Sequence Determination of Selected LAB Strains

The complete genome sequence of ten Limosilactobacillus mucosae (formerly Lactobacillus mucosae) [34] and three Leuconostoc suionicum (formerly Leuconostoc mesenteroides subs. suionicum) [35] strains were determined. Strains were grown using MRSCC broth medium at 35 °C for 24 h, then the cells were harvested and kept frozen in a –70 °C freezer until delivered to the sequencing facility. DNA preparation and sequence determination of the strains were performed by Xenovea Ltd. (Szeged, Hungary), except strain F1 which was performed by BIOMI Ltd. (Gödöllő, Hungary). De novo assembly of the raw reads was performed with SPAdes v3.0.0 software [36, 37] (https://cab.spbu.ru/software/spades/). After the de novo assembly, contigs below 500 bp were filtered out by using in-house Linux scripts. Contamination was removed using a BLAST search against the eukaryotic RefSeq sequences. RefSeq sequences were downloaded from NCBI. If the alignment length of the match was bigger than the half of the contig’s length we marked the scaffold as contamination and removed it from further analysis. The sequences of the cleaned draft genomes were deposited in the NCBI database, under accession number PRJNA926800.