Diversity and functions of the sheep faecal microbiota: a multi-omic characterization.
Little is currently known on the microbial populations colonizing the sheep large intestine, despite their expected key role in host metabolism, physiology and immunity. This study reports the first characterization of the sheep faecal microbiota composition and functions, obtained through the application of a multi-omic strategy. An optimized protocol was first devised for DNA extraction and amplification from sheep stool samples. Then, 16S rDNA sequencing, shotgun metagenomics and shotgun metaproteomics were applied to unravel taxonomy, genetic potential and actively expressed functions and pathways respectively. Under a taxonomic perspective, the sheep faecal microbiota appeared globally comparable to that of other ruminants, with Firmicutes being the main phylum. In functional terms, we detected 2097 gene and 441 protein families, finding that the sheep faecal microbiota was primarily involved in catabolism. We investigated carbohydrate transport and degradation activities and identified phylum-specific pathways, such as methanogenesis for Euryarchaeota and acetogenesis for Firmicutes. Furthermore, our approach enabled the identification of proteins expressed by the eukaryotic component of the microbiota. Taken together, these findings unveil structure and role of the distal gut microbiota in sheep, and open the way to further studies aimed at elucidating its connections with management and dietary variables in sheep farming.
Porto Conte Ricerche, Science and Technology Park of Sardinia, Tramariglio, Alghero, Italy.
Alessandro
A
Tanca
Porto Conte Ricerche, Science and Technology Park of Sardinia, Tramariglio, Alghero, Italy.
Cristina
C
Fraumene
Porto Conte Ricerche, Science and Technology Park of Sardinia, Tramariglio, Alghero, Italy.|Department of Biomedical Sciences, University of Sassari, Sassari, Italy.
Valeria
V
Manghina
Porto Conte Ricerche, Science and Technology Park of Sardinia, Tramariglio, Alghero, Italy.|Department of Biomedical Sciences, University of Sassari, Sassari, Italy.
Antonio
A
Palomba
Department of Biomedical Sciences, University of Sassari, Sassari, Italy.
Marcello
M
Abbondio
Department of Biomedical Sciences, University of Sassari, Sassari, Italy.
Massimo
M
Deligios
Porto Conte Ricerche, Science and Technology Park of Sardinia, Tramariglio, Alghero, Italy.
Daniela
D
Pagnozzi
Porto Conte Ricerche, Science and Technology Park of Sardinia, Tramariglio, Alghero, Italy.
Maria Filippa
MF
Addis
Porto Conte Ricerche, Science and Technology Park of Sardinia, Tramariglio, Alghero, Italy.|Department of Biomedical Sciences, University of Sassari, Sassari, Italy.
Sergio
0000-0001-6246-2794
S
Uzzau
D000818:Animals; D001105:Archaea / Q000145:classification* / Q000235:genetics / Q000378:metabolism; D001419:Bacteria / Q000145:classification* / Q000235:genetics / Q000378:metabolism; D016000:Cluster Analysis; D019641:DNA, Archaeal / Q000737:chemistry / Q000235:genetics; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D005243:Feces / Q000382:microbiology*; D000069196:Gastrointestinal Microbiome; D007420:Intestine, Large / Q000382:microbiology*; D053858:Metabolic Networks and Pathways; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D012756:Sheep / Q000382:microbiology*
D019641:DNA, Archaeal; D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S