Abstract
BackgroundGut microbial compositional and functional variation can affect health and production performance of farm animals. Analysing metabolites in biological samples provides information on the basic mechanisms that affect the well-being and production traits in farm animals. However, the extent to which host breeds affect the gut microbiome and serum metabolome in meat rabbits is still unknown. In this study, the differences in phylogenetic composition and functional capacities of gut microbiota in two commercial rabbit breeds Elco and Ira were determined by 16S rRNA gene and metagenomic sequencing. The alternations in serum metabolome in the two rabbit breeds were detected using ultra-performance liquid chromatography system coupled with quadrupole time of flight mass spectrometry (UPLC-QTOFMS).ResultsSequencing results revealed that there were significant differences in the gut microbiota of the two breeds studied, suggesting that host breeds affect structure and diversity of gut microbiota. Numerous breed-associated microorganisms were identified at different taxonomic levels and most microbial taxa belonged to the families Lachnospiraceae and Ruminococcaceae. In particular, several short-chain fatty acids (SCFAs) producing species including Coprococcus comes, Ruminococcus faecis, Ruminococcus callidus, and Lachnospiraceae bacterium NK4A136 could be considered as biomarkers for improving the health and production performance in meat rabbits. Additionally, gut microbial functional capacities related to bacterial chemotaxis, ABC transporters, and metabolism of different carbohydrates, amino acids, and lipids varied greatly between rabbit breeds. Several fatty acids, amino acids, and organic acids in the serum were identified as breed-associated, where certain metabolites could be regarded as biomarkers correlated with the well-being and production traits of meat rabbits. Correlation analysis between breed-associated microbial species and serum metabolites revealed significant co-variations, indicating the existence of cross-talk among host-gut microbiome-serum metabolome.ConclusionsOur study provides insight into how gut microbiome and serum metabolome of meat rabbits are affected by host breeds and uncovers potential biomarkers important for breed improvement of meat rabbits.
Highlights
Gut microbial compositional and functional variation can affect health and production performance of farm animals
Structure and diversity of gut microbiota in Elco and Ira rabbits To understand how host breeds affect gut microbial community structure, we performed redundancy analysis (RDA) analysis, which revealed that breeds exerted a stronger effect on gut microbial communities in comparison to gender and age (Fig. 1a)
The alpha diversity analysis showed that there were no significant differences in Chao1, ACE, observed species, and Good’s coverage between Elco and Ira rabbits, but Elco rabbits had significantly higher Shannon and Simpson indices than Ira rabbits (Fig. 1b and c, false discovery rate (FDR) adjusted P < 0.05)
Summary
Gut microbial compositional and functional variation can affect health and production performance of farm animals. The extent to which host breeds affect the gut microbiome and serum metabolome in meat rabbits is still unknown. Compositional and functional variation in the gut microbiota has been linked to the health and production performance of farm animals [2]. Understanding the mechanisms governing the maintenance and function of gut microbiota is crucial for farm animal industry. Both environmental (e.g., diet, medicine, and environmental hygiene) and host factors (e.g., genetics background, gender, and age) can shape the gut microbial communities [3]. Pandit et al identified several breed-specific biomarkers including the genera Clostridium, Blautia, Butyrivibrio, Ruminococcus, and Roseburia in the gut microbial communities of different broiler chicken breeds [5], while Cheng et al observed substantial changes in the metabolic capacities of xylose, ribose, and fucose in the gut microbiome of Lantang and Duroc pigs [6]
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