1887

Abstract

A fast-growing, non-chromogenic, acid-fast-staining bacterium (DL90) was isolated from a peat bog in northern Minnesota. On the basis of 16S rRNA gene sequence similarity (99.8 % identity with and 98 % with ) and chemotaxonomic data (fatty acid content), strain DL90 represents a member of the genus . Physiological tests (growth curves, biofilm formation, antibiotic sensitivity, colony morphologies and heat tolerance) and biochemical analysis (arylsulfatase activity and fatty acid profiles) distinguish DL90 from its closest relative . Phylogenomic reconstruction of the ‘’ clade, digital DNA–DNA hybridization (DDH) values of 61 %, and average nucleotide identity (ANI) values of approximately 95 % indicate that DL90 is likely to be diverged from . Thus, we propose that DL90 represents a novel species, given the name with the type strain being isolate DL90 (=JCM 32796=NCCB 100660).

  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2021-03-01
2022-01-19
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References

  1. Gupta RS, Lo B, Son J. Phylogenomics and comparative genomic studies robustly support division of the genus Mycobacterium into an embeded genus Mycobacterium and four novel genera. Front Microbiol 2018; 9:article 67 [View Article][PubMed]
    [Google Scholar]
  2. Kazda J. The Ecology of Mycobacteria Netherlands: Kuwer Academic Publishers; 2000
    [Google Scholar]
  3. Hannigan GD, Krivogorsky B, Fordice D, Welch JB, Dahl JL. Mycobacterium minnesotense sp. nov., a photochromogenic bacterium isolated from sphagnum peat bogs. Int J Syst Evol Microbiol 2013; 63:124–128 [View Article][PubMed]
    [Google Scholar]
  4. Telenti A, Marchesi F, Balz M, Bally F, Böttger EC et al. Rapid identification of Mycobacteria to the species level by polymerase chain reaction and restriction enzyme analysis. J Clin Microbiol 1993; 31:175–178 [View Article][PubMed]
    [Google Scholar]
  5. Tran PM, Dahl JL. Mycobacterium sarraceniae sp. nov. and Mycobacterium helvum sp. nov., isolated from the pitcher plant Sarracenia purpurea . Int J Syst Evol Microbiol 2016; 66:4480–4485 [View Article][PubMed]
    [Google Scholar]
  6. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014; 30:2114–2120 [View Article][PubMed]
    [Google Scholar]
  7. Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 2017; 13:e1005595 [View Article][PubMed]
    [Google Scholar]
  8. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article]
    [Google Scholar]
  9. Kumar S, Stecher G, Tamura K. mega7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article][PubMed]
    [Google Scholar]
  10. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403–410 [View Article][PubMed]
    [Google Scholar]
  11. Lee MD. GToTree: a user-friendly workflow for phylogenomics. Bioinformatics 2019; 35:4162–4164 [View Article]
    [Google Scholar]
  12. Hyatt D, LoCascio PF, Hauser LJ, Uberbacher EC. Gene and translation initiation site prediction in metagenomic sequences. Bioinformatics 2012; 28:2223–2230 [View Article][PubMed]
    [Google Scholar]
  13. Eddy SR. Accelerated profile HMM searches. PLoS Comput Biol 2011; 7:e1002195 [View Article][PubMed]
    [Google Scholar]
  14. Edgar RC. Muscle: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 2004; 5:113 [View Article][PubMed]
    [Google Scholar]
  15. Capella-Gutierrez S, Silla-Martinez JM, Gabaldon T. TrimAl: a tool for automatic alignment trimming. Bioinformatics 2009; 25:1972–1973
    [Google Scholar]
  16. Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 2015; 32:268–274 [View Article][PubMed]
    [Google Scholar]
  17. Hug LA, Baker BJ, Anantharaman K, Brown CT, Probst AJ et al. A new view of the tree of life. Nat Microbiol 2016; 1:16048 [View Article][PubMed]
    [Google Scholar]
  18. Konstantinidis KT, Tiedje JM. Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci U S A 2005; 102:2567–2572 [View Article][PubMed]
    [Google Scholar]
  19. Auch AF, von Jan M, Klenk H-P, 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][PubMed]
    [Google Scholar]
  20. Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol 2018; 36:996–1004 [View Article][PubMed]
    [Google Scholar]
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