acids, supporting gut integrity and systemic health.
Microbiome Diversity Metrics
Diversity metrics provide quantitative measures of microbiome complexity. Alpha diversity assesses diversity within a sample using indices like observed richness (count of distinct taxa), Shannon index (accounts for richness and evenness), and Pielou’s evenness (distribution uniformity). Beta diversity compares composition between samples, commonly using Aitchison distance after centered log-ratio transformation to respect compositional constraints. Visualization methods like principal component analysis (PCA) and statistical tests such as PERMANOVA identify factors explaining community differences.
Age-Related Changes and Longevity
Microbiome dynamics shift over an animal’s lifespan. In young mammals, microbial diversity often increases during gut maturation. However, studies of adult and elderly populations reveal varied patterns, including diversity declines or compositional drifts linked to aging-related inflammation and immunosenescence. Such shifts can weaken colonization resistance, reduce beneficial metabolite production, and favor opportunistic pathogens. Understanding age-driven microbiome changes helps identify biomarkers associated with healthspan and longevity across species.
Implications for Rabbit Health and Longevity
This research on adult female rabbits demonstrates that microbial richness and evenness decline steadily throughout reproductive life, with specific bacterial taxa decreasing in abundance. By comparing two genetic lines—one commercial and one selected for high longevity—investigators reveal genetic influences on gut community resilience. These findings suggest microbiome profiles as practical biomarkers for breeding programs aiming to enhance functional longevity, reduce early culling, and improve overall welfare in rabbit production.
