Supplementary data for "Cross-platform comparison of oral microbiome profiles under a unified reference database"

This dataset contains the supplementary figures and tables supporting the findings of the manuscript <b>"Cross-platform comparison of oral microbiome profiles under a unified reference database."</b>The dataset includes:<b>Supplementary Figure S1.</b><b> </b><b>Correlation of relative abundances at the (A) family and (B) species levels.</b> This figure complements Figure 2. Relative abundances for each taxon were plotted for all four samples (n=4), with each point representing a specific taxon within a single sample. The plot is shown on a log10 scale. The dashed black line indicates the line of identity (y=x), and the dashed red lines represent a 10-fold difference in abundance. For each plot, the 15 most abundant taxa are highlighted in color, while all other taxa are shown in gray. Point size is proportional to its average abundance across both platforms. Overall Spearman's rank correlation coefficient (ρ) is annotated in the top-left corner of each panel.<b>Supplementary Figure S2.</b><b> MA plots comparing Illumina and ONT abundances at all taxonomic levels.</b> (A) Phylum, (B) family, (C) genus, and (D) species. MA plots visualize the platform bias (log2 fold change, y-axis) against the average abundance (A-value, x-axis) for each taxon. The y-axis represents the log2 fold change of (ONT/Illumina abundance). The x-axis represents the mean abundance across both platforms on a log10 scale. The horizontal dashed line at y=0 indicates no bias. Points are colored by taxon only if they are among the 15 most abundant taxa for that rank; all others are shown in gray. This figure visually represents the data from Supplementary Table S2.<b>Supplementary Table S1. Merged abundance data used for correlation and bias analyses.</b> This Excel (.xlsx) file contains four sheets corresponding to different taxonomic ranks: "phylum," "family," "genus," and "species." Each sheet provides the complete, merged relative abundance data (%) for each taxon detected in each of the four samples (AP, BP, AS, BS) by both the Illumina and ONT platforms. This dataset forms the basis for the correlation analyses (Figure 2, Supplementary Figure S1) and systematic bias quantification (Table 3, Supplementary Figure S2).<b>Supplementary Table S2. Comprehensive per-taxon quantitative comparison and bias analysis. </b>This Excel (.xlsx) file contains four sheets corresponding to "phylum," "family," "genus," and "species." This table provides the complete statistics for all taxa detected at each rank, forming the basis for the data presented in Table 3 and Supplementary Figure S2. Columns provide the mean relative abundance (%) and standard deviation (SD) for both the Illumina and ONT platforms, as well as the calculated log2 fold change (ONT/Illumina) for each taxon.<b>Note:</b> The raw sequencing data (FASTQ files) generated in this study have been deposited in the DDBJ Sequence Read Archive (DRA) under accession BioProject accession number PRJDB39890. The R scripts used for analysis are available at (https://github.com/hmaru/2026_cross-platform-comparison) and archived in Zenodo (https://doi.org/10.5281/zenodo.17810740).