Comparison of the methodological differences between samples. Venn diagrams showing the number of differentially classified taxonomies after analyzing the recreated dataset for (A) ORIGINAL vs. QIIME, (B) ORGINAL vs. LAST, and (C) LAST vs. QIIME. ORIGINAL represents the recreated dataset of 1,028 error-free sequences obtained from the SILVA128 database of the bacterial taxonomy identified by the Illumina and MinION reads for A. tamarense and C. polykrikoides. LAST represents the results obtained by analyzing the ORIGINAL dataset with LAST alignment. QIIME represents the results obtained by analyzing the ORIGINAL dataset with the QIIME pipeline. (D) A heatmap of the relative abundance percentage change after analyzing the ORIGINAL data with the QIIME and LAST pipeline. The taxonomic ranks, from order to species, are shown for the taxonomies with an abundance level of at least 0.5%. (E) Example of sequence alignment composed of Illumina read and MinION reads for their representative sequences obtained from the SILVA128 database. (Top to Bottom) URB (EU328076.1.1447) sequence, Citreimonas, UO (EU246244.1.1424) sequence, Illumina reads classified as URB, Illumina reads classified as Citreimonas, UO, MB ALUS254_43 (E. AF359526.1.1401) sequence, MinION reads (1 and 2) classified as MB ALUS254_43 with a higher than 97% identity to URB sequence, and MinION reads (3 and 4) classified as MB ALUS254_43 with a higher than 97% identity to Citreimonas, UO sequence. The colors of the alignment represent the percentage identity between sequences. The consensus bar plot at the bottom represents the percentage of conserved sequences in the alignment. Abbreviations: AB ISHR1: alphaproteobacterium ISHR1; BECC 11(2013): bacterium enrichment culture clone 11(2013); FB KHS1: Flavobacteriaceae bacterium KHS1; MB ALUS253_43: marine bacterium ALUS253_43; RB MOLA13: Rhodobacteraceae bacterium MOLA 13; RB ZJ2218: Rhodobacteraceae bacterium ZJ2218; UAP: uncultured alphaproteobacterium; UAPS: uncultured alphaproteobacterium species; UB_genus: uncultured bacterium_genus; UGP: uncultured gamma proteobacterium; UO: uncultured organism; URB: uncultured Rhodobacteraceae bacterium.