Aquatic GAMUT Bacterial Community Target Metagenomics-454 Pyro

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 in September 2014. Briefly, water column samples were filtered onto 0.2 um membrane filters, which were dissolved and processed with MOBIO Power Soil DNA extraction kits. We sequenced bacterial DNA (PCR-amplified using V4-region specific primers) using 454-pyrosequencing (an older sequencing method with more limitations). We cleaned, clustered (using 97% OTU similarity cut-off) and aligned sequences using the Schloss 2011 protocol, and classified OTUs to taxonomy based on the SILVA bacteria database. Code used for analysis 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.

Schloss PD, Gevers D, Westcott SL. (2011). Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PloS ONE. 6:e27310.

本数据集的收集旨在深入探究河流细菌群落在不同城市化类型和不同季节中的连通性与多样性。该数据集涵盖了2014年9月，在iUTAH水生GAMUT站点（http://data.iutahepscor.org/mdf/Data/Gamut_Network/）的三个流域中，河流细菌群落的操作分类单元（OTU，细菌物种的替代指标）丰度。简而言之，水柱样本经过0.2微米膜过滤，并使用MOBIO Power Soil DNA提取试剂盒溶解和处理。通过V4区特异性引物进行PCR扩增的细菌DNA，采用454焦磷酸测序（一种具有更多局限性的较老测序方法）进行测序。随后，我们采用Schloss 2011协议对序列进行清洗、聚类（采用97% OTU相似性阈值）和比对，并根据SILVA细菌数据库对OTU进行分类。用于分析的代码可在https://github.com/erinfjones/mothurcode上获取。数据集中包含三个文件；stream_design.txt文件包含了站点和样本元数据（如采样日期），.shared文件中包含了按样本观察到的OTU计数，而.taxonomy文件中则包含了OTU的分类学分类。Schloss PD, Gevers D, Westcott SL. (2011). Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PloS ONE. 6:e27310。