Characterization of the rumen microbiota in dairy calves receiving copper or grape-pomace feed supplementatio

In this study, the rumen microbiota of Holstein-Friesian calves was characterized, and the effect of two feed supplementations on its composition was investigated. Fifteen male calves of an average age of 195 days were assigned to three groups: copper supplementation (cupric sulphate: 300 g/100L of drinking water), grape pomace supplementation (1 kg/head/ day), and control (no supplementation). The dietary treatment had a duration of 75 days. Copper is an essential trace elements; grape pomace is a source of polyphenols and resveratrol which have antioxidant and protective properties. Rumen fluid was sampled after slaughter for microbial-16S metabarcoding- sequencing. Taxonomic counts were then used to characterize the rumen microbiota and assess the impact of dietary supplementation. The average number of different microbial OTUs (operational taxonomic units) was highest in the grape-pomace group (1583) compared to the copper (1507) and control (1500) groups. The species richness indicators (Chao1, abundancebased coverage estimator-ACE) gave a similar picture. The Shannon and Simpson diversity indexes were very similar among groups. On the contrary, the Fisher’s alpha index showed a tendency of being higher in grape pomace group (256.4) than in copper and control ones (235.1 and 218.6 respectively). Overall, the most abundant microbial species in the rumen were Prevotella stercorea, Bacteroides uniformis and Ruminococcus flavefaciens, which accounted for 79% of total rumen bacteria. The same three species were the most abundant in the grape-pomace group (86% of the total), in controls (76% of total) and in the copper group (70% of total). Microbial counts were also used to classify calves in the three experimental groups. Random Forest (RF) was used for classification. When all OTUs were fitted to the classification model, the OOB (out-of-bag) classification error was high (66%). However, if only the four most relevant OTUs (from RF variable importance ranking) were fitted to the RF model, the OOB error dropped to 26.7%. The rumen microbiota in dairy calves seems to be dominated by few taxas. Feed supplementation with grape-pomace and copper did not have a profound impact on the overall composition of the rumen microbiota. However, specific microbial species and/or taxa were differentially abundant in the treatment groups, and allowed for a certain degree of discrimination between them.