| Summary: | The intestinal health of poultry is of great importance for birds’ growth and development; probiotics-driven shifts in gut microbiome can exert considerable indirect effect on birds’ welfare and production performance. The information about gut microbiota of ducks is scarce; by using high throughput metagenomic sequencing with Illumina Miseq we examined fecal bacterial diversity of Peking ducks grown on conventional and <i>Bacillus</i>-probiotic-enriched feed. The probiotic supplementation drastically decreased the presence of the opportunistic pathogen <i>Escherichia/Shigella</i>, which was the major and sole common dominant in all samples. Seventy other bacterial species in the ducks’ fecal assemblages were found to have probiotic-related differences, which were interpreted as beneficial for ducks’ health as was confirmed by the increased production performance of the probiotic-fed ducks. Bacterial α-biodiversity indices increased in the probiotic-fed group. The presented inventory of the duck fecal bacteriobiome can be very useful for the global meta-analysis of similar data in order to gain a better insight into bacterial functioning and interactions with other gut microbiota to improve poultry health, welfare and production performance.
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