Impact of dietary fiber/starch ratio in shaping caecal microbiota in rabbits

The objective of this experiment was to determine whether changing the dietary neutral detergent fiber (NDF)/starch ratio affected caecal microbiota when 4 different diets (diet A: 2.3 NDF/starch, diet B: 1.9, diet C: 1.4, diet D: 1.0) were formulated. A total of 200 weaned rabbits (35 days old, 50 per group) were used for the experiment, which started after an adaptation period of 7 days (i.e., day 42). Caecal contents were obtained from rabbits fed different NDF/starch diets at 52, 62, 72, and 82 days of life. The bacterial community structure was characterized by high-throughput 16S rRNA sequencing. Firmicutes, Actinobacteria, Synergistetes, and Tenericutes did not significantly change with diet or age. However, Bacteroidetes (P < 0.05), Proteobacteria (P < 0.01), and Verrucomicrobia (P < 0.05) reads were significantly affected by diet, and Proteobacteria (P < 0.01) and Verrucomicrobia (P < 0.05) reads were significantly influenced by age. At the genus level, Escherichia/Shigella (P < 0.01) was overrepresented in diet A (high fiber) relative to diet D (high starch) in 52- and 62-day-old rabbits. Venn diagrams and heat map plot analyses revealed that the number of gut species shared between animals with different diet treatments increased with age. These results suggest that dietary fiber per starch ratios and age significantly alter the composition of caecal microbiota in growing rabbits.