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Rumen bacteria, archaea and ciliate protozoa data from animal trial with Nordic Red dairy cows

Citation

Tapio, Ilma (2021), Rumen bacteria, archaea and ciliate protozoa data from animal trial with Nordic Red dairy cows, Dryad, Dataset, https://doi.org/10.5061/dryad.pvmcvdnk7

Abstract

Four multiparous dairy cows fitted with rumen cannula were used in a 4 × 4 Latin square with 2 × 2 factorial arrangement of treatments to examine how starch level and oil mixture impact dry matter (DM) intake and digestibility, milk yield and composition, rumen fermentation, ruminal methane (CH4) emissions, and microbial diversity. Experimental treatments were comprised of high (HS) or low (LS) levels of starch containing 0 or 30 g of a mixture of sunflower and fish oils (2:1 w/w) per kg diet DM (LSO and HSO, respectively). Digestibility was measured by total collection of feces and CH4 was measured using SF6 technique. Rumen microbial community was assessed by 16S/18S rRNA gene amplicon sequencing.

Usage Notes

Primers used in this study are described in Tapio et al. (2016).

Bacteria

File containing demultiplexed bacteria 16S rRNA gene (V5-6) fasta files for individual animals. Barcodes, forward and reverse primer sequences are trimmed. Primer sequences and metadata for each sample are provided in the file 'Sequence metadata.xlsx', that is also part of this Dryad data package.

Archaea

File containing demultiplexed archaea 16S rRNA gene (V9) fasta files for individual animals. Barcodes, forward and reverse primer sequences are trimmed. Primer sequences and metadata for each sample are provided in the file 'Sequence metadata.xlsx', that is also part of this Dryad data package.

Ciliate protozoa

File containing demultiplexed ciliate protozoa 18S rRNA gene fasta files for individual animals. Barcodes, forward and reverse primer sequences are trimmed. Primer sequences and metadata for each sample are provided in the file 'Sequence metadata.xlsx', that is also part of this Dryad data package.

Reference

Tapio I, Shingfield KJ, McKain N, Bonin A, Fischer D, Bayat AR, Vilkki J, Taberlet P, Snelling TJ, Wallace RJ. (2016) Oral samples as non-invasive proxies for assessing the composition of the rumen microbial community. PLoS ONE 11(3): e0151220. doi:10.1371/journal.pone.0151220.