1887

Abstract

The taxonomic status of the species was assessed. The 16S rRNA gene sequence, whole-genome sequence and phenotypic characterizations suggested that the type strain deposited in the American Type Culture Collection ( ATCC 700855) is a member of the species . Hence, ATCC 700855 cannot be used as a reference for taxonomic study. The type strain deposited in the German Collection of Microorganism and Cell Cultures GmbH (DSM 12182) is no longer listed in its online catalogue. Also, both the 16S rRNA gene and the whole-genome sequences of the original strain SR3 showed high sequence identity with those of (recently reclassified from ) as the most closely related species. Analysis of the two genomes showed average nucleotide identity based on and digital DNA–DNA hybridization values of 98.3 and 87.9 %, respectively. Based on these results, SR3 was considered to be a member of .

Funding
This study was supported by the:
  • a research grant from NARO Gender Equality Program
    • Principle Award Recipient: TohnoMasanori
  • JSPS KAKENHI (Award Grant Number JP21K14967)
    • Principle Award Recipient: KobayashiHisami
  • Genebank Project (Microorganism Section)
    • Principle Award Recipient: TohnoMasanori
  • a research grant from NARO Gender Equality Program
    • Principle Award Recipient: KobayashiHisami
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2021-08-11
2022-10-03
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References

  1. Mechichi T, Labat M, Patel BK, Woo TH, Thomas P et al. Clostridium methoxybenzovorans sp. nov., a new aromatic o-demethylating homoacetogen from an olive mill wastewater treatment digester. Int J Syst Evol Microbiol 1999; 49:1201–1209 [View Article]
    [Google Scholar]
  2. Tohno M, Kobayashi H, Nomura M, Kitahara M, Ohkuma M et al. Genotypic and phenotypic characterization of lactic acid bacteria isolated from Italian ryegrass silage. Anim Sci J 2012; 83:111–120 [View Article]
    [Google Scholar]
  3. Tohno M, Kitahara M, Uegaki R, Irisawa T, Ohkuma M et al. Lactobacillus hokkaidonensis sp. nov., isolated from subarctic timothy grass (Phleum pratense L.) silage. Int J Syst Evol Microbiol 2013; 63:2526–253 [View Article]
    [Google Scholar]
  4. Suzuki K, Sasaki J, Uramoto M, Nakase T, Komagata K. Agromyces mediolanus sp. nov., nom. rev., comb. nov., a species for “Corynebacterium mediolanum” Mamoli 1939 and for some aniline-assimilating bacteria which contain 2,4-diaminobutyric acid in the cell wall peptidoglycan. Int J Syst Bacteriol 1996; 46:88–93 [View Article]
    [Google Scholar]
  5. Chun J, Lee JH, Jung Y, Kim S, Kim S et al. EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int J Syst Evol Microbiol 2007; 57:2259–2261 [View Article]
    [Google Scholar]
  6. Chen Y, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 2018; 34:i884–i890 [View Article]
    [Google Scholar]
  7. Kajitani R, Toshimoto K, Noguchi H, Toyoda A, Ogura Y et al. Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads. Genome Res 2014; 24:1384–1395 [View Article]
    [Google Scholar]
  8. Tanizawa Y, Fujisawa T, Nakamura Y. DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication. Bioinformatics 2018; 34:1037–1039 [View Article]
    [Google Scholar]
  9. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [View Article]
    [Google Scholar]
  10. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article]
    [Google Scholar]
  11. Goris J, Klappenbach JA, Vandamme P, Coenye T, Konstantinidis KT et al. DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article]
    [Google Scholar]
  12. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [View Article]
    [Google Scholar]
  13. Ach AF, von Jan M, Klenk HP, Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010; 2:117–134 [View Article]
    [Google Scholar]
  14. Gundawar K, Kumari S, Sharma S, Grover V, Patil PB et al. Clostridium indicum sp. nov., a novel anaerobic bacterium isolated from the sludge of an industrial effluent. Int J Syst Evol Microbiol 2019; 69:672–678 [View Article]
    [Google Scholar]
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