Microbial Biogeography Study - Meyer et al. 2018 ISME-J

The V3 and V4 region of the 16S rRNA gene of the DNA and cDNA amplified using the primers 319F and 806R. Data are demultiplexed, quality-filtered, trimmed fasta files with primers removed. <br>OTU tables are from 2 community inference methods: DNA- based and RNA (cDNA)- based. OTU tables also differ by similarity threshold, i.e. 95, 97, 99, and 100% sequence similarity. None of these tables have been rarefied or normalized, thus differences in sequencing depth (i.e. sampling extent) across samples will vary. Naming convention is as follows: 'otu_table_rabi_uparse_{OTU sequence similarity threshold}_{community inference method}.txt'. Only OTU tables at 97% cutoff have taxonomic assignments. <br>'Rabi_geodist_matrix.txt' is a matrix of pairwise geographic distance (in meters) between samples. <br>'soil_chemical_data_pared.txt' is a table with soil chemical attributes as columns and samples as rows. <br>'Sampling_effort_DD.R' is an R function that performs a single rarefaction of a community matrix, calculates the slope of the distance-decay relationship of that community, then repeats iteratively.<br>Please cite: Meyer et al. 2018 ISME-J, DOI: 10.1038/s41396-018-0103-3本数据集包含使用引物319F与806R扩增得到的DNA及互补DNA（complementary DNA，cDNA）的16S核糖体RNA（16S rRNA）基因V3、V4区域。所得数据为已完成样本拆分（demultiplexed）、质量过滤、截短的FASTA（FASTA）格式文件，且已移除引物序列。 操作分类单元（Operational Taxonomic Unit，OTU）表基于两种群落推断方法生成，分别为基于DNA的方法与基于RNA（cDNA）的方法；同时OTU表还依据序列相似性阈值进行划分，阈值涵盖95%、97%、99%及100%。所有表格均未进行稀疏化或标准化处理，因此不同样本间的测序深度（即采样规模）存在差异。其命名规则为：`otu_table_rabi_uparse_{OTU序列相似性阈值}_{群落推断方法}.txt`。仅阈值为97%的OTU表附带物种分类注释信息。 `Rabi_geodist_matrix.txt`为样本间两两地理距离矩阵，单位为米。 `soil_chemical_data_pared.txt`为土壤化学属性数据表，列代表各项土壤化学指标，行代表对应样本。 `Sampling_effort_DD.R`为一款R语言函数，其功能为对群落矩阵执行单次稀疏化操作，计算该群落的距离衰减关系斜率，并迭代重复上述流程。 请引用该数据集相关文献：Meyer 等人于2018年发表于《ISME Journal》的研究，DOI：10.1038/s41396-018-0103-3