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)