Comparative Analysis on the Duodenal Microbiota Community in Geese Fed with the All-grass or Basal Diet

Geese (Anser cygnoides) possess stronger ability of roughage digestion and utilization than other poultries, hence, it has become the focus of attention of scientists. Duodenal, jejunum and ileum were mainly participated in food digestion and nutrient absorption, while the cecum was responsible for biological fermentation. Effects on the geese's cecal microbiota community by feeding with the all-grass diet have been investigated, however, whether it had an influence on the geese's duodenal microbiota community remains unexplored. To address this problem, geese feeding with the basal diet for 28 days (G1), the basal diet for 28 days and the all-grass diet for the following 14 days (G2), the basal diet for 42 days (G3) were selected, respectively. The duodenal segments of geese were collected and the hypervariable V3-V4 region of the bacterial 16S rRNA gene was sequencing. A total of 4 main phyla and 16 main genera were identified. Moreover, we also successfully identified that two taxa including the Helcococcus and Clostridium could be used as distinguishing biomarkers specific to G2. The functional profiles of the duodenum microbiota were mainly involved in the membrane transport (e.g. ABC transporters), amino acid metabolism, energy metabolism, metabolism of cofactors and vitamins, and cellular processes and signaling pathways in geese feeding with the all-grass diet. In conclusion, the all-grass diet could impact the composition of duodenal microbiota. However, to resolve the underlying mechanism of the fiber digesting and utilization in geese's gut microbiota, the whole intestinal system needs to be assessed by further studies.