Postnatal development of the rabbit caecal microbiota composition and activity

Abstract

This study describes the development of the rabbit caecum microbiota and its metabolic activities from the neonatal (day 2) until the subadult period (day 70). The caecal microbiota was analysed using 16S rRNA gene approaches coupled with capillary electrophoresis single-stranded conformation polymorphism (CE-SSCP) and qPCR. At day 2, rabbits harboured population levels up to 8.4, 7.2 and 7.4log10 copy numberg-1 full caecum of the total bacteria, Bacteroides-Prevotella and Firmicutes groups, respectively. These populations reached their maximum levels from day 14 for Firmicutes groups (10.8log10 copy numberg-1 caecal content) and day 21 (11.4 and 10.7log10 copy numberg-1 caecal content of the total bacteria and the Bacteroides-Prevotella group, respectively). The archaeal population could be detected only from day 7 onwards (5.5log10 copy numberg-1 full caecum) and reached its maximum level at day 35 (7.4log10 copy numberg-1 caecal content). Similarity analysis, diversity calculation and quantitative evaluation of the stability of bacterial community CE-SSCP profiles provided some evidence that the caecal microbiota develops progressively from a simple and unstable community after birth into a complex and climax community in subadult rabbits. Meanwhile, the microbial activity evolved with the progressive decrease of the propionate/butyrate ratio towards a rabbit-specific value <1. © 2011 INRA. FEMS Microbiology Ecology © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd.