Data from: Metagenomic and near full-length 16S rRNA sequence data in support of the phylogenetic analysis of the rumen bacterial community in steers

Amplicon sequencing utilizing next-generation platforms has significantly transformed how research is conducted, specifically microbial ecology. However, primer and sequencing platform biases can confound or change the way scientists interpret these data. The Pacific Biosciences RSII instrument may also preferentially load smaller fragments, which may also be a function of PCR product exhaustion during sequencing. To further examine theses biases, data is provided from 16S rRNA rumen community analyses. Specifically, data from the relative phylum-level abundances for the ruminal bacterial community are provided to determine between-sample variability. Direct sequencing of metagenomic DNA was conducted to circumvent primer-associated biases in 16S rRNA reads and rarefaction curves were generated to demonstrate adequate coverage of each amplicon. PCR products were also subjected to reduced amplification and pooling to reduce the likelihood of PCR product exhaustion during sequencing on the Pacific Biosciences platform. The taxonomic profiles for the relative phylum-level and genus-level abundance of rumen microbiota as a function of PCR pooling for sequencing on the Pacific Biosciences RSII platform were provided.
Data is within this article and raw ruminal MiSeq sequence data is available from the NCBI Sequence Read Archive (SRA Accession SRP047292). Additional descriptive information is associated with NCBI BioProject PRJNA261425. http://www.ncbi.nlm.nih.gov/bioproject/PRJNA261425/ Resources in this dataset:Resource Title: NCBI Sequence Read Archive (SRA Accession SRP047292). File Name: Web Page, url: https://www.ncbi.nlm.nih.gov/sra/SRX704260 1 ILLUMINA (Illumina MiSeq) run: 978,195 spots, 532.9M bases, 311.6Mb downloads.

利用下一代测序平台进行的扩增子测序已显著改变了研究方法，尤其是在微生物生态学领域。然而，引物和测序平台偏差可能会混淆或改变科学家对数据的解读方式。太平洋生物科学RSII仪器可能更倾向于加载较小的片段，这可能是由于测序过程中PCR产物耗竭的结果。为进一步研究这些偏差，提供了来自16S rRNA瘤胃群落分析的数据。具体而言，提供了瘤胃细菌群落在相对门水平丰度方面的数据，以确定样本间的变异性。为了绕过与引物相关的16S rRNA读取偏差，进行了宏基因组DNA的直接测序，并生成了稀释曲线以展示每个扩增子的充分覆盖。PCR产物也进行了减量扩增和混池处理，以降低在太平洋生物科学平台上测序过程中PCR产物耗竭的可能性。提供了相对门水平和属水平丰度的瘤胃微生物群落分类学概况，这些概况是作为PCR混池测序在太平洋生物科学RSII平台上的函数。数据包含在本文中，且原始瘤胃MiSeq测序数据可在NCBI序列读取档案（SRA登录号SRP047292）中获取。与NCBI生物项目PRJNA261425相关联的附加描述性信息。http://www.ncbi.nlm.nih.gov/bioproject/PRJNA261425/ 本数据集包含以下资源：资源标题：NCBI序列读取档案（SRA登录号SRP047292）。文件名：网页，URL：https://www.ncbi.nlm.nih.gov/sra/SRX704260 1 ILLUMINA（Illumina MiSeq）运行：978,195个斑点，532.9M个碱基，311.6Mb下载量。