Metagenome analysis of gut microbial in both the caged and non-caged ducks

Abstract

The different duck husbandry techniques, the type of feeds, and environments are believed to have an impact on the diversity of duck's gut microbiome. This research has the objective to examine the diversity of gut microbiome of duck in different husbandry models, i.e., cage and non-cage. The research design was an exploratory study. Duck samples were taken purposively from both cage (CG) and non-cage (NCG) methods at local duck farms in Gunungpati, Semarang, Central Java, Indonesia. Five grams of duck intestinal samples were prepared for DNA isolation, 16S rRNA gene amplification in the V3-V4 region and were sequenced with Next Generation Sequencing (NGS) method: metagenomics. The 16S metagenomic analysis was performed using QIIME2 (Ver. 2019.4). The most dominant gut bacteria that found in both CG and NCG was Family Enterobacteriaceae, Phylum Proteobacteria and followed by Lactobacillaceae from Phylum Firmicutes. However, the bacterial diversity map in family level was not shown a significant trend between CG and NCG. There were 851 shared species belongs to NCG and CG; it means that more than 800 same bacteria species build up the gut ecosystem both in NCG and CG. It is likely because of similar feed and environmental condition from the two husbandries. The diversity of duck gut microbiome in Gunungpati may be closely related to feeding, rearing techniques, and environments. The number of bacteria species in the non-caged duck (NCG) was higher than CG or caged duck.