DOI: 10.5061/dryad.1b07d
title: Data from: Oral samples as non-invasive proxies for assessing the composition of the rumen microbial community

description: Microbial community analysis was carried out on ruminal digesta obtained
 directly via rumen fistula and buccal fluid, regurgitated digesta (bolus)
 and faeces of dairy cattle to assess if non-invasive samples could be used
 as proxies for ruminal digesta. Samples were collected from five cows
 receiving grass silage based diets containing no additional lipid or four
 different lipid supplements in a 5 x 5 Latin square design. Extracted DNA
 was analysed by qPCR and by sequencing 16S and 18S rRNA genes or the
 fungal ITS1 amplicons. Faeces contained few protozoa, and bacterial,
 fungal and archaeal communities were substantially different to ruminal
 digesta. Buccal and bolus samples gave much more similar profiles to
 ruminal digesta, although fewer archaea were detected in buccal and bolus
 samples. Bolus samples overall were most similar to ruminal samples. The
 differences between both buccal and bolus samples and ruminal digesta were
 consistent across all treatments. It can be concluded that either proxy
 sample type could be used as a predictor of the rumen microbial community,
 thereby enabling more convenient large-scale animal sampling for
 phenotyping and possible use in future animal breeding programs aimed at
 selecting cattle with a lower environmental footprint.
description: Archaea sequence
 dataPrimers 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.archaea.tar.gzBacteria sequence dataPrimers 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.bacteria.tar.gzFungi sequence dataPrimers 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.fungi.tar.gzProtozoa sequence dataPrimers 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.protozoa.tar.gzSequence metadataThis file contains information on animal ID's, primer sequences, sampling periods and diets.