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Communication Dans Un Congrès Année : 2023

Diet-induced changes in rumen epimural microbiota structure and predicted metabolic pathways in dairy goats

Résumé

At the interface between the rumen contents and the host’s internal milieu, the microorganisms colonising the rumen epithelium are likely to influence the physiology of their host and play a critical role in stabilizing the rumen ecosystem and animal health. However, their composition and metabolic activities remain considerably less documented than those of the microbial groups associated with the liquid phase and particles of the fermentation medium. To assess how diet affects the composition of the epithelial microbiota in rumen cannulated dairy goats, we sampled the epithelia of 12 dry animals fed a forage diet (F) and 12 lactating animals fed a mixed diet rich in non-structural carbohydrates (C). The procedure included temporary emptying and double rinsing of the rumen then rubbing two swabs on the roof and lateral surface of the dorsal rumen. After DNA extraction, the V4-V5 hypervariable region of the 16S rRNA gene was amplified. Using the Illumina MiSeq platform and the metabarcoding pipeline FROGS, 2033746 sequences were clustered into 1929 OTUs that were assigned using the 138 SILVA 16S database. A predictive analysis of the functional genes in the epimural microbiota was done using the procedure from PICRUSt2 and Metacyc database at hierarchical level 2 pathways and linear discriminant analysis effect size of functional abundances (LEfSe) was performed. The dominant phyla were Bacteroidota (relative abundances of 34% in F vs 43% in C, P=0.003), Firmicutes (40% in F vs 27% in C, P=0.0001) and Proteobacteria (4% in F vs 18% in C, P=0.0001) followed by Euryarcheota (6.4% in F vs 16.8% in C, P=0.0001), Fibrobacterota (1.51%) and Spirochaetota (0.96% in F vs 1.79% in C, P=0.007). The epithelial microbiota of F goats had a higher richness (P=0.001) but similar Shannon and Simpson indexes compared to microbiota of the C goats. Principal coordinate analysis based on bray-curtis distances revealed clear clustering of epithelial communities by diet along the first principal axis. Among the thirty-nine metabolic pathways that were identified in all samples, a total of 21 metabolic functions of the ruminal epithelial microbiota discriminated F and C goats. The 3 main enriched metabolic pathways of the epithelial microbiota of the C goats were the fatty acids and lipid biosynthesis, cell structure biosynthesis and fermentation whereas those enriched in the F goats were the amino acid biosynthesis and nucleoside and nucleotide biosynthesis / degradation. These results suggest an effect of dietary chemical composition on microbial primary metabolism in response to differing limiting nutritional factors as well as a higher microbial cell turnover in F communities due to potential more active regeneration of rumen epithelium. In conclusion, the two diets shaped these epimural communities, either directly or through ecological interactions that remain to be identified.

Dates et versions

hal-04484599 , version 1 (29-02-2024)

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Citer

Valérie Berthelot, Meriem Charef-Mansouri, Laurent Broudiscou. Diet-induced changes in rumen epimural microbiota structure and predicted metabolic pathways in dairy goats. 11. International Symposium on the Nutrition of Herbivores (ISNH 2023), Jun 2023, Florianópolis, Brazil. pp.591-592, ⟨10.1016/j.anscip.2023.04.075⟩. ⟨hal-04484599⟩
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