Composition of intestinal bacterial community in ducks through high-throughput amplicon sequencing of 16S rRNA gene

Abstract

Little research has been conducted on the gut microbiome of the duck, although global duck meat production is steadily rising. The aim of the present study was to compare the composition of caecal microbiota of Cherry Valley ducks with the results of previous research. In total, 120 one-day-old ducks were purchased from a commercial hatchery and randomly assorted into 12 pens which had wheat straw litter as bedding material. On day 42, caecal chymus samples were collected from 12 pens including 2 ducks per pen. Samples in each pen were pooled after DNA extraction and analyzed by 16S rRNA gene targeted Illumina MiSeq sequencing. Bacteroidetes (59.36%), Firmicutes (30.70%), Proteobacteria (5.45%) were the dominant phyla in the caecum. At the genus level, Bacteroides, Prevotella, Megamonas, Barnesiella, Helicobacter were most abundant (31.35%, 17.20%, 6.78%, 3.79% and 2.49% respectively)