The genome sequences from this study are available from GenBank under the following accession no: CP003249.1 (T. oshimai JL-2 chromosome), CP003250.1 (T. oshimai JL-2 megaplasmid pTHEOS01), CP003251.1 (T. oshimai JL-2 plasmid pTHEOS02), CP003252.1 (T. thermophilus JL-18 chromosome), CP003253.1 (T. thermophilus JL-18 plasmid pTTJL1801), and CP003254.1 (T. thermophilus JL-18 plasmid pTTJL1802).