Diversity and functions of the sheep faecal microbiota: a multi-omic characterization.

Alessandro Tanca,Massimo Deligios,Daniela Pagnozzi,Maria Filippa Addis,Valeria Manghina,Marcello Abbondio,Antonio Palomba,Sergio Uzzau,Cristina Fraumene

doi:10.1111/1751-7915.12462

Alessandro Tanca, Massimo Deligios + Show 7 more

Open Access

https://doi.org/10.1111/1751-7915.12462

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Abstract

SummaryLittle 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.

Highlights

SummaryLittle is currently known on the microbial populations colonizing the sheep large intestine, despite their expected key role in host metabolism, physiology and immunity
A well-balanced microbiota, with highly diverse taxonomic content and stability, appears of paramount importance throughout the whole digestive system, where a bidirectional driving force between microbial metabolic circuits and mucosal physiology allows to maintain a stable microbiota and a healthy gut and, an overall healthy and productive organism. In keeping with these premises, we investigated composition and functions of the microbial populations associated with the final tract of the sheep large intestine, where the last stage of plant mass digestion occurs with a significant potential contribution to host energy harvesting and physiology homeostasis
As described in the “Experimental procedures” section, samples were subjected to differential centrifugation (DC) or direct lysis (DL); DNA was extracted from both preparations after enzymatic and mechanical lysis with QIAamp Fast DNA Stool or with the E.Z.N.A

Summary

Little is currently known on the microbial populations colonizing the sheep large intestine, despite their expected key role in host metabolism, physiology and immunity. In keeping with these premises, we investigated composition and functions of the microbial populations associated with the final tract of the sheep large intestine, where the last stage of plant mass digestion occurs with a significant potential contribution to host energy harvesting and physiology homeostasis To reach this aim, we employed an integrated, multi-omic strategy, comprising 16S rDNA and shotgun metagenomic sequencing, to unravel microbiota structure and genetic potential, as well as metaproteomics, to identify and characterize functions and pathways actively expressed by the sheep faecal microbial communities

Results and discussion

Conclusions

Experimental procedures