sp. nov., a ciprofloxacin-resistant bacterium from a human clinical specimen; reclassification of as comb. nov. and emended description of the genus Free

Abstract

The taxonomic position of strain 15-057A, an acidophilic actinobacterium isolated from the bronchial lavage of an 80-year-old male, was determined using a polyphasic approach incorporating morphological, phenotypic, chemotaxonomic and genomic analyses. Pairwise 16S rRNA gene sequence similarities calculated using the GGDC web server between strain 15-057A and its closest phylogenetic neighbours, NBRC 12779 and TH49, were 99.7 and 97.6 %, respectively. The G+C content of isolate 15-057A was determined to be 72.6 mol%. DNA–DNA relatedness and average nucleotide identity between isolate 15-057A and DSM 40009 were 29.2±2.5 % and 85.97 %, respectively. Chemotaxonomic features of isolate 15-057A were consistent with its assignment within the genus : the whole-cell hydrolysate contained -diaminopimelic acid as the diagnostic diamino acid and glucose, mannose and ribose as cell-wall sugars; the major menaquinone was MK9(H); the polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, glycophospholipid, aminoglycophospholipid and an unknown lipid; the major fatty acids were anteiso-C and isoC. Phenotypic and morphological traits distinguished isolate 15-057A from its closest phylogenetic neighbours. The results of our taxonomic analyses showed that strain 15-057A represents a novel species within the evolutionary radiation of the genus for which the name sp. nov. is proposed. The type strain is 15-057A (=DSM 106435=ATCC BAA-2934).

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2019-02-11
2024-03-29
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References

  1. Waksman SA, Henrici AT. The Nomenclature and Classification of the Actinomycetes. J Bacteriol 1943; 46:337–341[PubMed]
    [Google Scholar]
  2. Kim SB, Lonsdale J, Seong CN, Goodfellow M. Streptacidiphilus gen. nov., acidophilic actinomycetes with wall chemotype I and emendation of the family Streptomycetaceae (Waksman and Henrici (1943)AL) emend. Rainey et al. 1997. Antonie van Leeuwenhoek 2003; 83:107–116 [View Article][PubMed]
    [Google Scholar]
  3. Cho SH, Han JH, Ko HY, Kim SB. Streptacidiphilus anmyonensis sp. nov., Streptacidiphilus rugosus sp. nov. and Streptacidiphilus melanogenes sp. nov., acidophilic actinobacteria isolated from Pinus soils. Int J Syst Evol Microbiol 2008; 58:1566–1570 [View Article][PubMed]
    [Google Scholar]
  4. Golinska P, Ahmed L, Wang D, Goodfellow M. Streptacidiphilus durhamensis sp. nov., isolated from a spruce forest soil. Antonie van Leeuwenhoek 2013; 104:199–206 [View Article][PubMed]
    [Google Scholar]
  5. Golinska P, Kim BY, Dahm H, Goodfellow M. Streptacidiphilus hamsterleyensis sp. nov., isolated from a spruce forest soil. Antonie van Leeuwenhoek 2013; 104:965–972 [View Article][PubMed]
    [Google Scholar]
  6. Huang Y, Cui Q, Wang L, Rodriguez C, Quintana E et al. Streptacidiphilus jiangxiensis sp. nov., a novel actinomycete isolated from acidic rhizosphere soil in China. Antonie van Leeuwenhoek 2004; 86:159–165 [View Article][PubMed]
    [Google Scholar]
  7. Song W, Duan L, Jin L, Zhao J, Jiang S et al. Streptacidiphilus monticola sp. nov., a novel actinomycete isolated from soil. Int J Syst Evol Microbiol 2018; 68:1757–1761 [View Article][PubMed]
    [Google Scholar]
  8. Wang L, Huang Y, Liu Z, Goodfellow M, Rodríguez C. Streptacidiphilus oryzae sp. nov., an actinomycete isolated from rice-field soil in Thailand. Int J Syst Evol Microbiol 2006; 56:1257–1261 [View Article][PubMed]
    [Google Scholar]
  9. Roh SG, Kim MK, Park S, Yun BR, Park J et al. Streptacidiphilus pinicola sp. nov., isolated from pine grove soil. Int J Syst Evol Microbiol 2018; 68:3149–3155 [View Article][PubMed]
    [Google Scholar]
  10. Golinska P, Dahm H, Goodfellow M. Streptacidiphilus toruniensis sp. nov., isolated from a pine forest soil. Antonie van Leeuwenhoek 2016; 109:1583–1591 [View Article][PubMed]
    [Google Scholar]
  11. Goodfellow M, Williams ST. Ecology of actinomycetes. Annu Rev Microbiol 1983; 37:189–216 [View Article][PubMed]
    [Google Scholar]
  12. Williams ST, Lanning S, Wellington EMH. Ecology of actinomycetes. In Goodfellow M, Mordarski M, Williams ST. (editors) The Biology of the Actinomycetes London: Academic Press; 1984 pp. 481–528
    [Google Scholar]
  13. Williams ST, Khan MR. Antibiotics-a soil microbiologist's viewpoint. Postepy Hig Med Dosw 1974; 28:395–408[PubMed]
    [Google Scholar]
  14. Williams ST, Robinson CS. The role of streptomycetes in decomposition of chitin in acidic soils. Microbiology 1981; 127:55–63 [View Article]
    [Google Scholar]
  15. Williams ST, Flowers TH. The influence of pH on starch hydrolysis by neutrophilic and acidophilic actinomycetes. Microbios 1987; 20:99–106
    [Google Scholar]
  16. Backus EJ, Tresner HD, Campbell TH. The nucleocidin and alazopetin producing organisms: two new species of Streptomyces . Antibiot Chemother 1957; 7:532–541[PubMed]
    [Google Scholar]
  17. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
    [Google Scholar]
  18. Berd D. Laboratory identification of clinically important aerobic actinomycetes. Appl Microbiol 1973; 25:665–681[PubMed]
    [Google Scholar]
  19. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974; 28:226–231[PubMed]
    [Google Scholar]
  20. Lechavalier MP, Lechevalier HA. Composition of whole-cell hydrolysates as a criterion in the classification of aerobic actinomycetes. In Prauser H. (editor) The Actinomycetales Jena: Gustav Fischer Verlag; 1970 pp. 311–316
    [Google Scholar]
  21. Collins MD. 11 Analysis of isoprenoid quinones. Meth Microbiol 1985; 18:329–366
    [Google Scholar]
  22. Minnikin DE, Goodfellow M. Lipid composition in the classification and identification of nocardiae and related taxa. In Goodfellow M, Brownell GH, Serrano JA. (editors) The Biology of the Nocardiae London: Academic Press; 1976 pp. 160–219
    [Google Scholar]
  23. Kroppenstedt RM, Goodfellow M. The family Thermomonosporaceae: Actinocorallia, Actinomadura, Spirillispora and Thermomonospora . In Dworkin M, Falkow K, Schleifer KH, Stackebrandt E. (editors) The Prokaryotes Archaea and Bacteria: Firmicutes, Actinomycetes, 3rd ed. vol. 3 New York: Springer; 2006 pp. 682–724
    [Google Scholar]
  24. Miller LT. Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. J Clin Microbiol 1982; 16:584–586[PubMed]
    [Google Scholar]
  25. Kuykendall LD, Roy MA, O'Neill JJ, Devine TE. Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum . Int J Syst Bacteriol 1988; 38:358–361 [View Article]
    [Google Scholar]
  26. Sasser MJ. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, Technical Note 101, Microbial ID. USA: Inc, Newark, Del; 1990
    [Google Scholar]
  27. Kämpfer P. Genus incertae sedis II. Streptacidiphilus Kim, Lonsdale, Seong and Goodfellow 2003a, 1219VP (Effective publication: Kim, Lonsdale, Seong and Goodfellow 2003b, 115.). In Godfellow M, Kämpfer P, Busse HJ, Trujillo ME, Suzuki K-I et al. (editors) Bergey’s Manual of Systematic Bacteriology, 2nd ed. vol. 5. The Actinobacteria, Part B New York: Springer; 2012 pp. 1777–1805
    [Google Scholar]
  28. Groth I, Rodríguez C, Schütze B, Schmitz P, Leistner E et al. Five novel Kitasatospora species from soil: Kitasatospora arboriphila sp. nov., K. gansuensis sp. nov., K. nipponensis sp. nov., K. paranensis sp. nov. and K. terrestris sp. nov. Int J Syst Evol Microbiol 2004; 54:2121–2129 [View Article][PubMed]
    [Google Scholar]
  29. Duggar BM. Aureomycin; a product of the continuing search for new antibiotics. Ann N Y Acad Sci 1948; 51:177–181 [View Article][PubMed]
    [Google Scholar]
  30. Labeda DP, Dunlap CA, Rong X, Huang Y, Doroghazi JR et al. Phylogenetic relationships in the family Streptomycetaceae using multi-locus sequence analysis. Antonie van Leeuwenhoek 2017; 110:563–583 [View Article][PubMed]
    [Google Scholar]
  31. Baldacci E, Grein A. Streptomyces avellaneus and Streptomyces libani: two new species characterized by a hazel-nut brown (avellaneus) aerial mycelium. Giornale di Microbiologia 1966; 14:185–198
    [Google Scholar]
  32. Liu Z, Rodríguez C, Wang L, Cui Q, Huang Y et al. Kitasatospora viridis sp. nov., a novel actinomycete from soil. Int J Syst Evol Microbiol 2005; 55:707–711 [View Article][PubMed]
    [Google Scholar]
  33. Groth I, Schütze B, Boettcher T, Pullen CB, Rodriguez C et al. Kitasatospora putterlickiae sp. nov., isolated from rhizosphere soil, transfer of Streptomyces kifunensis to the genus Kitasatospora as Kitasatospora kifunensis comb. nov., and emended description of Streptomyces aureofaciens Duggar 1948. Int J Syst Evol Microbiol 2003; 53:2033–2040 [View Article][PubMed]
    [Google Scholar]
  34. Vaas LA, Sikorski J, Michael V, Göker M, Klenk HP. Visualization and curve-parameter estimation strategies for efficient exploration of phenotype microarray kinetics. PLoS One 2012; 7:e34846 [View Article][PubMed]
    [Google Scholar]
  35. Vaas LA, Sikorski J, Hofner B, Fiebig A, Buddruhs N et al. opm: an R package for analysing OmniLog(R) phenotype microarray data. Bioinformatics 2013; 29:1823–1824 [View Article][PubMed]
    [Google Scholar]
  36. Weyant RS, Moss CW, Weaver RE, Hollis DG, Jordan JJ et al. Identification of Unusual Pathogenic Gram-Negative Aerobic and Facultatively Anaerobic Bacteria, 2nd ed. Baltimore, MD: Williams & Wilkins; 1966
    [Google Scholar]
  37. Kämpfer P. Genus streptomyce. In Goodfellow M, Kämpfer P, Busse HJ, Trujillo ME, Suzuki KI, Ludwig W, Whitman WB. (editors) Bergy’s manual of systematic baceriology, 2nd ed. vol. 5 New York: Springer; 2012 pp. 1455–1767
    [Google Scholar]
  38. Clinical and Laboratory Standards Institute Susceptibility Testing of Mycobacteria, Nocardiae, and Other Aerobic Actinomycetes; Approved Standards M24-A Wayne, IN: Clinical Laboratory Standards Institute; 2011
    [Google Scholar]
  39. Lasker BA, Bell M, Klenk HP, Spröer C, Schumann C et al. Nocardia vulneris sp. nov., isolated from wounds of human patients in North America. Antonie van Leeuwenhoek 2014; 106:543–553 [View Article][PubMed]
    [Google Scholar]
  40. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article][PubMed]
    [Google Scholar]
  41. Meier-Kolthoff JP, Göker M, Spröer C, Klenk HP. When should a DDH experiment be mandatory in microbial taxonomy?. Arch Microbiol 2013; 195:413–418 [View Article][PubMed]
    [Google Scholar]
  42. 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][PubMed]
    [Google Scholar]
  43. Meier-Kolthoff JP, Hahnke RL, Petersen J, Scheuner C, Michael V et al. Complete genome sequence of DSM 30083(T), the type strain (U5/41(T)) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy. Stand Genomic Sci 2014; 9:2 [View Article][PubMed]
    [Google Scholar]
  44. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article][PubMed]
    [Google Scholar]
  45. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  46. Kluge AG, Farris JS. Quantitative phyletics and the evolution of anurans. Syst Zool 1969; 18:1–32 [View Article]
    [Google Scholar]
  47. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312–1313 [View Article][PubMed]
    [Google Scholar]
  48. Goloboff PA, Farris JS, Nixon KC. TNT, a free program for phylogenetic analysis. Cladistics 2008; 24:774–786 [View Article]
    [Google Scholar]
  49. Pattengale ND, Alipour M, Bininda-Emonds OR, Moret BM, Stamatakis A. How many bootstrap replicates are necessary?. J Comput Biol 2010; 17:337–354 [View Article][PubMed]
    [Google Scholar]
  50. Swofford DL. PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods), Version 4.0 Sunderland: Sinauer Associates; 2002
    [Google Scholar]
  51. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article][PubMed]
    [Google Scholar]
  52. 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]
  53. Nouioui I, Carro L, García-López M, Meier-Kolthoff JP, Woyke T et al. Genome-based taxonomic classification of the phylum Actinobacteria . Front Microbiol 2018; 9:9 [View Article][PubMed]
    [Google Scholar]
  54. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014; 30:2114–2120 [View Article][PubMed]
    [Google Scholar]
  55. 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][PubMed]
    [Google Scholar]
  56. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J et al. The sequence alignment/map format and SAMtools. Bioinformatics 2009; 25:2078–2079 [View Article][PubMed]
    [Google Scholar]
  57. Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv 2013; 3:13033997
    [Google Scholar]
  58. Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 2014; 9:e112963 [View Article][PubMed]
    [Google Scholar]
  59. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P 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][PubMed]
    [Google Scholar]
  60. Mesbah M, Premachandran U, Whitman WB. Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 1989; 39:159–167 [View Article]
    [Google Scholar]
  61. Kim M, Oh HS, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article][PubMed]
    [Google Scholar]
  62. Wayne LG, Moore WEC, Stackebrandt E, Kandler O, Colwell RR et al. Report of the ad Hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 1987; 37:463–464 [View Article]
    [Google Scholar]
  63. Kim YR, Park S, Kim TS, Kim MK, Han JH et al. Draft genome sequence of Streptacidiphilus oryzae TH49T, an acidophilic actinobacterium isolated from soil. Genome Announc 2015; 3:e0070300715 [View Article][PubMed]
    [Google Scholar]
  64. Pope MK, Green B, Westpheling J. The bldB gene encodes a small protein required for morphogenesis, antibiotic production, and catabolite control in Streptomyces coelicolor . J Bacteriol 1998; 180:1556–1562[PubMed]
    [Google Scholar]
  65. Labeda DP, Dunlap CA, Rong X, Huang Y, Doroghazi JR et al. Phylogenetic relationships in the family Streptomycetaceae using multi-locus sequence analysis. Antonie van Leeuwenhoek 2017; 110:563–583 [View Article][PubMed]
    [Google Scholar]
  66. Hanage WP, Fraser C, Spratt BG. Fuzzy species among recombinogenic bacteria. BMC Biol 2005; 3:6 [View Article][PubMed]
    [Google Scholar]
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