Journal of Animal Science and Technology

Korean Society of Animal Sciences and Technology (한국축산학회)
권호 표지
DOI QR코드

DOI QR Code

Complete genome sequence of Enterococcus faecium strain AK_C_05 with potential characteristics applicable in livestock industry

  • Hyunok Doo (Department of Animal Biotechnology, Dankook University) ;
  • Jin Ho Cho (Division of Food and Animal Science, Chungbuk National University) ;
  • Minho Song (Division of Animal and Dairy Science, Chungnam National University) ;
  • Eun Sol Kim (Department of Animal Biotechnology, Dankook University) ;
  • Sheena Kim (Department of Animal Biotechnology, Dankook University) ;
  • Gi Beom Keum (Department of Animal Biotechnology, Dankook University) ;
  • Jinok Kwak (Department of Animal Biotechnology, Dankook University) ;
  • Sriniwas Pandey (Department of Animal Biotechnology, Dankook University) ;
  • Sumin Ryu (Department of Animal Biotechnology, Dankook University) ;
  • Yejin Choi (Department of Animal Biotechnology, Dankook University) ;
  • Juyoun Kang (Department of Animal Biotechnology, Dankook University) ;
  • Hyeun Bum Kim (Department of Animal Biotechnology, Dankook University) ;
  • Ju-Hoon Lee (Department of Food Animal Biotechnology, Seoul National University)
  • Received : 2023.08.02
  • Accepted : 2023.09.25
  • Published : 2024.03.31
Download PDF
⟨ Previous Next ⟩

Abstract

The Enterococcus faecium (E. faecium) strain AK_C_05 was isolated from cheonggukjang, the Korean traditional food, collected from a local market in South Korea. In this report, we presented the complete genome sequence of E. faecium strain AK_C_05. The genome of E. faecium strain AK_C_05 genome consisted of one circular chromosome (2,691,319 bp) with a guanine + cytosine (GC) content of 38.3% and one circular plasmid (177,732 bp) with a GC content of 35.48%. The Annotation results revealed 2,827 protein-coding sequences (CDSs), 18 rRNAs, and 68 tRNA genes. It possesses genes, which encodes enzymes such as alpha-galactosidase (EC 3.2.1.22), beta-glucosidase (EC 3.2.1.21) and alpha-L-arabinofuranosidase (EC 3.2.1.55) enabling efficient utilization of carbohydrates. Based on Clusters of Orthologous Groups analysis, E. faecium strain AK_C_05 showed specialization in carbohydrate transport and metabolism indicating the ability to generate energy using a variety of carbohydrates.

Keywords

References

  1. Franz CMAP, Stiles ME, Schleifer KH, Holzapfel WH. Enterococci in foods-a conundrum for food safety. Int J Food Microbiol. 2003;88:105-22. https://doi.org/10.1016/S0168-1605(03)00174-0 
  2. Bhardwaj A, Gupta H, Kapila S, Kaur G, Vij S, Malik RK. Safety assessment and evaluation of probiotic potential of bacteriocinogenic Enterococcus faecium KH 24 strain under in vitro and in vivo conditions. Int J Food Microbiol. 2010;141:156-64. https://doi.org/10.1016/j.ijfoodmicro.2010.05.001 
  3. Sato Y, Kuroki Y, Oka K, Takahashi M, Rao S, Sukegawa S, et al. Effects of dietary supplementation with Enterococcus faecium and Clostridium butyricum, either alone or in combination, on growth and fecal microbiota composition of post-weaning pigs at a commercial farm. Front Vet Sci. 2019;6:26. https://doi.org/10.3389/fvets.2019.00026 
  4. Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013;29:1072-5. https://doi.org/10.1093/bioinformatics/btt086 
  5. Simao FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015;31:3210-2. https://doi.org/10.1093/bioinformatics/btv351 
  6. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, et al. The RAST server: rapid annotations using subsystems technology. BMC Genom. 2008;9:75. https://doi.org/10.1186/1471-2164-9-75 
  7. Cantalapiedra CP, Hernandez-Plaza A, Letunic I, Bork P, Huerta-Cepas J. eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Mol Biol Evol. 2021;38:5825-9. https://doi.org/10.1093/molbev/msab293 
  8. Chen L, Yang J, Yu J, Yao Z, Sun L, Shen Y, et al. VFDB: a reference database for bacterial virulence factors. Nucleic Acids Res. 2005;33:D325-8. https://doi.org/10.1093/nar/gki008 
  9. McArthur AG, Waglechner N, Nizam F, Yan A, Azad MA, Baylay AJ, et al. The comprehensive antibiotic resistance database. Antimicrob Agents Chemother. 2013;57:3348-57. https://doi.org/10.1128/aac.00419-13 
  10. Li B, Zhan M, Evivie SE, Jin D, Zhao L, Chowdhury S, et al. Evaluating the safety of potential probiotic Enterococcus durans KLDS6.0930 using whole genome sequencing and oral toxicity study. Front Microbiol. 2018;9:1943. https://doi.org/10.3389/fmicb.2018.01943