Data from: Oral samples as non-invasive proxies for assessing the composition of the rumen microbial community

Tapio I, Shingfield KJ, McKain N, Bonin A, Fischer D, Bayat AR, Vilkki J, Taberlet P, Snelling TJ, Wallace RJ

Date Published: April 27, 2016

DOI: http://dx.doi.org/10.5061/dryad.1b07d

 

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Title Archaea sequence data
Downloaded 4 times
Description Primers used for PCR amplification of bacteria and archaea 16S rRNA genes, ciliate protozoa 18S rRNA genes and anaerobic fungi ITS1 genes were designed in silico using ecoPrimers, the OBITools software suite (http://www.grenoble.prabi.fr/trac/OBITools) and a database created from sequences stored in GenBank. PCR amplicons were combined in equal volumes and purified (QIAquick PCR purification kit, Qiagen, Germany). After library preparation using a standard protocol with only five PCR cycles, amplicons were sequenced using the MiSeq technology from Illumina (Fasteris, SA, Geneva, Switzerland), which produced 250-base paired-end reads for all markers, other than for archaea (100-base paired-end reads). Alignment of paired-end reads, sample assignment and removal of sequences with ambiguous nucleotides and sequences of lengths outside the empirical sequence length distribution were performed with the OBITools software suite. Primer sequences and metadata for each sample are provided in the file 'Sequence metadata.xlsx', that is also part of this Dryad data package.
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Title Bacteria sequence data
Downloaded 4 times
Description Primers used for PCR amplification of bacteria and archaea 16S rRNA genes, ciliate protozoa 18S rRNA genes and anaerobic fungi ITS1 genes were designed in silico using ecoPrimers, the OBITools software suite (http://www.grenoble.prabi.fr/trac/OBITools) and a database created from sequences stored in GenBank. PCR amplicons were combined in equal volumes and purified (QIAquick PCR purification kit, Qiagen, Germany). After library preparation using a standard protocol with only five PCR cycles, amplicons were sequenced using the MiSeq technology from Illumina (Fasteris, SA, Geneva, Switzerland), which produced 250-base paired-end reads for all markers, other than for archaea (100-base paired-end reads). Alignment of paired-end reads, sample assignment and removal of sequences with ambiguous nucleotides and sequences of lengths outside the empirical sequence length distribution were performed with the OBITools software suite. Primer sequences and metadata for each sample are provided in the file 'Sequence metadata.xlsx', that is also part of this Dryad data package.
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Title Fungi sequence data
Downloaded 2 times
Description Primers used for PCR amplification of bacteria and archaea 16S rRNA genes, ciliate protozoa 18S rRNA genes and anaerobic fungi ITS1 genes were designed in silico using ecoPrimers, the OBITools software suite (http://www.grenoble.prabi.fr/trac/OBITools) and a database created from sequences stored in GenBank. PCR amplicons were combined in equal volumes and purified (QIAquick PCR purification kit, Qiagen, Germany). After library preparation using a standard protocol with only five PCR cycles, amplicons were sequenced using the MiSeq technology from Illumina (Fasteris, SA, Geneva, Switzerland), which produced 250-base paired-end reads for all markers, other than for archaea (100-base paired-end reads). Alignment of paired-end reads, sample assignment and removal of sequences with ambiguous nucleotides and sequences of lengths outside the empirical sequence length distribution were performed with the OBITools software suite. Primer sequences and metadata for each sample are provided in the file 'Sequence metadata.xlsx', that is also part of this Dryad data package.
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Title Protozoa sequence data
Downloaded 3 times
Description Primers used for PCR amplification of bacteria and archaea 16S rRNA genes, ciliate protozoa 18S rRNA genes and anaerobic fungi ITS1 genes were designed in silico using ecoPrimers, the OBITools software suite (http://www.grenoble.prabi.fr/trac/OBITools) and a database created from sequences stored in GenBank. PCR amplicons were combined in equal volumes and purified (QIAquick PCR purification kit, Qiagen, Germany). After library preparation using a standard protocol with only five PCR cycles, amplicons were sequenced using the MiSeq technology from Illumina (Fasteris, SA, Geneva, Switzerland), which produced 250-base paired-end reads for all markers, other than for archaea (100-base paired-end reads). Alignment of paired-end reads, sample assignment and removal of sequences with ambiguous nucleotides and sequences of lengths outside the empirical sequence length distribution were performed with the OBITools software suite. Primer sequences and metadata for each sample are provided in the file 'Sequence metadata.xlsx', that is also part of this Dryad data package.
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Title Sequence metadata
Downloaded 9 times
Description This file contains information on animal ID's, primer sequences, sampling periods and diets.
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When using this data, please cite the original publication:

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. http://dx.doi.org/10.1371/journal.pone.0151220

Additionally, please cite the Dryad data package:

Tapio I, Shingfield KJ, McKain N, Bonin A, Fischer D, Bayat AR, Vilkki J, Taberlet P, Snelling TJ, Wallace RJ (2016) Data from: Oral samples as non-invasive proxies for assessing the composition of the rumen microbial community. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.1b07d
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