Tracking the Source of Escherichia coli isolated from Somerset, Baroon Pocket and Wivenhoe dams Using the B-glucuronidase gene : data

The collection contains a lab notebook, as well as associated spreadsheets, documents, images, and phylogenetic analysis files. The data was collected as part of a UWSRA funded project investigating the reduction of selected biological and chemical contaminants in South East Queensland reservoirs and associated waterways. The data is part of an ongoing method development research program funded by the Water Quality Research Centre with Seqwater as industry partners. E.coli isolates were collected by Seqwater from Wivenhoe Dam, Somerset Dam and Baroon Pocket Dam, and provided as live cultures to the research team at the Smart Water Research Centre. The isolates were checked for purity and stored in nutrient broth & 30% glycerol at -80oC until analysed. A 518 base pair fragment of the beta-glucuronidase gene from all E. coli isolates was amplified, using the polymerase chain reaction and sequenced. The sequence data from unknown isolates was compared to a library of known E. coli beta-glucuronidase gene sequences. Multiple sequence alignments were performed using ClustalX. Gap-only columns in the multiple sequence alignment were removed and final editing of the alignment was performed in BioEdit to yield an aligned 518 base pair fragment. Phylogenetic analysis involved the construction of phylogentic trees using the Neighbour-Joining method. The NJ tree was generated using MEGA version 5 employing the Maximum Composite Likelihood model/method and 1,000 bootstrap replicates.

本数据集包含实验室记录本（lab notebook）以及相关的电子表格（spreadsheets）、文档、图像和系统发育分析文件（phylogenetic analysis files）。该数据为一项由UWSRA资助的研究项目的组成部分，旨在探究昆士兰州东南部（South East Queensland）水库及关联水道中部分生物与化学污染物的消减工作。本数据同时隶属于水质研究中心（Water Quality Research Centre）资助的一项持续开展的方法学开发研究计划，合作产业伙伴为Seqwater。大肠杆菌（E.coli）分离株由Seqwater从怀文霍水库（Wivenhoe Dam）、萨默塞特水库（Somerset Dam）及巴隆口袋水库（Baroon Pocket Dam）采集，并以活培养物形式交付给智能水研究中心（Smart Water Research Centre）的研究团队。研究人员对这些分离株进行了纯度核验，并将其保存在营养肉汤（nutrient broth）与30%甘油（glycerol）的混合体系中，置于-80℃环境下直至后续分析环节。研究人员通过聚合酶链式反应（polymerase chain reaction）扩增了所有大肠杆菌分离株的β-葡萄糖醛酸酶基因（beta-glucuronidase gene）的518碱基对（base pair）片段，并完成测序。将未知分离株的序列数据与已知大肠杆菌β-葡萄糖醛酸酶基因序列数据库进行比对。研究使用ClustalX开展多序列比对（multiple sequence alignments），移除多序列比对中仅含空位的列，并借助BioEdit对比对结果进行最终编辑，得到最终对齐的518碱基对片段。系统发育分析采用邻接法（Neighbour-Joining method）构建系统发育树，借助MEGA 5版本（MEGA version 5），采用最大复合似然模型（Maximum Composite Likelihood model）方法，并结合1000次自举重复（bootstrap replicates），生成邻接树。