Whole-metagenome shotgun sequencing of pig faecal microbiome
Open Access
- 1 January 2021
- journal article
- research article
- Published by Taylor & Francis Ltd in Italian Journal of Animal Science
- Vol. 20 (1), 1147-1155
- https://doi.org/10.1080/1828051x.2021.1952910
Abstract
Here, we sequenced the faecal microbiome of a local pig breed by using whole-metagenome sequencing. Metagenomic data revealed that the faecal microbiome consists of a complex and intricate admixture of microbes belonging to all domains of life, including viruses. Most of sequencing reads were mapped to multiple reference sequences of Bacteria (99.35%) whereas the remaining reads (0.65%) were assigned to different microbes belonging to Archaea, Eukarya, and viruses. The predominant bacterial phylum was Firmicutes (∼86%), whereas Ascomycota division (fungi) was the most abundant eukaryotic phyla found. BLAST homology search showed that viral reads could be assigned to a total of 13 viral families of which 7 were present in all metagenomes. Bioinformatics analysis identified a catalogue of microbial genes encoding 231,428 unique proteins grouped in 3,169 functional groups and involved in 275 biochemical pathways. This study represents a first attempt to explore the faecal microbiome of a local pig breed in order to expand our knowledge about the taxonomic and functional profiles of microbes associated with this rare and endangered-maintained pig breed.Keywords
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