Nanopore data

Datasets describing community composition of EcoPlate wells inoculated with lake water analyzed by 16S rRNA gene sequencing with Nanopore MinION. OTUs were assembled with an in-house pipeline by Hofer, C. 2022. Master thesis: Long-read MinION data for microbial community analysis. Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Switzerland. Here we provide OTU and taxonomy table and OTUs_Nanopore lists the sequences of the OTUs.Only syringe samples (see project description) were analyzed by Nanopore sequencing. 24 samples were sequenced, grown on four different subtrates (D-cellobiose, L-serine, N-acetyl-D-glucosamine, putrescine) inoculated with syringe samples from Sampling 1 and 2 (n = 3). Putrescine enrichments were disregarded in the corresponding publication due to a lack of successful enrichments available for Illumina sequencing. More information about the sampling conditions can be found in the project description.Sample_info provides information for the sample names given in the OTU table. Information is formated as barcode_substrate_sampling. Values: Barcode = 01-24, substrate = cellobiose/serine/glucosamine/putrescine, Sampling = S1/S2. For example, 01_cellobiose_S1 describes a community inoculated with lake water from a sampling 1 syringe sample grown in D-cellobiose.

本数据集描述了接种湖水的EcoPlate微孔板孔内微生物群落组成，该样本采用纳米孔MinION（Nanopore MinION）平台通过16S rRNA基因测序进行分析。操作分类单元（Operational Taxonomic Unit，OTU）由霍费尔（Hofer, C.）于2022年完成的硕士学位论文《用于微生物群落分析的长读长纳米孔数据》中开发的内部分析流程组装完成，该论文隶属于瑞士苏黎世大学植物与微生物生物学系湖沼学工作站。本数据集提供了OTU表、分类学表，以及存储OTU序列的OTUs_Nanopore列表。仅注射器采集样本（详见项目说明文档）通过纳米孔测序开展分析。本次研究共完成24份样本的测序，这些样本分别接种于4种不同底物：D-纤维二糖、L-丝氨酸、N-乙酰-D-氨基葡萄糖、腐胺，且接种样本均来自采样1与采样2的注射器采集湖水样本，每组设置3个生物学重复（n=3）。由于缺乏可用于Illumina测序的成功富集样本，腐胺富集组在对应发表论文中未被纳入分析。更多采样条件相关细节可查阅项目说明文档。sample_info文件用于说明OTU表中各样本名称的对应信息，命名格式为barcode_substrate_sampling。各字段取值规则如下：Barcode（条形码）取值范围为01-24；substrate（底物）可选值为cellobiose/serine/glucosamine/putrescine（即纤维二糖、丝氨酸、氨基葡萄糖、腐胺）；Sampling（采样批次）可选值为S1/S2。例如，01_cellobiose_S1代表一份接种自采样1的注射器湖水样本，并在D-纤维二糖培养基中培养得到的微生物群落样本。