Rumen microbiome in dairy calves fed copper and grape-pomace dietary supplementations: Composition and predicted functional profile

Loor, Juan J, Biscarini, Filippo ORCID: https://orcid.org/0000-0002-3901-2354, Palazzo, Fiorentina, Castellani, Federica, Masetti, Giulia, Grotta, Lisa, Cichelli, Angelo and Martino, Giuseppe 2018. Rumen microbiome in dairy calves fed copper and grape-pomace dietary supplementations: Composition and predicted functional profile. PLoS ONE 13 (11) , e0205670. 10.1371/journal.pone.0205670

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Abstract

The rumen microbiome is fundamental for the productivity and health of dairy cattle and diet is known to influence the rumen microbiota composition. In this study, grape-pomace, a natural source of polyphenols, and copper sulfate were provided as feed supplementation in 15 Holstein-Friesian calves, including 5 controls. After 75 days of supplementation, genomic DNA was extracted from the rumen liquor and prepared for 16S rRNA-gene sequencing to characterize the composition of the rumen microbiota. From this, the rumen metagenome was predicted to obtain the associated gene functions and metabolic pathways in a cost-effective manner. Results showed that feed supplementations did alter the rumen microbiome of calves. Copper and grape-pomace increased the diversity of the rumen microbiota: the Shannon’s and Fisher’s alpha indices were significantly different across groups (p-values 0.045 and 0.039), and Bray-Curtis distances could separate grape-pomace calves from the other two groups. Differentially abundant taxa were identified: in particular, an uncultured Bacteroidales UCG-001 genus and OTUs from genus Sarcina were the most differentially abundant in pomace-supplemented calves compared to controls (p-values 0.003 and 0.0002, respectively). Enriched taxonomies such as Ruminiclostridium and Eubacterium sp., whose functions are related to degradation of the grape- pomace constituents (e.g. flavonoids or xyloglucan) have been described (p-values 0.027/0.028 and 0.040/0.022 in Pomace vs Copper and Controls, respectively). The most abundant predicted metagenomic genes belonged to the arginine and proline metabolism and the two- component (sensor/responder) regulatory system, which were increased in the supplemented groups. Interestingly, the lipopolysaccharide biosynthetic pathway was decreased in the two supplemented groups, possibly as a result of antimicrobial effects. Methanogenic taxa also responded to the feed supplementation, and methane metabolism in the rumen was the second most different pathway (up-regulated by feed supplementations) between experimental groups.

Item Type:	Article
Date Type:	Published Online
Status:	Published
Schools:	Medicine
Publisher:	Public Library of Science
ISSN:	1932-6203
Funders:	EU FP7-IAPP
Date of First Compliant Deposit:	3 December 2018
Date of Acceptance:	29 September 2018
Last Modified:	14 Aug 2023 07:10
URI:	https://orca.cardiff.ac.uk/id/eprint/117296

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