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. 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.