Complete genome sequence of Leuconostoc suionicum DSM 20241T provides insights into its functional and metabolic features

Standards in Genomic Sciences, Jul 2017

The genome of Leuconostoc suionicum DSM 20241T (=ATCC 9135T = LMG 8159T = NCIMB 6992T) was completely sequenced and its fermentative metabolic pathways were reconstructed to investigate the fermentative properties and metabolites of strain DSM 20241T during fermentation. The genome of L. suionicum DSM 20241T consists of a circular chromosome (2026.8 Kb) and a circular plasmid (21.9 Kb) with 37.58% G + C content, encoding 997 proteins, 12 rRNAs, and 72 tRNAs. Analysis of the metabolic pathways of L. suionicum DSM 20241T revealed that strain DSM 20241T performs heterolactic acid fermentation and can metabolize diverse organic compounds including glucose, fructose, galactose, cellobiose, mannose, sucrose, trehalose, arbutin, salcin, xylose, arabinose and ribose.

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Complete genome sequence of Leuconostoc suionicum DSM 20241T provides insights into its functional and metabolic features

Chun et al. Standards in Genomic Sciences Complete genome sequence of T Leuconostoc suionicum DSM 20241 provides insights into its functional and metabolic features Byung Hee Chun 0 1 Se Hee Lee 0 3 Hye Hee Jeon 1 Dong-Woon Kim 2 Che Ok Jeon 1 0 Equal contributors 1 Department of Life Science, Chung-Ang University , 84, HeukSeok-Ro, Dongjak-Gu, Seoul 06974 , Republic of Korea 2 Animal Nutrition and Physiology Team, National Institute of Animal Science , RDA, Jeollabukdo 55365 , Republic of Korea 3 Microbiology and Functionality Research Group, World Institute of Kimchi , Gwangju 61755 , Republic of Korea The genome of Leuconostoc suionicum DSM 20241T (=ATCC 9135T = LMG 8159T = NCIMB 6992T) was completely sequenced and its fermentative metabolic pathways were reconstructed to investigate the fermentative properties and metabolites of strain DSM 20241T during fermentation. The genome of L. suionicum DSM 20241T consists of a circular chromosome (2026.8 Kb) and a circular plasmid (21.9 Kb) with 37.58% G + C content, encoding 997 proteins, 12 rRNAs, and 72 tRNAs. Analysis of the metabolic pathways of L. suionicum DSM 20241T revealed that strain DSM 20241T performs heterolactic acid fermentation and can metabolize diverse organic compounds including glucose, fructose, galactose, cellobiose, mannose, sucrose, trehalose, arbutin, salcin, xylose, arabinose and ribose. Leuconostoc suionicum; Complete genome; Lactic acid bacteria; KEGG; Fermentative metabolic pathway Introduction The genus Leuconostoc comprises Gram-positive, facultatively anaerobic, intrinsically vancomycin-resistant, catalase-negative, spherical heterofermentative lactic acid bacteria which are involved in the fermentation of plant materials (such as kimchi), dairy products, meats, vegetable sausages and beverages [ 1–7 ]. Strain DSM 20241T (=ATCC 9135T =LMG 8159T =NCIMB 6992T) of the genus Leuconostoc was isolated in Sweden in 1972. It was originally classified as a subspecies of L. mesenteroides, but was recently reclassified as a novel species –L. suionicum–based on its whole genome sequence [ 4 ]. Here, we present the taxonomic and genomic features of L. suionicum DSM 20241T. In addition, we investigated the metabolic properties of L. suionicum DSM 20241T and reconstructed the metabolic pathways of organic compounds to estimate the fermentative metabolites in L. suionicum DSM 20241T. Organism information Classification and features L. suionicum DSM 20241T belongs to the family Leuconostocaceae, order Lactobacillales, class Bacilli and phylum Firmicutes. Strain DSM 20241T is a Grampositive, facultatively anaerobic, non-motile, nonsporulating, catalase-negative coccus, with a diameter of 0.5–0.7 μm (Fig. 1). It can be grown in MRS broth at 10–40 °C, with an optimal growth temperature of 30 °C [ 4 ]. Strain DSM 20241T ferments a wide variety of carbon sources including D-glucose, arbutin, melibiose, sucrose, turanose, N-acetylglucosamine, cellobiose, galactose, gentiobiose, amygdalin, L-arabinose, esculin, ferric citrate, D-fructose, D-mannose, lactose, maltose, methyl α-D-glucopyranoside, salicin, trehalose, D-xylose, potassium 5-ketogluconate, mannitol and ribose to produce gas and acids (Table 1); however, it does not ferment glycerol, erythritol, D-arabinose, L-xylose, D-adonitol, methyl β-D-xylopyranoside, L-sorbose, methyl α-D-mannopyranoside, L-rhamnose, dulcitol, inositol, D-sorbitol, inulin, D-melezitose, starch, glycogen, xylitol, D-lyxose, D-tagatose, fucose, D-arabitol, L-arabitol, potassium gluconate, potassium 2-ketogluconate or raffinose [ 4, 8 ]. Phylogenetic analysis using the 16S rRNA gene sequences with validated type strains showed that L. suionicum DSM 20241T is most closely related to the subspecies of the species L. mesenteroides: L. mesenteroides subsp. mesenteroides, L. mesenteroides subsp. jonggajibkimchii, L. mesenteroides subsp. cremoris, and L. mesenteroides subsp. dextranicum with very high 16S rRNA gene sequence similarities (>99.73%; Fig. 2). Genome sequencing information Genome project history L. suionicum DSM 20241T was selected owing to its taxonomic significance for the species L. mesenteroides and was obtained from the German Collection of Microorganisms and Cell Cultures. The complete sequences of the chromosome and plasmid of strain DSM 20241T were deposited in GenBank with the accession numbers CP015247–48. The project information and its association with MIGS version 2.0 [ 9 ] are summarized in Table 2. Growth conditions and genomic DNA preparation L. suionicum DSM 20241T was cultured in MRS broth (BD Biosciences, CA, USA) at 30 °C for 24 h until the early stationary phase. Genomic DNA was extracted according to a standard phenol-chloroform extraction and ethanol precipitation procedure [ 10 ]. DNA quality (OD260/OD280 > 1.8) and concentration were measured using a NanoDrop ND-1000 spectrophotometer (Synergy Mx, Biotek, VT, USA). Genome sequencing and assembly The genome of strain D (...truncated)


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Byung Hee Chun, Se Hee Lee, Hye Hee Jeon, Dong-Woon Kim, Che Ok Jeon. Complete genome sequence of Leuconostoc suionicum DSM 20241T provides insights into its functional and metabolic features, Standards in Genomic Sciences, 2017, pp. 38, Volume 12, Issue 1, DOI: 10.1186/s40793-017-0256-0