Abstract
Gut microbiome contributes to host health by maintaining homeostasis, increasing digestive efficiency, and facilitating the development of immune system. Wild greylag geese (Anser anser) and ruddy shelducks (Tadorna ferruginea), migrating along the central Asian flyway, appear to be one of the most popular species in the rare birds rearing industries of China. However, the structure and function of the gut microbial communities associated with these two bird species remain poorly understood. Here, for the first time, we compared gut metagenomes from greylag geese to ruddy shelducks and investigated the similarities and differences between these two bird species in detail. Taxonomic classifications revealed the top three bacterial phyla, Firmicutes, Proteobacteria, and Fusobacteria, in both greylag geese and ruddy shelducks. Furthermore, between the two species, 12 bacterial genera were found to be more abundant in ruddy shelducks and 41 genera were significantly higher in greylag geese. A total of 613 genera (approximately 70%) were found to be present in both groups. Metabolic categories related to carbohydrate metabolism, metabolism of cofactors and vitamins, lipid metabolism, amino acid metabolism, and glycan biosynthesis and metabolism were significantly more abundant in ruddy shelducks, while greylag geese were enriched in nucleotide metabolism and energy metabolism. The herbivorous greylag geese gut microbiota harbored more carbohydrate‐active enzymes than omnivorous ruddy shelducks. In our study, a range of antibiotic resistance categories were also identified in the gut microbiota of greylag geese and ruddy shelducks. In addition to providing a better understanding of the composition and function of wild birds gut microbiome, this comparative study provides reference values of the artificial domestication of these birds.
Highlights
Animals are colonized by rich and complex communities of microorganisms, both externally and internally (Colston & Jackson, 2016; McFall-Ngai et al, 2013)
The output data encompassed a total of 38,306.65 Mb of raw reads, with an average of 6,384.44 Mb per sample (Supporting Information Table S1)
To investigate the antibiotic resistance genes (ARGs) present in the gut microbiota of greylag geese and ruddy shelducks, the unigenes identified in the metagenome data were screened for antibiotic resistance factors using the Comprehensive Antibiotic Resistance Database (CARD)
Summary
Animals are colonized by rich and complex communities of microorganisms, both externally (e.g., on skin and feathers) and internally (e.g., in the gastrointestinal and reproductive tracts) (Colston & Jackson, 2016; McFall-Ngai et al, 2013). A wealth of studies have shown that gut microbiome plays an important role in several fundamental and crucial processes in humans and other animal hosts, such as development (Malmuthuge, Griebel, & Guan, 2015), immune homeostasis (Ahern, Faith, & Gordon, 2014), nutrient assimilation (Kau, Ahern, Griffin, Goodman, & Gordon, 2011), vitamins synthesis and sterols metabolism (O’Mahony, Clarke, Borre, Dinan, & Cryan, 2015), and diseases (e.g., obesity, diabetes, and cancer) (Kinross, Darzi, & Nicholson, 2011; Lee & Hase, 2014). Metagenomic sequencing was performed to compare the gut microbial compositions and functions of two bird species, greylag geese (Anser anser) and ruddy shelducks (Tadorna ferruginea) These birds belong to the same family (Anatidae) and are two ecologically and economically important waterfowl. The results of this study provide a deeper exploration of the gut microbiomes of wild geese and ducks and may provide useful information for the further application of probiotic strains (isolated from the feces of wild geese and ducks) in the artificial rearing of these birds
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