Effect of host breeds on gut microbiome and serum metabolome in meat rabbits

Abstract

Background Gut 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). Results Sequencing 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. Conclusions Our 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.

Structural and Functional Alterations of Gut Microbiota in Males With Hyperuricemia and High Levels of Liver Enzymes

“…In our study, some species that are known as SCFAs (e.g. butanoate) producer [Roseburia hominis (32,33), Odoribacter splanchnicus (34), Ruminococcus callidus (35), Lachnospiraceae bacterium 3_1_46FAA (36), Bacteroides uniformis (37) and Butyricimonas synergistica (38)], together with the metabolic pathway of producing butanoate (CENTFERM-PWY and PWY-6590) were enriched in the healthy controls. Importantly, both of the two pathways had significantly positive correlations with the above bacterials.…”

Integrated Bacterial and Fungal Diversity Analysis Reveals the Gut Microbial Alterations in Diarrheic Giraffes

“…Alloprevotella can produce moderate amounts of acetate and succinate and decrease lifetime cardiovascular disease risk ( Downes et al, 2013 ; Ricaboni et al, 2016 ; Xin et al, 2019 ). Some genera such as Coprococcus and Ruminiclostridium have been demonstrated to produce short-chain fatty acids, which is beneficial to regulate energy intake and maintain the morphology and function of intestine and intestinal epithelial cells ( Tan et al, 2014 ; Ye et al, 2021 ). Moreover, Ruminiclostridium , as an intestinal beneficial bacterium, is involved in the positive regulation of the growth performance and decrease of gastrointestinal diseases of animals ( Tan et al, 2014 ).…”

Metagenomic Analysis Reveals New Microbiota Related to Fiber Digestion in Pigs

“…In this study, we also found that the relative contribution to GH5_1 of R. albus reaches 72.11% and only R. callidus contains GH48 family in all potential bacterial biomarkers of H_NDF group. R. callidus is a producer of short-chain fatty acids (SCFAs), which can be used as a bacterial biomarker for improving the health and production performance of meat rabbits ( Ye et al, 2021 ). S. bovis is a kind of separable bacteria existing in the rumen contents of yak, which can utilize cellobiose, arabinose, mannose, glucose, etc.…”