1887

Abstract

A Gram-stain-negative, rod-shaped, non-motile, non-spore-forming, aerobic bacterium, designated type strain SSI9, was isolated from sand fly ( Scopoli; ) rearing substrate and subjected to polyphasic taxonomic analysis. Strain SSI9 contained phosphatidylethanolamine as a major polar lipid, MK-7 as the predominant quinone, and Cω6/Cω, iso-C, iso-C 3-OH and C as the major cellular fatty acids. Phylogenetic analysis based on 16S rRNA gene sequences revealed that SSI9 represents a member of the genus , of the family Sphingobacteriaceae sharing 96.5–88.0 % sequence similarity with other species of the genus . The results of multilocus sequence analysis using the concatenated sequences of the housekeeping genes A, C and L indicated that SSI9 formed a separate branch in the genus . The genome of SSI9 is 5 197 142 bp with a DNA G+C content of 41.8 mol% and encodes 4395 predicted coding sequences, 49 tRNAs, and three complete rRNAs and two partial rRNAs. SSI9 could be distinguished from other species of the genus with validly published names by several phenotypic, chemotaxonomic and genomic characteristics. On the basis of the results of this polyphasic taxonomic analysis, the bacterial isolate represents a novel species within the genus , for which the name sp. nov. is proposed. The type strain is SSI9 (=ATCC TSD-210=LMG 31664=NRRL B-65603).

Funding
This study was supported by the:
  • Carolina Center of Cancer Nanotechnology Excellence, University of North Carolina - Chapel Hill (US)
    • Principle Award Recipient: GideonWasserberg
  • National Institute of Allergy and Infectious Diseases (Award 1R01AI123327-01)
    • Principle Award Recipient: GideonWasserberg
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004809
2021-05-06
2021-06-24
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/71/5/ijsem004809.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004809&mimeType=html&fmt=ahah

References

  1. Yabuuchi E, Kaneko T, Yano I, Moss CW, Miyoshi N. Sphingobacterium gen. nov., Sphingobacterium spiritivorum comb. nov., Sphingobacterium multivorum comb. nov., Sphingobacterium mizutae sp. nov., and Flavobacterium indologenes sp. nov.: glucose-nonfermenting Gram-negative rods in CDC groups IIk-2 and IIb. Int J Syst Bacteriol 1983; 33:580–598 [View Article]
    [Google Scholar]
  2. Wauters G, Janssens M, De Baere T, Vaneechoutte M, Deschaght P. Isolates belonging to CDC group II-i belong predominantly to Sphingobacterium mizutaii Yabuuchi et al. 1983: emended descriptions of S. mizutaii and of the genus Sphingobacterium. Int J Syst Evol Microbiol 2012; 62:2598–2601 [View Article][PubMed]
    [Google Scholar]
  3. Lee D-H, Hur JS, Kahng H-Y. Sphingobacterium cladoniae sp. nov., isolated from lichen, Cladonia sp., and emended description of Sphingobacterium siyangense. Int J Syst Evol Microbiol 2013; 63:755–760 [View Article][PubMed]
    [Google Scholar]
  4. Sun L-N, Zhang J, Chen Q, He J, Li S-P. Sphingobacterium caeni sp. nov., isolated from activated sludge. Int J Syst Evol Microbiol 2013; 63:2260–2264 [View Article][PubMed]
    [Google Scholar]
  5. Yoo S-H, Weon H-Y, Jang H-B, Kim B-Y, Kwon S-W et al. Sphingobacterium composti sp. nov., isolated from cotton-waste composts. Int J Syst Evol Microbiol 2007; 57:1590–1593 [View Article][PubMed]
    [Google Scholar]
  6. Yabe S, Aiba Y, Sakai Y, Hazaka M, Kawahara K et al. Sphingobacterium thermophilum sp. nov., of the phylum Bacteroidetes, isolated from compost. Int J Syst Evol Microbiol 2013; 63:1584–1588 [View Article][PubMed]
    [Google Scholar]
  7. Siddiqi MZ, Muhammad Shafi S, Choi KD, Im W-T, Aslam Z. Sphingobacterium jejuense sp. nov., with ginsenoside-converting activity, isolated from compost. Int J Syst Evol Microbiol 2016; 66:4433–4439 [View Article][PubMed]
    [Google Scholar]
  8. Albert RA, Waas NE, Pavlons SC, Pearson JL, Ketelboeter L et al. Sphingobacterium psychroaquaticum sp. nov., a psychrophilic bacterium isolated from Lake Michigan water. Int J Syst Evol Microbiol 2013; 63:952–958 [View Article][PubMed]
    [Google Scholar]
  9. Jiang S, Chen M, Su S, Yang M, Li A et al. Sphingobacterium arenae sp. nov., isolated from sandy soil. Int J Syst Evol Microbiol 2014; 64:248–253 [View Article][PubMed]
    [Google Scholar]
  10. Xiao T, He X, Cheng G, Kuang H, Ma X et al. Sphingobacterium hotanense sp. nov., isolated from soil of a Populus euphratica forest, and emended descriptions of Sphingobacterium daejeonense and Sphingobacterium shayense. Int J Syst Evol Microbiol 2013; 63:815–820 [View Article][PubMed]
    [Google Scholar]
  11. Liu B, Yang X, Sheng M, Yang Z, Qiu J et al. Sphingobacterium olei sp. nov., isolated from oil-contaminated soil. Int J Syst Evol Microbiol 2020; 70:1931–1939 [View Article][PubMed]
    [Google Scholar]
  12. Chaudhary DK, Kim J. Sphingobacterium terrae sp. nov., isolated from oil-contaminated soil. Int J Syst Evol Microbiol 2018; 68:609–615 [View Article][PubMed]
    [Google Scholar]
  13. Liu J, Yang L-L, Xu C-K, Xi J-Q, Yang F-X et al. Sphingobacterium nematocida sp. nov., a nematicidal endophytic bacterium isolated from tobacco. Int J Syst Evol Microbiol 2012; 62:1809–1813 [View Article][PubMed]
    [Google Scholar]
  14. Li Y, Xu G-T, Chang J-P, Guo L-M, Yang X-Q et al. Sphingobacterium corticis sp. nov., isolated from bark of Populus × euramericana. Int J Syst Evol Microbiol 2017; 67:3860–3864 [View Article][PubMed]
    [Google Scholar]
  15. Li Y, Guo L-M, Chang J-P, Yang X-Q, Xie S-J et al. Sphingobacterium corticibacter sp. nov., isolated from bark of Populus × euramericana. Int J Syst Evol Microbiol 2019; 69:1870–1874 [View Article][PubMed]
    [Google Scholar]
  16. Schmidt VS, Wenning M, Scherer S, sp Slactis. Sphingobacterium lactis sp. nov. and Sphingobacterium alimentarium sp. nov., isolated from raw milk and a dairy environment. Int J Syst Evol Microbiol 2012; 62:1506–1511 [View Article][PubMed]
    [Google Scholar]
  17. Marayati BF, Schal C, Ponnusamy L, Apperson CS, Rowland TE et al. Attraction and oviposition preferences of Phlebotomus papatasi (Diptera: Psychodidae), vector of Old-World cutaneous leishmaniasis, to larval rearing media. Parasit Vectors 2015; 8:663 [View Article][PubMed]
    [Google Scholar]
  18. Lane D. 16S/23S rRNA sequencing London, UK: John Wiley and Sons; 1991
    [Google Scholar]
  19. Ponnusamy L, Xu N, Nojima S, Wesson DM, Schal C et al. Identification of bacteria and bacteria-associated chemical cues that mediate oviposition site preferences by Aedes aegypti. Proc Natl Acad Sci U S A 2008; 105:9262–9267 [View Article][PubMed]
    [Google Scholar]
  20. Kim O-S, Cho Y-J, Lee K, Yoon S-H, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012; 62:716–721 [View Article][PubMed]
    [Google Scholar]
  21. Benson D, Karsch-Mizrachi I, Lipman D, Ostell J. Genbank. 2009. Nucleic Acids Res 2009D26–D31
    [Google Scholar]
  22. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. mega X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article][PubMed]
    [Google Scholar]
  23. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article][PubMed]
    [Google Scholar]
  24. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  25. 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]
  26. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
    [Google Scholar]
  27. Liu L, Hui N, Liang L-X, Zhang X-X, Li L-B et al. Sphingobacterium haloxyli sp. nov., an endophytic bacterium isolated from Haloxylon ammodendron stems in Kumtag desert. Int J Syst Evol Microbiol 2018; 68:3279–3284 [View Article][PubMed]
    [Google Scholar]
  28. Wang X, Zhang C-F, Yu X, Hu G, Yang H-X. Sphingobacterium chuzhouense sp. nov., isolated from farmland soil. Int J Syst Evol Microbiol 2016; 66:4968–4974 [View Article][PubMed]
    [Google Scholar]
  29. Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 2006; 33:152–155
    [Google Scholar]
  30. Kim M, Oh H-S, Park S-C, 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]
  31. 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]
  32. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Ciufo S. Prokaryotic genome annotation pipeline. The NCBI Handbook [Internet], 2nd edition. US: National Center for Biotechnology Information; 2013
    [Google Scholar]
  33. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75–15 [View Article]
    [Google Scholar]
  34. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:2182 [View Article][PubMed]
    [Google Scholar]
  35. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article][PubMed]
    [Google Scholar]
  36. Rodriguez-R LM, Konstantinidis KT. Bypassing cultivation to identify bacterial species. Microbe 2014; 9:111–118 [View Article]
    [Google Scholar]
  37. 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]
  38. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article][PubMed]
    [Google Scholar]
  39. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids; 1990
  40. Bligh EG, Dyer WJ. A rapid method of total lipid extraction and purification. Can J Biochem Physiol 1959; 37:911–917 [View Article][PubMed]
    [Google Scholar]
  41. Tindall BJ, Sikorski J, Smibert RA, Krieg NR. Phenotypic characterization and the principles of comparative systematics. Methods General Mol Microbiol 2007330–393
    [Google Scholar]
  42. Tindall BJ. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990; 13:128–130 [View Article]
    [Google Scholar]
  43. Tindall BJ. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 1990; 66:199–202 [View Article]
    [Google Scholar]
  44. Zhao P, Zhou Z, Chen M, Lin W, Zhang W et al. Sphingobacterium gobiense sp. nov., isolated from soil of the Gobi Desert. Int J Syst Evol Microbiol 2014; 64:3931–3935 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004809
Loading
/content/journal/ijsem/10.1099/ijsem.0.004809
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited this month Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error