Comparative metagenomics of the gut microbiota in wild greylag geese (Anser anser) and ruddy shelducks (Tadorna ferruginea)

• Published in: MicrobiologyOpen (Weinheim) 2019-05, Vol.8 (5), p.e00725-n/a
• Main Authors: Wang, Wen, Zheng, Sisi, Li, Laixing, Yang, Yongsheng, Liu, Yingbao, Wang, Aizhen, Sharshov, Kirill, Li, Yao
• Format: Article
• Language: English
• Subjects: Amino acids; Animals; Anser anser; Antibiotic resistance; antibiotic resistance genes; Antibiotics; Aquatic birds; Bacteria - classification; Bacteria - genetics; Big Data; Biosynthesis; Bird migration; Birds; Carbohydrate metabolism; Carbohydrates; carbohydrate‐active enzymes; China; Cofactors; Comparative studies; Computer centers; Data analysis; Datasets; Deoxyribonucleic acid; Digestive system; DNA; Domestication; Drug resistance; Ducks - microbiology; Energy metabolism; Enzymes; Feces; Gastrointestinal Microbiome; Gastrointestinal tract; Geese - microbiology; Genera; Genomics; Glycan; greylag geese; gut metagenomes; Homeostasis; Immune system; Intestinal microflora; Laboratories; Lipid metabolism; Lipids; Metagenome; Metagenomics; Microbial activity; Microbiomes; Microbiota; Microorganisms; Nucleotides; Original; Rare species; ruddy shelducks; Species classification; Structure-function relationships; Studies; Tadorna ferruginea; Vitamins; Wildfowl
• ISSN: 2045-8827; 2045-8827
• DOI: 10.1002/mbo3.725

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. Analysis of the overall functional profiles in this study indicated that the gut microbes associated with greylag geese (Anser anser) and ruddy shelducks (Tadorna ferruginea) exhibited high metabolic activities. The unigenes matched to level 1 and level 2 KEGG functional categories were shown in this Figure. In detail, the dominant functional categories included metabolism (59.89%), genetic information processing (13.37%), and environmental information processing (9.65%) in the KEGG database.