Bacterial ASV-pH preference-functional gene associations

Presence/absence of 332 gene types significantly associated to bacterial pH preference in representative genomes of bacterial taxa from soil and freshwater habitats. The subset of 56 genes required to run the predictive model is also included. While the model only requires the pH preference and presence/absence of each gene in columns as input, the files include a column ASV and Dataset that allow matching them to their corresponding 16S rDNA reference sequences. If the intention is to run the model on the 56_genes_pHpreference_soil_freshwater.csv file, these two columns need to be removed. <br> Files pH_preferences_ASVs_*.csv indicate all ASVs with inferred pH preferences in the study. Note that these values are higher than those found in the 56_genes_pHpreference_soil_freshwater.csv, because not all ASVs could be matched to a reference genome. For more information check supplementary table 1 in the original paper - https://www.science.org/doi/10.1126/sciadv.adf8998. The 16S rDNA representative sequences of all ASVs can be found in the Representative sequences folder, in case the intention is to match those sequences to their corresponding inferred pH preferences.

本数据集涵盖土壤与淡水生境细菌类群代表性基因组中，332种与细菌pH偏好性显著相关的基因类型的存在/缺失情况。同时附带运行该预测模型所需的56个基因子集。尽管该模型仅需以各基因的pH偏好性及存在/缺失情况作为列输入，但数据文件中额外包含ASV（Amplicon Sequence Variant）和Dataset两列，可用于将条目匹配至对应的16S rDNA参考序列。若需针对56_genes_pHpreference_soil_freshwater.csv文件运行该模型，则需移除这两列。<br>pH_preferences_ASVs_*.csv文件包含本研究中所有带有推定pH偏好性的ASV。需注意，该文件中的数值高于56_genes_pHpreference_soil_freshwater.csv中的数值，原因在于并非所有ASV均可匹配至参考基因组。如需获取更多详情，请查阅原论文的补充表1——https://www.science.org/doi/10.1126/sciadv.adf8998。所有ASV的16S rDNA代表性序列可在Representative sequences文件夹中获取，用于将这些序列与其对应的推定pH偏好性进行匹配。