FIGURE 3.

Relative abundance of 16S rRNA at the genus level. We used the Human Oral Microbiome Database (HOMD) to assign taxonomy to the 16S rRNA from the MinION reads. For the short‐read metagenomes, we used the taxonomy of the ribosomal gene S7 with the Genome Taxonomy Database (GTDB). We processed the 16S rRNA amplicons with the Minimum Entropy Decomposition (MED) algorithm and used Silva version 132 to assign taxonomy. Genera representing less than 1% of a sample were pooled as rare (in light grey). Samples noted as TD correspond to an additional sampling performed 2 weeks after the initial pool of samples used for the long‐read extractions. PB, DNeasy PowerSoil with modified bead beating; GT, Qiagen Genomic Tip 20/G with enzymatic treatment; PC, phenol–chloroform; AE, agarose encasement. The designations “_1” and “_2” indicate replicate 1 and replicate 2, respectively