Metagenomic reconstructions of caecal microbiome in Landes, Roman and Zhedong White geese

ABSTRACT

1. The caecal microbiota in geese play a crucial role in determining the host’s health, disease status and behaviour, as evidenced by extensive epidemiological data. The present investigation conducted 10× metagenomic sequencing of caecal content samples obtained from three distinct goose species, namely Landes geese, Roman geese and Zhedong White geese (n = 5), to explore the contribution of the gut microbiome to carbohydrate metabolism.

2. In total, 337GB of Illumina data were generated, which identified 1,048,575 complete genes and construction of 331 metagenomic bins, encompassing 78 species from nine phyla. Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria and Bacteria were identified as the dominant phyla while Prevotella, Bacteroides, Streptococcus, and Subdoligranulum were the most abundant genera in the caecum of geese.

3. The genes were allocated to 375 pathways using the Kyoto Encyclopedia of Genes and Genome (KEGG) analysis. The most abundant classes in the caecum of geese were confirmed to be glycoside hydrolases (GHs), glycosyl transferases (GTs), as identified through the carbohydrate-active enzyme (CAZyme) database mapping. Subdoligranulum variabile and Mediterraneibacter glycyrrhizinilyticus were discovered to potentially facilitate carbohydrate digestion in geese.

4. Notwithstanding, further investigation and validation are required to establish a connection between these species and CAZymes. Based on binning analysis, Mediterraneibacter glycyrrhizinilyticus and Ruminococcus sp. CAG:177 are potential species in LD geese that contribute to the production of fatty liver.

KEYWORDS:

• Geese
• caecal microbiome
• metagenome
• MAGs
• CAZymes

Disclosure statement

No potential conflict of interest was reported by the author(s).

Data availability statement

Metagenomic sequencing data were submitted to the NCBI Sequence Read Archive (SRA) database under the study Accession SUB11630667 (https://www.ncbi.nlm.nih.gov/sra/PRJNA850683).

Supplementary material

Supplemental data for this article can be accessed online at https://doi.org/10.1080/00071668.2023.2239172.

Additional information

Funding

This research was funded by the China Agriculture Research System of MOF and MARA [CARS-42-27].