Authors:Letterio Giuffrèa, Domenico Giosa, Grazia Galeano, Riccardo Aiese Cigliano, Andreu Paytuví-Gallart, Anna Maria Sutera, Giuseppe Tardiolo, Alessandro Zumbo, Orazio Romeo, Enrico D’Alessandro


  • Dipartimento di Scienze Veterinarie, Università di Messina, Messina, Italy
  • Sequentia Biotech, Barcelona, Spain

Publication: Italian Journal of Animal Science

Date: August 2021

Full paper: Whole-metagenome shotgun sequencing of pig faecal microbiome


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.