Aquatic GAMUT Bacterial Community Target Metagenomics-HiSeq

This data was collected as part of a study to understand the connectivity and diversity of stream bacteria communities in streams flowing from high to low elevation through different types of urbanization and in different seasons. The dataset contains OTU (operational taxonomic units, the bacterial surrogate for species) abundance for bacteria at iUTAH aquatic GAMUT sites (http://data.iutahepscor.org/mdf/Data/Gamut_Network/) in three watersheds at 3 time points (November 2014, February 2015, and May 2015). Briefly, we filtered water column samples onto 0.2 um membrane filters, which were dissolved and processed with MOBIO Power Soil DNA extraction kits (alternate low protocol yield using phenol chloroform). We sequenced bacterial DNA (PCR-amplified using V4 region specific primers) using Illumina Hi-Seq. We cleaned, clustered (using 97% OTU similarity cut-off) and aligned sequences using the Kozich et al. 2013 protocol, and classified OTUs to taxonomy based on the SILVA bacteria database. Code used for processing is available at https://github.com/erinfjones/mothurcode.

There are three files; site and sample metadata (e.g. date sampled) is included in the file stream_design.txt, observed OTU counts by sample are in the .shared file, and the taxonomic classification of OTUs is in the .taxonomy file.

Also included are zipped folders containing raw fastq files.

Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD. (2013): Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Applied and Environmental Microbiology. 79(17):5112-20.

本数据集系一项研究之成果，旨在探究不同城市化类型和季节背景下，自高海拔流向低海拔的溪流中细菌群落之间的连接性和多样性。数据集收录了iUTAH水生GAMUT站点（http://data.iutahepscor.org/mdf/Data/Gamut_Network/）三个流域在三个时间点（2014年11月、2015年2月和2015年5月）的细菌操作分类单元（OTU，细菌物种的替代指标）丰度。简要而言，研究团队将水柱样品过滤至0.2微米的膜过滤器上，之后使用MOBIO Power Soil DNA提取试剂盒（采用酚-氯仿的替代低产率方案）进行溶解和处理。通过Illumina Hi-Seq平台对细菌DNA（使用V4区域特异性引物进行PCR扩增）进行测序。随后，研究团队采用Kozich等人在2013年的协议对序列进行清洗、聚类（使用97% OTU相似度截止值）和比对，并根据SILVA细菌数据库对OTU进行分类。用于处理的数据处理代码可在https://github.com/erinfjones/mothurcode上获取。数据集包含三个文件；包含采样日期等站点和样本元数据的文件为stream_design.txt，每个样本的观察OTU计数文件为.shared文件，而OTU的分类学分类文件为.taxonomy文件。此外，还包括包含原始fastq文件的压缩文件夹。Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD. (2013): Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Applied and Environmental Microbiology. 79(17):5112-20.