Analysis of the bacterial diversity in the rumen of Creole goats receiving two different diets by PCR Denaturing Gradient Gel Electrophoresis and q-PCR.

GRILLI, D.; KOPECNY, J; MRAZEK, J; PAEZ LAMA, S.; SOSA, MA; ARENAS, GN.

Aberdeen, Escocia.

Simposio; 9th Joint Symposium: Gut Microbiology. Rowett Institute of Nutrition and Health, University of Aberdeen, Scotland (UK) and the Institut National de la Recherche Agronomique, Clermont-Ferrand-Theix (France).; 2014

Rowett Institute of Nutrition and Health, University of Aberdeen, Scotland (UK) and the Institut National de la Recherche Agronomique, Clermont-Ferrand-Theix (France).

PCR-DGGE and qPCR were associated in a two-step approach to determine both the abundance and diversity of the bacterial community characterizing the rumen of Creole goats for whom the diet was switched from alfalfa hay/corn (AH/C) to native forages. Total bacteria and bacteria belonging to the phyla Firmicutes, Actinobacteria, Bacteroidetes and γ-Proteobacteria were quantified by qPCR using primers targeting the 16S rRNA gene. The V3 region of the 16S rRNA from the total DNA isolated from the rumen of goats was amplified by PCR and the resulting products were separated on DGGE gels. To determine the banding patterns in terms of structural diversity, clearly distinguishable bands per gel strip were analyzed by two ways. The similarities of all gel tracks were calculated, and then a cluster analysis of the matrix of similarity values were performed. The H index of diversity from the DGGE banding pattern of samples was calculated. Results demonstrated that goats fed on a native diet showed a greater bacterial diversity in their rumens than goats receiving a AH/C diet. A predominance of unknown bacterial taxa was observed. The major bacterial taxon identified in rumen samples was Firmicutes. No significant differences in the concentrations of total ruminal bacteria, Firmicutes, Bacteroidetes or γ-Proteobacteria were observed. However, the proportion of Actinobacteria was significantly higher in goats fed on native diet than those fed on a AH/C diet. Findings from PCR-DGGE and qPCR analysis suggest that the bacterial community in the rumen of Creole goats can be modified by the diet.