Journal of Microbiology and Biotechnology

The Korean Society for Microbiology and Biotechnology (한국미생물·생명공학회)
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Genome-Based Reclassification of Strain KIST612, Previously Classified as Eubacterium limosum, into a New Strain of Eubacterium callanderi

  • Ji-Yeon Kim (School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology) ;
  • Byeongchan Kang (School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology) ;
  • Soyoung Oh (School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology) ;
  • Yeji Gil (School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology) ;
  • In-Geol Choi (Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University) ;
  • In Seop Chang (School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology)
  • Received : 2023.04.07
  • Accepted : 2023.05.08
  • Published : 2023.08.28
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Abstract

The strain KIST612, initially identified as E. limosum, was a suspected member of E. callanderi due to differences in phenotype, genotype, and average nucleotide identity (ANI). Here, we found that E. limosum ATCC 8486T and KIST612 are genetically different in their central metabolic pathways, such as that of carbon metabolism. Although 16S rDNA sequencing of KIST612 revealed high identity with E. limosum ATCC 8486T (99.2%) and E. callanderi DSM 3662T (99.8%), phylogenetic analysis of housekeeping genes and genome metrics clearly indicated that KIST612 belongs to E. callanderi. The phylogenies showed that KIST612 is closer to E. callanderi DSM 3662T than to E. limosum ATCC 8486T. The ANI between KIST612 and E. callanderi DSM 3662T was 99.8%, which was above the species cut-off of 96%, Meanwhile, the ANI value with E. limosum ATCC 8486T was not significant, showing only 94.6%. The digital DNA-DNA hybridization (dDDH) results also supported the ANI values. The dDDH between KIST612 and E. callanderi DSM 3662T was 98.4%, whereas between KIST612 and E. limosum ATCC 8486T , it was 57.8%, which is lower than the species cut-off of 70%. Based on these findings, we propose the reclassification of E. limosum KIST612 as E. callanderi KIST612.

Keywords

Acknowledgement

This work was supported by the National Research Foundation of Korea (NRF) grant funded by the Korean government (MSIT) [NRF-2021R1A5A1028138].

References

  1. Chang IS, Kim DH, Kim BH, Shin PK, Yoon JH, Lee JS, et al. 1997. Isolation and identification of carbon monxide utilzing anaerobe, Eubacterium limosum KIST612. Microbiol. Biotechnol. Lett. 25: 1-8.
  2. Roh H, Ko HJ, Kim D, Choi DG, Park S, Kim S, et al. 2011. Complete genome sequence of a carbon monoxide-utilizing acetogen, Eubacterium limosum KIST612. J. Bacteriol. 193: 307-308. https://doi.org/10.1128/JB.01217-10
  3. Kang S, Song Y, Jin S, Shin J, Bae J, Kim DR, et al. 2020. Adaptive laboratory evolution of Eubacterium limosum ATCC 8486 on carbon monoxide. Front. Microbiol. 11: 402.
  4. Shin J, Bae J, Lee H, Kang S, Jin S, Song Y, et al. 2023. Genome-wide CRISPRi screen identifies enhanced autolithotrophic phenotypes in acetogenic bacterium Eubacterium limosum. Proc. Natl. Acad. Sci. USA 120: e2216244120.
  5. Jeong J, Kim JY, Park B, Choi IG, Chang IS. 2020. Genetic engineering system for syngas-utilizing acetogen, Eubacterium limosum KIST612. Bioresour. Technol. Rep. 11: 100452.
  6. Dietrich HM, Kremp F, Oppinger C, Ribaric L, Muller V. 2021. Biochemistry of methanol-dependent acetogenesis in Eubacterium callanderi KIST612. Environ. Microbiol. 23: 4505-4517. https://doi.org/10.1111/1462-2920.15643
  7. Kang H, Park B, Oh S, Pathiraja D, Kim JY, Jung S, et al. 2021. Metabolism perturbation caused by the overexpression of carbon monoxide dehydrogenase/Acetyl-CoA synthase gene complex accelerated gas to acetate conversion rate of Eubacterium limosum KIST612. Bioresour. Technol. 341: 125879.
  8. Kim JY, Park S, Jeong J, Lee M, Kang B, Jang SH, et al. 2021. Methanol supply speeds up synthesis gas fermentation by methylotrophic-acetogenic bacterium, Eubacterium limosum KIST612. Bioresour. Technol. 321: 124521.
  9. Chowdhury NP, Litty D, Muller V. 2022. Biosynthesis of butyrate from methanol and carbon monoxide by recombinant Acetobacterium woodii. Int. Microbiol. 25: 551-560. https://doi.org/10.1007/s10123-022-00234-z
  10. Paek J, Shin Y, Kim JS, Kim H, Kook JK, Paek WK, et al. 2017. Description of Absiella argi gen. nov., sp. nov., and transfer of Eubacterium dolichum and Eubacterium tortuosum to the genus Absiella as Absiella dolichum comb. nov. and Absiella tortuosum comb. nov. Anaerobe 48: 70-75. https://doi.org/10.1016/j.anaerobe.2017.07.006
  11. Shetty SA, Zuffa S, Bui TPN, Aalvink S, Smidt H, De Vos WM. 2018. Reclassification of Eubacterium hallii as Anaerobutyricum hallii gen. nov., comb. nov., and description of Anaerobutyricum soehngenii sp. nov., a butyrate and propionate-producing bacterium from infant faeces. Int. J. Syst. Evol. Microbiol. 68: 3741-3746. https://doi.org/10.1099/ijsem.0.003041
  12. Kageyama A, Benno Y, Nakase T. 1999. Phylogenetic and phenotypic evidence for the transfer of Eubacterium aerofaciens to the genus Collinsella as Collinsella aerofaciens gen. nov., comb. nov. Int. J. Syst. Evol. Microbiol. 49: 557-565. https://doi.org/10.1099/00207713-49-2-557
  13. Taras D, Simmering R, Collins MD, Lawson PA, Blaut M. 2002. Reclassification of Eubacterium formicigenerans Holdeman and Moore 1974 as Dorea formicigenerans gen. nov., comb. nov., and description of Dorea longicatena sp. nov., isolated from human faeces. Int. J. Syst. Evol. Microbiol. 52: 423-428. https://doi.org/10.1099/00207713-52-2-423
  14. Sakamoto M, Iino T, Ohkuma M. 2017. Faecalimonas umbilicata gen. nov., sp. nov., isolated from human faeces, and reclassification of Eubacterium contortum, Eubacterium fissicatena and Clostridium oroticum as Faecalicatena contorta gen. nov., comb. nov., Faecalicatena fissicatena comb. nov. and Faecalicatena orotica comb. nov. Int. J. Syst. Evol. Microbiol. 67: 1219-1227. https://doi.org/10.1099/ijsem.0.001790
  15. De Maesschalck C, Van Immerseel F, Eeckhaut V, De Baere S, Cnockaert M, Croubels S, et al. 2014. Faecalicoccus acidiformans gen. nov., sp. nov., isolated from the chicken caecum, and reclassification of Streptococcus pleomorphus (Barnes et al. 1977), Eubacterium biforme (Eggerth 1935) and Eubacterium cylindroides (Cato et al. 1974) as Faecalicoccus pleomorphus comb. nov., Holdemanella biformis gen. nov., comb. nov. and Faecalitalea cylindroides gen. nov., comb. nov., respectively, within the family Erysipelotrichaceae. Int. J. Syst. Evol. Microbiol. 64: 3877-3884. https://doi.org/10.1099/ijs.0.064626-0
  16. Hedberg ME, Moore ERB, Svensson-Stadler L, Horstedt P, Baranov V, Hernell O, et al. 2012. Lachnoanaerobaculum gen. nov., a new genus in the Lachnospiraceae: characterization of Lachnoanaerobaculum umeaense gen. nov., sp. nov., isolated from the human small intestine, and Lachnoanaerobaculum orale sp. nov., isolated from saliva, and reclassification of Eubacterium saburreum (Prevot 1966) Holdeman and Moore 1970 as Lachnoanaerobaculum saburreum comb. nov. Int. J. Syst. Evol. Microbiol. 62: 2685-2690. https://doi.org/10.1099/ijs.0.033613-0
  17. Madeira F, Pearce M, Tivey ARN, Basutkar P, Lee J, Edbali O, et al. 2022. Search and sequence analysis tools services from EMBL-EBI in 2022. Nucleic Acids Res. 50: W276-W279. https://doi.org/10.1093/nar/gkac240
  18. Tamura K, Stecher G, Kumar S. 2021. MEGA11: molecular evolutionary genetics analysis version 11. Mol. Biol. Evol. 38: 3022-3027. https://doi.org/10.1093/molbev/msab120
  19. Chaudhari NM, Gupta VK, Dutta C. 2016. BPGA- an ultra-fast pan-genome analysis pipeline. Sci. Rep. 6: 24373.
  20. Yoon S-H, Ha S, Lim J, Kwon S, Chun J. 2017. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 110: 1281-1286. https://doi.org/10.1007/s10482-017-0844-4
  21. Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Goker M. 2022. TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res. 50: D801-D807. https://doi.org/10.1093/nar/gkab902
  22. Edgar RC. 2010. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26: 2460-2461. https://doi.org/10.1093/bioinformatics/btq461
  23. Kanehisa M, Goto S. 2000. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28: 27-30. https://doi.org/10.1093/nar/28.1.27
  24. Kanehisa M, Sato Y, Morishima K. 2016. BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J. Mol. Biol. 428: 726-731. https://doi.org/10.1016/j.jmb.2015.11.006
  25. Darzi Y, Letunic I, Bork P, Yamada T. 2018. iPath3.0: interactive pathways explorer v3. Nucleic Acids Res. 46: W510-W513. https://doi.org/10.1093/nar/gky299
  26. Edgar RC. 2018. Updating the 97% identity threshold for 16S ribosomal RNA OTUs. Bioinformatics 34: 2371-2375. https://doi.org/10.1093/bioinformatics/bty113
  27. Mountfort DO, Grant WD, Clarke R, Asher RA. 1988. Eubacterium callanderi sp. nov. that demethoxylates O-methoxylated aromatic acids to volatile fatty acids. Int. J. Syst. Evol. Microbiol. 38: 254-258. https://doi.org/10.1099/00207713-38-3-254