The supplementation with Lactobacillus sakei as probiotic on the ileal and cecal microbiota of mule ducks during overfeeding was investigated using high-throughput 16S rRNA gene-based pyrosequencing and real-time PCR. The ducks were overfed with or without L. sakei for 12 d with 56% ground corn and 42% whole corn. Samples were collected before the overfeeding period (at 12 wk), at 13 wk (meal 12 of overfeeding), and at 14 wk (meal 24), 3 h postfeeding. Whatever the digestive segment and the level of intake, Firmicutes, Bacteroidetes, and Proteobacteria were the dominant phyla in the bacterial community of mule ducks (at least 90%). Before overfeeding, ileal samples were dominated by Clostridia, Bacteroidia, and Gammaproteobacteria (80% and up), and cecal samples by Bacteroidia and Clostridia (around 85%). The richness and diversity decreased in the ileum and increased in the ceca after overfeeding. Overfeeding increased the relative abundance of Firmicutes and especially the Lactobacillus group in ileal samples. Nonmetric multidimensional scaling profiles separated the bacterial communities with respect to overfeeding only in cecal samples. Richness indicators decreased after L. sakei has been added at mid-overfeeding only in the ileum. In the ceca, the decrease of these indexes only occurred at the end of overfeeding. The addition of L. sakei triggers major changes in the ileum, whereas the ceca are not affected. Lactobacillus sakei decreased the relative abundance of Bacteroides at mid-overfeeding and the relative abundance of Enterobacteria at the end of overfeeding in the ileum.
Keywords: 454 pyrosequencing; duck microbial diversity; overfeeding; probiotic; real-time PCR.