Characterization of Weissella koreensis SK Isolated from Kimchi Fermented at Low Temperature (around 0 °C) Based on Complete Genome Sequence and Corresponding Phenotype
Abstract
:1. Introduction
2. Materials and Methods
2.1. Isolation and Identification of LAB
2.2. Polymerase Chain Reaction (PCR)-Denaturing Gradient Gel Electrophoresis (DGGE)
2.3. Whole Genome Sequencing, Assembly, and Annotation
2.4. Plasmid Preparation and Digestion
2.5. Phenotypic Properties
2.5.1. Carbohydrate Assimilation
2.5.2. Growth at Different Temperatures
2.5.3. Cell Viability According to pH Level
2.5.4. Arginine Catabolic Ability
2.5.5. Biogenic Amine Production
2.6. Statistical Analysis
3. Results and Discussion
3.1. Kimchi Samples and Isolation of LAB
3.2. Genome Properties of W. koreensis SK
3.3. Phenotypic Characteristics of W. koreensis SK
3.3.1. Carbohydrate Assimilation
3.3.2. Growth at Different Temperatures
3.3.3. Tolerance to Acid and Alkali Conditions
3.3.4. Biogenic Amine (BA) Production and Other Virulence Traits
3.3.5. Growth of W. koreensis SK in MRS Supplemented with Arginine and Citrulline
3.4. Arginine and Glucose Metabolism by W. koreensis SK
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Feature | SK | KACC 15510 | WiKim0080 | CBA3615 | ||||
---|---|---|---|---|---|---|---|---|
Chromo- Some | Plasmid | Chromo- Some | Plasmid | Chromo- Some | Plasmid | Chromo- Some | Plasmid | |
Genome size (bp) | 1,451,607 | 10,481 | 1,422,478 | 18,992 | 1,495,237 | 31,842 9934 | 1,491,842 | 19,971 |
G+C content (%) | 35.5 | 36.9 | 35.5 | 36.7 | 35.5 | 40.0 27.5 | 35.4 | 38.7 |
Total genes (no.) | 1389 | 11 | 1379 | 24 | 1454 | 32 11 | 1443 | 27 |
Protein coding sequences (no.) | 1318 | 11 | 1308 | 24 | 1382 | 32 11 | 1371 | 27 |
rRNAs (no.) | 15 | - | 15 | - | 15 | - | 15 | - |
tRNAs (no.) | 56 | - | 56 | - | 57 | - | 57 | - |
GenBank Accession No. | CP043431 | CP043432 | CP002899 | CP002900 | CP026847 | CP026848 CP026849 | CP046070 | CP046071 |
Assembly level 1 | Complete | Complete | Complete | Chromosome | ||||
Source | Kimchi | Kimchi | Kimchi | Kimchi | ||||
Reference | This study 2 | [27] | [10] | [28] |
ORF | ORF Length (a.a) | Related Protein (Length of a.a) | Identity (%) | Accession No. of Related Protein |
---|---|---|---|---|
1 | 411 | mobilization protein [Weissella koreensis] (411) | 99.76 | WP_104914736.1 |
2 | 384 | MULTISPECIES: RepB family plasmid replication initiator protein [Leuconostocaceae] (384) | 98.18 | WP_102753750.1 |
3 | 151 | CopY/TcrY family copper transport repressor [Weissella confusa] (151) | 100.00 | WP_135469337.1 |
4 | 58 | heavy-metal-associated domain-containing protein [Weissella soli] (58) | 100.00 | WP_147153977.1 |
5 | 692 | MULTISPECIES: cadmium-translocating P-type ATPase [Leuconostocaceae] (692) | 99.86 | WP_004909401.1 |
6 | 127 | MULTISPECIES: glyoxalase/bleomycin resistance/extradiol dioxygenase family protein [Weissella] (127) | 100.00 | WP_104914740.1 |
7 | 242 | MULTISPECIES: fructose permease [Leuconostoc] (242) | 98.76 | WP_071952482.1 |
Substrate | Culture | Content | Incubation Time | ||
---|---|---|---|---|---|
0 h | 24 h | 72 h | |||
Arginine /Citrulline | MRS | Glutamic acid | 614.69 ± 17.96 a,C | 666.74 ± 9.16 a,B | 719.00 ± 16.48 a,A |
Glutamine | N.D 1 | N.D | N.D | ||
Citrulline | 11.38 ± 3.85 c,A | 3.07 ± 0.85 c,B | 3.91 ± 0.20 c,B | ||
Arginine | 301.38 ± 62.79 b,A | 7.48 ± 2.65 b,B | 5.09 ± 1.74 b,B | ||
Ornithine | 38.78 ± 10.09 b,B | 93.25 ± 13.10 c,A | 99.16 ± 8.37 c,A | ||
NH3 | 453.06 ± 49.30 a,A | 462.52 ± 46.27 b,A | 443.97 ± 10.23 c,A | ||
MRS-A | Glutamic acid | 611.92 ± 17.25 a,C | 677.89 ± 5.39 a,B | 739.63 ± 11.00 a,A | |
Glutamine | N.D | N.D | N.D | ||
Citrulline | 47.90 ± 11.75 b,C | 841.70 ± 75.64 b,A | 676.13 ± 12.60 b,B | ||
Arginine | 7713.34 ± 34.57 a,A | 62.25 ± 9.10 a,B | 41.68 ± 1.07 a,B | ||
Ornithine | 55.81 ± 21.42 b,B | 6569.52 ± 327.28 a,A | 7174.73 ± 148.56 a,A | ||
NH3 | 465.11 ± 8.64 a,B | 2334.97 ± 182.86 a,A | 2321.34 ± 143.57 a,A | ||
MRS-C | Glutamic acid | 617.07 ± 16.83 a,C | 676.51 ± 12.01 a,B | 725.21 ± 10.52 a,A | |
Glutamine | N.D | N.D | N.D | ||
Citrulline | 6687.78 ± 5.11 a,A | 4504.69 ± 199.02 a,B | 2155.59 ± 69.07 a,C | ||
Arginine | 229.10 ± 0.08 b,A | 5.01 ± 1.60 b,B | 4.95 ± 0.24 b,B | ||
Ornithine | 1010.71 ± 63.32 a,A | 3048.81 ± 76.68 b,B | 4254.92 ± 193.10 b,C | ||
NH3 | 479.51 ± 32.06 a,B | 697.32 ± 112.75 b,B | 938.11 ± 29.22 b,A | ||
Glucose | MRS | Lactic acid | 209.00 ± 9.85 a,C | 5917.63 ± 201.77 b,B | 7556.81 ± 31.06 a,A |
Formic acid | 144.36 ± 1.12 a,B | 180.37 ± 1.05 b,A | 198.10 ± 17.70 a,A | ||
Acetic acid | 4396.08 ± 49.64 a,C | 4538.84 ± 4.50 a,B | 4730.90 ± 28.87 a,A | ||
EtOH | N.D | 354.56 ± 10.03 b,B | 431.56 ± 1.16 b,A | ||
Citric acid | 1947.97 ± 38.88 a,A | 1870.40 ± 22.09 a,A | 1895.47 ± 38.77 a,A | ||
MRS-A | Lactic acid | 210.14 ± 2.50 a,B | 6965.00 ± 255.56 a,A | 7078.32 ± 9.72 b,A | |
Formic acid | 145.69 ± 19.66 a,B | 233.16 ± 4.01 a,A | 228.98 ± 15.42 a,A | ||
Acetic acid | 4351.16 ± 54.43 a,B | 4539.66 ± 25.54 a,A | 4534.56 ± 34.99 bA | ||
EtOH | N.D | 458.74 ± 23.58 a,A | 464.78 ± 4.60 a,A | ||
Citric acid | 1932.38 ± 57.61 a,B | 1817.38 ± 7.87 a,A,B | 1832.65 ± 13.49 a,b,A | ||
MRS-C | Lactic acid | 194.64 ± 3.72 a,C | 5339.90 ± 192.18 b,B | 7166.88 ± 223.21 a,b,A | |
Formic acid | 148.02 ± 30.62 a,A | 207.75 ± 14.47 a,b,A | 197.35 ± 3.49 a,A | ||
Acetic acid | 4220.48 ± 238.05 a,A | 4475.87 ± 2.93 b,A | 4481.72 ± 69.85 b,A | ||
EtOH | N.D | 323.44 ± 15.38 b,B | 444.94 ± 5.91 b,A | ||
Citric acid | 1825.29 ± 108.46 a,A | 1823.65 ± 35.44 a,A | 1767.00 ± 41.11 a,A |
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Mun, S.Y.; Chang, H.C. Characterization of Weissella koreensis SK Isolated from Kimchi Fermented at Low Temperature (around 0 °C) Based on Complete Genome Sequence and Corresponding Phenotype. Microorganisms 2020, 8, 1147. https://doi.org/10.3390/microorganisms8081147
Mun SY, Chang HC. Characterization of Weissella koreensis SK Isolated from Kimchi Fermented at Low Temperature (around 0 °C) Based on Complete Genome Sequence and Corresponding Phenotype. Microorganisms. 2020; 8(8):1147. https://doi.org/10.3390/microorganisms8081147
Chicago/Turabian StyleMun, So Yeong, and Hae Choon Chang. 2020. "Characterization of Weissella koreensis SK Isolated from Kimchi Fermented at Low Temperature (around 0 °C) Based on Complete Genome Sequence and Corresponding Phenotype" Microorganisms 8, no. 8: 1147. https://doi.org/10.3390/microorganisms8081147